bioRxiv Channel: 4D Nucleome https://biorxiv.org This feed contains articles for bioRxiv Channel "4D Nucleome " bioRxiv bioRxiv https://biorxiv.org <![CDATA[ The 3D genome organization of Drosophila melanogaster through data integration ]]> https://biorxiv.org/cgi/content/short/099911v1?rss=1" Li, Q. Tjong, H. Li, X. Gong, K. Zhou, X. J. Chiolo, I. Alber, F. 2017-01-15 doi:10.1101/099911 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization ]]> https://biorxiv.org/cgi/content/short/095802v1?rss=1" nView larger version (49K):norg.highwire.dtl.DTLVardef@79c6c5org.highwire.dtl.DTLVardef@e8e61forg.highwire.dtl.DTLVardef@5c2eedorg.highwire.dtl.DTLVardef@cf7f3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nora, E. P. Goloborodko, A. Valton, A.-L. Gibcus, J. Uebsersohn, A. Abdennur, N. Dekker, J. Mirny, L. Bruneau, B. 2016-12-21 doi:10.1101/095802 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Cohesin dependent compaction of mitotic chromosomes ]]> https://biorxiv.org/cgi/content/short/094946v1?rss=1" Schalbetter, S. A. Goloborodko, A. Fudenberg, G. Belton, J. M. Miles, C. Yu, M. Dekker, J. Mirny, L. Baxter, J. 2016-12-17 doi:10.1101/094946 Cold Spring Harbor Laboratory Press 2016-12-17 <![CDATA[ Two independent modes of chromosome organization are revealed by cohesin removal ]]> https://biorxiv.org/cgi/content/short/094185v1?rss=1" Schwarzer, W. Abdennur, N. Goloborodko, A. Pekowska, A. Fudenberg, G. Loe-Mie, Y. Fonseca, N. A. Huber, W. Haering, C. Mirny, L. Spitz, F. 2016-12-15 doi:10.1101/094185 Cold Spring Harbor Laboratory Press 2016-12-15 <![CDATA[ CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics ]]> https://biorxiv.org/cgi/content/short/093476v1?rss=1" Hansen, A. S. Pustova, I. Cattoglio, C. Tjian, R. Darzacq, X. 2016-12-12 doi:10.1101/093476 Cold Spring Harbor Laboratory Press 2016-12-12 <![CDATA[ HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATION ]]> https://biorxiv.org/cgi/content/short/090001v1?rss=1" Belaghzal, H. Dekker, J. Gibcus, J. H. 2016-11-27 doi:10.1101/090001 Cold Spring Harbor Laboratory Press 2016-11-27 <![CDATA[ FISH-ing for captured contacts: towards reconciling FISH and 3C ]]> https://biorxiv.org/cgi/content/short/081448v1?rss=1" Fudenberg, G. Imakaev, M. 2016-10-17 doi:10.1101/081448 Cold Spring Harbor Laboratory Press 2016-10-17 <![CDATA[ Comparative analysis of 2D and 3D distance measurements to study spatial genome organization ]]> https://biorxiv.org/cgi/content/short/076893v1?rss=1" Elizabeth Finn Gianluca Pegoraro Sigal Shachar Tom Misteli 2016-09-23 doi:10.1101/076893 Cold Spring Harbor Laboratory Press 2016-09-23 <![CDATA[ Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome ]]> https://biorxiv.org/cgi/content/short/071357v1?rss=1" Tsung-Han Hsieh Geoffrey Fudenberg Anton Goloborodko Oliver Rando 2016-08-24 doi:10.1101/071357 Cold Spring Harbor Laboratory Press 2016-08-24 <![CDATA[ Compaction and segregation of sister chromatids via active loop extrusion ]]> https://biorxiv.org/cgi/content/short/038281v1?rss=1" Anton Goloborodko Maxim V. Imakaev John F. Marko Leonid A. Mirny 2016-01-30 doi:10.1101/038281 Cold Spring Harbor Laboratory Press 2016-01-30 <![CDATA[ Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers ]]> https://biorxiv.org/cgi/content/short/110239v1?rss=1" Yan, J. Chen, S.-A. A. Local, A. Liu, T. Qiu, Y. Lee, A.-Y. Jung, I. Preissl, S. Rivera, C. M. Wang, C. Ishii, H. Fang, R. Ye, Z. Ge, K. Hu, M. Ren, B. 2017-02-21 doi:10.1101/110239 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ Comprehensive characterization of neutrophil genome topology ]]> https://biorxiv.org/cgi/content/short/100198v1?rss=1" Zhu, Y. Gong, K. Denholtz, M. Chandra, V. Kamps, M. P. Alber, F. Murre, C. 2017-01-15 doi:10.1101/100198 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQ ]]> https://biorxiv.org/cgi/content/short/074294v1?rss=1" Rongxin Fang Miao Yu Guoqiang Li Sora Chee Tristin Liu Anthony Schmitt Bing Ren 2016-09-09 doi:10.1101/074294 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture ]]> https://biorxiv.org/cgi/content/short/103614v1?rss=1" Schreiber, J. Libbrecht, M. Bilmes, J. Noble, W. 2017-01-27 doi:10.1101/103614 Cold Spring Harbor Laboratory Press 2017-01-27 <![CDATA[ Software tools for visualizing Hi-C data ]]> https://biorxiv.org/cgi/content/short/086017v1?rss=1" Yardimci, G. G. Noble, W. S. 2016-11-07 doi:10.1101/086017 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ Massively multiplex single-cell Hi-C ]]> https://biorxiv.org/cgi/content/short/065052v1?rss=1" Vijay Ramani Xinxian Deng Kevin L Gunderson Frank J Steemers Christine M Disteche William S Noble Zhijun Duan Jay Shendure 2016-07-23 doi:10.1101/065052 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH ]]> https://biorxiv.org/cgi/content/short/101477v1?rss=1" Takei, Y. Shah, S. Harvey, S. Qi, L. S. Cai, L. 2017-01-18 doi:10.1101/101477 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Real-time chromatin dynamics at the single gene levelduring transcription activation ]]> https://biorxiv.org/cgi/content/short/111179v1?rss=1" Germier, T. Kocanova, S. Walther, N. Bancaud, A. Shaban, H. A. Sellou, H. Politi, A. Ellenberg, J. Gallardo, F. Bystricky, K. 2017-02-23 doi:10.1101/111179 Cold Spring Harbor Laboratory Press 2017-02-23 <![CDATA[ Direct visualization of transcriptional activation by physical enhancer-promoter proximity ]]> https://biorxiv.org/cgi/content/short/099523v1?rss=1" Chen, H. Fujioka, M. Gregor, T. 2017-01-11 doi:10.1101/099523 Cold Spring Harbor Laboratory Press 2017-01-11 <![CDATA[ A Dynamic Mode of Mitotic Bookmarking by Transcription Factors ]]> https://biorxiv.org/cgi/content/short/066464v1?rss=1" Sheila S Teves Luye An Anders S Hansen Liangqi Xie Xavier Darzacq Robert Tjian 2016-07-28 doi:10.1101/066464 Cold Spring Harbor Laboratory Press 2016-07-28 <![CDATA[ The p150N domain of Chromatin Assembly Factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer ]]> https://biorxiv.org/cgi/content/short/082339v1?rss=1" Matheson, T. Kaufman, P. 2016-10-21 doi:10.1101/082339 Cold Spring Harbor Laboratory Press 2016-10-21 <![CDATA[ Visualizing adenosine to inosine RNA editing in single mammalian cells ]]> https://biorxiv.org/cgi/content/short/088146v1?rss=1" Mellis, I. A. Gupte, R. K. Raj, A. Rouhanifard, S. H. 2016-11-16 doi:10.1101/088146 Cold Spring Harbor Laboratory Press 2016-11-16 <![CDATA[ The 4D Nucleome Project ]]> https://biorxiv.org/cgi/content/short/103499v1?rss=1" Dekker, J. Belmont, A. S. Guttman, M. Leshyk, V. O. Lis, J. T. Lomvardas, S. Mirny, L. A. O'Shea, C. C. Park, P. J. Ren, B. Ritland, J. C. Shendure, J. Zhong, S. The 4D Nucleome Network, 2017-01-26 doi:10.1101/103499 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Repli-seq: genome-wide analysis of replication timing by next-generation sequencing ]]> https://biorxiv.org/cgi/content/short/104653v1?rss=1" Marchal, C. Sasaki, T. Vera, D. Wilson, K. Sima, J. Rivera-Mulia, J.-C. Trevilla Garcia, C. Nogues, C. Nafie, E. Gilbert, D. M. 2017-02-14 doi:10.1101/104653 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions ]]> https://biorxiv.org/cgi/content/short/112268v1?rss=1" Wang, Y. Zhang, B. Zhang, L. An, L. Xu, J. Li, D. Choudhary, M. N. Li, Y. Hu, M. Hardison, R. Wang, T. Yue, F. 2017-02-27 doi:10.1101/112268 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ HiCPlus: Resolution Enhancement of Hi-C interaction heatmap ]]> https://biorxiv.org/cgi/content/short/112631v1?rss=1" Zhang, Y. An, L. Hu, M. Tang, J. Yue, F. 2017-03-01 doi:10.1101/112631 Cold Spring Harbor Laboratory Press 2017-03-01 <![CDATA[ A fluorogenic nanobody array tag for prolonged single molecule imaging in live cells ]]> https://biorxiv.org/cgi/content/short/111690v1?rss=1" Ghosh, R. Draper, W. Franklin, J. M. Shi, Q. Liphardt, J. 2017-02-27 doi:10.1101/111690 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ Detecting hierarchical 3-D genome domain reconfiguration with network modularity ]]> https://biorxiv.org/cgi/content/short/089011v1?rss=1" Norton, H. K. Huang, H. Emerson, D. J. Kim, J. Gu, S. Bassett, D. S. Phillips-Cremins, J. E. 2016-11-22 doi:10.1101/089011 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome ]]> https://biorxiv.org/cgi/content/short/105676v1?rss=1" Dawson, W. Plewczynski, D. 2017-02-03 doi:10.1101/105676 Cold Spring Harbor Laboratory Press 2017-02-03 <![CDATA[ HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient ]]> https://biorxiv.org/cgi/content/short/101386v1?rss=1" Yang, T. Zhang, F. Yardimci, G. G. Hardison, R. C. Noble, W. S. Yue, F. Li, Q. 2017-01-18 doi:10.1101/101386 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Formation of Chromosomal Domains by Loop Extrusion ]]> https://biorxiv.org/cgi/content/short/024620v1?rss=1" Geoffrey Fudenberg Maxim Imakaev Carolyn Lu Anton Goloborodko Nezar Abdennur Leonid A Mirny 2015-08-14 doi:10.1101/024620 Cold Spring Harbor Laboratory Press 2015-08-14 <![CDATA[ ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy ]]> https://biorxiv.org/cgi/content/short/115436v1?rss=1" Morganella, S. Oedegaard, O. Alexander, S. Ries, J. Fitzgerald, T. Ellenberg, J. Birney, E. 2017-03-09 doi:10.1101/115436 Cold Spring Harbor Laboratory Press 2017-03-09 <![CDATA[ The dynamic three-dimensional organization of the diploid yeast genome ]]> https://biorxiv.org/cgi/content/short/091827v1?rss=1" Kim, S. Liachko, I. Brickner, D. G. Cook, K. Noble, W. S. Brickner, J. H. Shendure, J. Dunham, M. 2016-12-05 doi:10.1101/091827 Cold Spring Harbor Laboratory Press 2016-12-05 <![CDATA[ Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells ]]> https://biorxiv.org/cgi/content/short/083212v1?rss=1" Danko, C. G. Wang, Z. Rice, E. J. Chu, T. Martins, A. L. Tait Wojno, E. Lis, J. T. Kraus, L. W. Siepel, A. 2016-10-25 doi:10.1101/083212 Cold Spring Harbor Laboratory Press 2016-10-25 <![CDATA[ HiGlass: Web-based Visual Comparison And Exploration Of Genome Interaction Maps ]]> https://biorxiv.org/cgi/content/short/121889v1?rss=1" Kerpedjiev, P. Abdennur, N. Lekschas, F. McCallum, C. Dinkla, K. Strobelt, H. Luber, J. M. Ouellette, S. B. Ahzir, A. Kumar, N. Hwang, J. Alver, B. H. Pfister, H. Mirny, L. A. Park, P. J. Gehlenborg, N. 2017-03-31 doi:10.1101/121889 Cold Spring Harbor Laboratory Press 2017-03-31 <![CDATA[ HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples ]]> https://biorxiv.org/cgi/content/short/123588v1?rss=1" Lekschas, F. Bach, B. Kerpedjiev, P. Gehlenborg, N. Pfister, H. 2017-04-03 doi:10.1101/123588 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ A Versatile Compressed Sensing Scheme For Faster And Less Phototoxic 3D Fluorescence Microscopy ]]> https://biorxiv.org/cgi/content/short/125815v1?rss=1" Woringer, M. Darzacq, X. Zimmer, C. Mir, M. 2017-04-10 doi:10.1101/125815 Cold Spring Harbor Laboratory Press 2017-04-10 <![CDATA[ Nuclear Microenvironments Modulate Transcription From Low-Affinity Enhancers ]]> https://biorxiv.org/cgi/content/short/128280v1?rss=1" Crocker, J. Tsai, A. Muthusamy, A. K. Lavis, L. D. Singer, R. H. Stern, D. L. 2017-04-18 doi:10.1101/128280 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ An Integrative Framework For Detecting Structural Variations In Cancer Genomes ]]> https://biorxiv.org/cgi/content/short/119651v1?rss=1" Dixon, J. Xu, J. Dileep, V. Zhan, Y. Song, F. Le, V. T. Yardimci, G. G. Chakraborty, A. Bann, D. V. Wang, Y. Clark, R. Zhang, L. Yang, H. Liu, T. Iyyanki, S. An, L. Pool, C. Sasaki, T. Mulia, J. C. R. Ozadam, H. Lajoie, B. R. Kaul, R. Buckley, M. Lee, K. Diegel, M. Pezic, D. Ernst, C. Hadjur, S. Odom, D. T. Stamatoyannopoulos, J. A. Broach, J. R. Hardison, R. Ay, F. Noble, W. S. Dekker, J. Gilbert, D. M. Yue, F. 2017-03-28 doi:10.1101/119651 Cold Spring Harbor Laboratory Press 2017-03-28 <![CDATA[ A Comparison Between Single Cell RNA Sequencing And Single Molecule RNA FISH For Rare Cell Analysis ]]> https://biorxiv.org/cgi/content/short/138289v1?rss=1" Torre, E. A. Dueck, H. Shaffer, S. Gospocic, J. Gupte, R. Bonasio, R. Kim, J. Murray, J. Raj, A. 2017-05-18 doi:10.1101/138289 Cold Spring Harbor Laboratory Press 2017-05-18 <![CDATA[ Gene Expression Recovery For Single Cell RNA Sequencing ]]> https://biorxiv.org/cgi/content/short/138677v1?rss=1" Huang, M. Wang, J. Torre, E. Dueck, H. Shaffer, S. Bonasio, R. Murray, J. Raj, A. Li, M. Zhang, N. R. 2017-05-16 doi:10.1101/138677 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Cohesin Loss Eliminates All Loop Domains, Leading To Links Among Superenhancers And Downregulation Of Nearby Genes ]]> https://biorxiv.org/cgi/content/short/139782v1?rss=1" Rao, S. Huang, S.-C. Glenn St. Hilaire, B. Engreitz, J. M. Perez, E. M. Kieffer-Kwon, K.-R. Sanborn, A. L. Johnstone, S. E. Bochkov, I. D. Huang, X. Shamim, M. S. Omer, A. D. Bernstein, B. E. Casellas, R. Lander, E. S. Lieberman Aiden, E. 2017-05-18 doi:10.1101/139782 Cold Spring Harbor Laboratory Press 2017-05-18 <![CDATA[ Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development ]]> https://biorxiv.org/cgi/content/short/142026v1?rss=1" 10 billion total reads)nC_LIO_LIMulti-loop interaction communities identified surrounding key macrophage genes.nC_LIO_LIMulti-loop communities connect dynamic enhancers through both static and newly acquired DNA loops, forming hubs of activationnC_LIO_LIMacrophage activation hubs are enriched for AP-1 bound long-range enhancer interactions, suggesting cell-type specific TFs drive changes in 3D structure and transcription through regulatory DNA loopsnC_LI ]]> Phanstiel, D. H. Van Bortle, K. Spacek, D. V. Hess, G. T. Saad Shamim, M. Machol, I. Love, M. I. Lieberman Aiden, E. Bassik, M. C. Snyder, M. P. 2017-05-25 doi:10.1101/142026 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map ]]> https://biorxiv.org/cgi/content/short/099804v1?rss=1" Eagen, K. P. Lieberman Aiden, E. Kornberg, R. D. 2017-01-12 doi:10.1101/099804 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images -- How Reliable Is It? ]]> https://biorxiv.org/cgi/content/short/145110v1?rss=1" Tu, L.-C. Huisman, M. Chung, Y.-C. Smith, C. Grunwald, D. 2017-06-02 doi:10.1101/145110 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPs ]]> https://biorxiv.org/cgi/content/short/156091v1?rss=1" Noma, A. Smith, C. S. Huisman, M. Martin, R. M. Moore, M. J. Grunwald, D. 2017-06-26 doi:10.1101/156091 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Cell cycle dynamics of chromosomal organisation at single-cell resolution ]]> https://biorxiv.org/cgi/content/short/094466v1?rss=1" Nagano, T. Lubling, Y. Varnai, C. Dudley, C. Leung, W. Baran, Y. Mandelson Cohen, N. Wingett, S. Fraser, P. Tanay, A. 2016-12-15 doi:10.1101/094466 Cold Spring Harbor Laboratory Press 2016-12-15 <![CDATA[ CRISPR/Cas9-mediated Knock-in of an Optimized TetO Repeat for Live Cell Imaging of Endogenous Loci ]]> https://biorxiv.org/cgi/content/short/162156v1?rss=1" Tasan, I. Sustackova, G. Zhang, L. Kim, J. Sivaguru, M. HamediRad, M. Wang, Y. Genova, J. Ma, J. Belmont, A. S. Zhao, H. 2017-07-12 doi:10.1101/162156 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome ]]> https://biorxiv.org/cgi/content/short/165340v1?rss=1" Bonora, G. Deng, X. Fang, H. Ramani, V. Qui, R. Berletch, J. Filippova, G. N. Duan, Z. Schendure, J. Noble, W. S. Disteche, C. M. 2017-07-19 doi:10.1101/165340 Cold Spring Harbor Laboratory Press 2017-07-19 <![CDATA[ Heterogeneity and Intrinsic Variation in Spatial Genome Organization ]]> https://biorxiv.org/cgi/content/short/171801v1?rss=1" Finn, E. Pegoraro, G. Brandao, H. B. Valton, A.-L. Oomen, M. E. Dekker, J. Mirny, L. Misteli, T. 2017-08-02 doi:10.1101/171801 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2 ]]> https://biorxiv.org/cgi/content/short/171819v1?rss=1" Gao, X. D. Tu, L.-C. Mir, A. Dekker, J. Shaffer, S. A. Zhu, L. J. Wolfe, S. A. Sontheimer, E. J. 2017-08-02 doi:10.1101/171819 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ Spot-On: robust model-based analysis of single-particle tracking experiments ]]> https://biorxiv.org/cgi/content/short/171983v1?rss=1" Hansen, A. S. Woringer, M. Grimm, J. B. Lavis, L. D. Tjian, R. Darzacq, X. 2017-08-03 doi:10.1101/171983 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture ]]> https://biorxiv.org/cgi/content/short/177766v1?rss=1" Gassler, J. Brandao, H. B. Imakaev, M. Flyamer, I. M. Ladstatter, S. Bickmore, W. A. Peters, J.-M. Mirny, L. A. Tachibana-Konwalski, K. 2017-08-17 doi:10.1101/177766 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Building a genome browser with GIVE ]]> https://biorxiv.org/cgi/content/short/177832v1?rss=1" Cao, X. Zheng, A. Zhong, S. 2017-08-18 doi:10.1101/177832 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing ]]> https://biorxiv.org/cgi/content/short/104844v1?rss=1" Cao, J. Packer, J. S. Ramani, V. Cusanovich, D. A. Huynh, C. Daza, R. Qiu, X. Lee, C. Furlan, S. N. Steemers, F. J. Adey, A. Waterston, R. H. Trapnell, C. Shendure, J. 2017-02-02 doi:10.1101/104844 Cold Spring Harbor Laboratory Press 2017-02-02 <![CDATA[ Reversed graph embedding resolves complex single-cell developmental trajectories ]]> https://biorxiv.org/cgi/content/short/110668v1?rss=1" Qiu, X. Mao, Q. Tang, Y. Wang, L. Chawla, R. Pliner, H. Trapnell, C. 2017-02-21 doi:10.1101/110668 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ Chromatin accessibility dynamics of myogenesis at single cell resolution ]]> https://biorxiv.org/cgi/content/short/155473v1?rss=1" Pliner, H. Packer, J. McFaline-Figueroa, J. Cusanovich, D. Daza, R. Srivatsan, S. Qiu, X. Jackson, D. Minkina, A. Adey, A. Steemers, F. Shendure, J. Trapnell, C. 2017-06-26 doi:10.1101/155473 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ PBAF’s genomic binding dynamics are regulated via bromodomain-acetyl-lysine interactions and select chromatin states ]]> https://biorxiv.org/cgi/content/short/111674v1?rss=1" Kenworthy, C. A. Wong, V. Dziuba, P. Lavis, L. D. Liu, W.-L. Singer, R. H. Coleman, R. A. 2017-08-10 doi:10.1101/111674 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ p53 dynamically directs TFIID assembly on target gene promoters ]]> https://biorxiv.org/cgi/content/short/083014v1?rss=1" Coleman, R. A. Qiao, Z. Singh, S. K. Peng, C. S. Cianfrocco, M. Zhang, Z. Song, L. Piasecka, A. Aldeborgh, H. Basishvili, G. Rice, W. Liu, W.-L. 2016-10-24 doi:10.1101/083014 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ Fast, robust and precise 3D localization for arbitrary point spread functions ]]> https://biorxiv.org/cgi/content/short/172643v1?rss=1" Li, Y. Mund, M. Hoess, P. Matti, U. Nijmeijer, B. Jimenez Sabinina, V. Ellenberg, J. Schoen, I. Ries, J. 2017-08-08 doi:10.1101/172643 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture ]]> https://biorxiv.org/cgi/content/short/142604v1?rss=1" Li, H. Kalhor, R. Li, B. Su, T. Berk, A. Kurdistani, S. Alber, F. Chen, L. 2017-05-26 doi:10.1101/142604 Cold Spring Harbor Laboratory Press 2017-05-26 <![CDATA[ Ki-67 Contributes To Normal Cell Cycle Progression And Inactive X Heterochromatin In p21 Checkpoint-Proficient Human Cells ]]> https://biorxiv.org/cgi/content/short/134767v1?rss=1" Sun, X. Bizhanova, A. Matheson, T. D. Yu, J. Zhu, J. L. Kaufman, P. D. 2017-05-05 doi:10.1101/134767 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ Dense Bicoid Hubs Accentuate Binding along the Morphogen Gradient ]]> https://biorxiv.org/cgi/content/short/133124v1?rss=1" Mir, M. Reimer, A. Haines, J. E. Li, X.-Y. Stadler, M. Garcia, H. Eisen, M. E. Darzacq, X. 2017-05-01 doi:10.1101/133124 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ PGS: a dynamic and automated population-based genome structure software ]]> https://biorxiv.org/cgi/content/short/103358v1?rss=1" Hua, N. Tjong, H. Shin, H. Gong, K. Zhou, X. J. Alber, F. 2017-01-26 doi:10.1101/103358 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Correlative live and super-resolution imaging reveals the dynamic structure of replication domains ]]> https://biorxiv.org/cgi/content/short/189373v1?rss=1" Xiang, W. Roberti, M. J. Heriche, J.-K. Huet, S. Alexander, S. Ellenberg, J. 2017-09-17 doi:10.1101/189373 Cold Spring Harbor Laboratory Press 2017-09-17 <![CDATA[ Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries ]]> https://biorxiv.org/cgi/content/short/191213v1?rss=1" Sun, J. Zhou, L. Emerson, D. J. Gilgenast, T. G. Titus, K. Beagan, J. A. Phillips-Cremins, J. E. 2017-09-20 doi:10.1101/191213 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Fluorescence polarization control for on-off switching of single molecules at cryogenic temperatures ]]> https://biorxiv.org/cgi/content/short/204776v1?rss=1" Hulleman, C. Huisman, M. Moerland, R. Grunwald, D. Stallinga, S. Rieger, B. 2017-10-17 doi:10.1101/204776 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies ]]> https://biorxiv.org/cgi/content/short/206094v1?rss=1" Allahyar, A. Vermeulen, C. Bouwman, B. Krijger, P. Verstegen, M. Geeven, G. van Kranenburg, M. Pieterse, M. Straver, R. Haarhuis, J. Teunissen, H. Renkens, I. Kloosterman, W. Rowland, B. de Wit, E. de Ridder, J. de Laat, W. 2017-10-19 doi:10.1101/206094 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks ]]> https://biorxiv.org/cgi/content/short/085241v1?rss=1" Singh, S. Yang, Y. Poczos, B. Ma, J. 2016-11-02 doi:10.1101/085241 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ HUGIn: Hi-C Unifying Genomic Interrogator ]]> https://biorxiv.org/cgi/content/short/117531v1?rss=1" Martin, J. S. Xu, Z. Reiner, A. P. Mohlke, K. L. Sullivan, P. Ren, B. Hu, M. Li, Y. 2017-03-16 doi:10.1101/117531 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells ]]> https://biorxiv.org/cgi/content/short/118737v1?rss=1" Kubo, N. Ishii, H. Gorkin, D. Meitinger, F. Xiong, X. Fang, R. Liu, T. Ye, Z. Li, B. Dixon, J. Desai, A. Zhao, H. Ren, B. 2017-03-20 doi:10.1101/118737 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Supercoiling DNA locates mismatches ]]> https://biorxiv.org/cgi/content/short/130567v1?rss=1" Dittmore, A. Brahmachari, S. Takagi, Y. Marko, J. F. Neuman, K. C. 2017-04-25 doi:10.1101/130567 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ Torque and buckling in stretched intertwined double-helix DNAs ]]> https://biorxiv.org/cgi/content/short/135905v1?rss=1" Marko, J. Brahmachari, S. 2017-05-09 doi:10.1101/135905 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Facilitated Dissociation Of Transcription Factors From Single DNA Binding Sites ]]> https://biorxiv.org/cgi/content/short/135947v1?rss=1" Kamar, R. I. Banigan, E. J. Erbas, A. Giuntoli, R. D. Olvera de la Cruz, M. Johnson, R. C. Marko, J. F. 2017-05-09 doi:10.1101/135947 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ qSR: A software for quantitative analysis of single molecule and super-resolution data ]]> https://biorxiv.org/cgi/content/short/146241v1?rss=1" Andrews, J. O. Narayanan, A. Spille, J.-H. Cho, W.-K. Thaler, J. D. Cisse, I. I. 2017-06-05 doi:10.1101/146241 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking ]]> https://biorxiv.org/cgi/content/short/153098v1?rss=1" Kaewsapsak, P. Shechner, D. M. Mallard, W. Rinn, J. L. Ting, A. Y. 2017-06-21 doi:10.1101/153098 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program. ]]> https://biorxiv.org/cgi/content/short/158352v1?rss=1" Dileep, V. Gilbert, D. M. 2017-06-30 doi:10.1101/158352 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ A Fluorogenic Array Tag for Temporally Unlimited Single Molecule Tracking ]]> https://biorxiv.org/cgi/content/short/159004v1?rss=1" Ghosh, R. P. Franklin, M. J. Draper, W. E. Shi, Q. Liphardt, J. T. 2017-07-03 doi:10.1101/159004 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays ]]> https://biorxiv.org/cgi/content/short/174649v1?rss=1" Gibcus, J. H. Samejima, K. Goloborodko, A. Samejima, I. Naumova, N. Kanemaki, M. Xie, L. Paulson, J. R. Earnshaw, W. C. Mirny, L. A. Dekker, J. 2017-08-10 doi:10.1101/174649 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution ]]> https://biorxiv.org/cgi/content/short/184846v1?rss=1" Ma, W. Ay, F. Lee, C. Gulsoy, G. Deng, X. Cook, S. Hesson, J. Cavanaugh, C. Ware, C. B. Krumm, A. Shendure, J. Blau, C. A. Disteche, C. M. Noble, W. S. Duan, Z. 2017-09-05 doi:10.1101/184846 Cold Spring Harbor Laboratory Press 2017-09-05 <![CDATA[ Measuring the reproducibility and quality of Hi-C data ]]> https://biorxiv.org/cgi/content/short/188755v1?rss=1" Yardimci, G. Ozadam, H. Sauria, M. E. G. Ursu, O. Yan, K.-K. Yang, T. Chakraborty, A. Kaul, A. Lajoie, B. R. Song, F. Zhan, Y. Ay, F. Gerstein, M. Kundaje, A. Li, Q. Taylor, J. Yue, F. Dekker, J. Noble, W. S. 2017-09-14 doi:10.1101/188755 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ High-throughput identification of RNA nuclear enrichment sequences ]]> https://biorxiv.org/cgi/content/short/189654v1?rss=1" Shukla, C. J. McCorkindale, A. L. Gerhardinger, C. Korthauer, K. D. Cabili, M. N. Shechner, D. M. Irizarry, R. A. Maass, P. G. Rinn, J. L. 2017-09-15 doi:10.1101/189654 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics ]]> https://biorxiv.org/cgi/content/short/195966v1?rss=1" Ma, H. Tu, L.-C. Naseri, A. Chung, Y.-C. Grunwald, D. Zhang, S. Pederson, T. 2017-09-29 doi:10.1101/195966 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Chromatin Organization by an Interplay of Loop Extrusion and Compartmental Segregation ]]> https://biorxiv.org/cgi/content/short/196261v1?rss=1" Nuebler, J. Fudenberg, G. Imakaev, M. Abdennur, N. Mirny, L. 2017-10-03 doi:10.1101/196261 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ Nucleation of multiple buckled structures in intertwined DNA double helices ]]> https://biorxiv.org/cgi/content/short/196345v1?rss=1" Brahmachari, S. Gunn, K. H. Giuntoli, R. D. Mondragon, A. Marko, J. F. 2017-09-30 doi:10.1101/196345 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Mechanics and buckling of biopolymeric shells and cell nuclei ]]> https://biorxiv.org/cgi/content/short/197566v1?rss=1" Banigan, E. J. Stephens, A. D. Marko, J. F. 2017-10-02 doi:10.1101/197566 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Juicebox.js provides a cloud-based visualization system for Hi-C data ]]> https://biorxiv.org/cgi/content/short/205740v1?rss=1" Robinson, J. Turner, D. Durand, N. C. Thorvaldsdottir, H. Mesirov, J. P. Aiden, E. L. 2017-10-19 doi:10.1101/205740 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins ]]> https://biorxiv.org/cgi/content/short/206367v1?rss=1" Stephens, A. D. Liu, P. Z. Banigan, E. J. Almassalha, L. M. Backman, V. Adam, S. A. Goldman, R. Marko, J. 2017-10-29 doi:10.1101/206367 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Dynamic and Selective Low-Complexity Domain Interactions Revealed by Live-Cell Single-Molecule Imaging ]]> https://biorxiv.org/cgi/content/short/208710v1?rss=1" Chong, S. Dugast-Darzacq, C. Liu, Z. Dong, P. Dailey, G. Banala, S. Lavis, L. Darzacq, X. Tjian, R. 2017-10-25 doi:10.1101/208710 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ A Cell Type-Specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs ]]> https://biorxiv.org/cgi/content/short/212928v1?rss=1" Joeng, M. Huang, X. Zhang, X. Su, J. Shamim, M. Bochkov, I. Reyes, J. Jung, H. Heikamp, E. Presser Aiden, A. Li, W. Lieberman Aiden, E. Goodell, M. 2017-11-09 doi:10.1101/212928 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Removing unwanted variation between samples in Hi-C experiments ]]> https://biorxiv.org/cgi/content/short/214361v1?rss=1" Fletez-Brant, K. Qiu, Y. Gorkin, D. U. Hu, M. Hansen, K. D. 2017-11-06 doi:10.1101/214361 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ CHRAC/ACF Contribute to the Repressive Ground State of Chromatin ]]> https://biorxiv.org/cgi/content/short/218768v1?rss=1" Scacchetti, A. Brueckner, L. Jain, D. Schauer, T. Zhang, X. Schnorrer, F. van Steensel, B. Straub, T. Becker, P. B. 2017-11-13 doi:10.1101/218768 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Quantitative imaging of chromatin decompaction in living cells ]]> https://biorxiv.org/cgi/content/short/219253v1?rss=1" 100 nm. This decompaction is linked to active transcription but is not sensitive to the histone deacetylase inhibitor trichostatin A or to deletion of the histone acetyl transferase Gcn5. By contrast, the deletion of SNF2 (encoding the ATPase of the SWI/SNF chromatin remodeling complex) or the deactivation of the histone chaperone complex FACT lead to a strongly reduced decompaction without significant effects on transcriptional induction. Our findings are consistent with nucleosome remodeling and eviction activities being major contributors to chromatin reorganization during transcription but also suggest that transcription can occur in the absence of detectable decompaction. ]]> Dultz, E. Mancini, R. Polles, G. Vallotton, P. Alber, F. Weis, K. 2017-11-15 doi:10.1101/219253 Cold Spring Harbor Laboratory Press 2017-11-15 <![CDATA[ Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus ]]> https://biorxiv.org/cgi/content/short/219683v1?rss=1" Quinodoz, S. A. Ollikainen, N. Tabak, B. Palla, A. Schmidt, J. M. Detmar, E. Lai, M. Shishkin, A. Bhat, P. Trinh, V. Aznauryan, E. Russell, P. Cheng, C. Jovanovic, M. Chow, A. McDonel, P. Garber, M. Guttman, M. 2017-11-18 doi:10.1101/219683 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Allele-specific control of replication timing and genome organization during development ]]> https://biorxiv.org/cgi/content/short/221762v1?rss=1" Rivera-Mulia, J. C. Dimond, A. Vera, D. Trevilla-Garcia, C. Sasaki, T. Zimmerman, J. Dupont, C. Gribnau, J. Fraser, P. Gilbert, D. M. 2017-11-21 doi:10.1101/221762 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Single-molecule fluorescent amplification of RNA using clampFISH probes ]]> https://biorxiv.org/cgi/content/short/222794v1?rss=1" 400x) signal amplification. We show that clampFISH signal enables detection with low magnification microscopy and separation of cells by RNA levels via flow cytometry. Additionally, we show that the modular design of clampFISH probes enables multiplexing, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH works in tissue samples. ]]> Rouhanifard, S. H. Dunagin, M. Mellis, I. A. Bayatpour, S. Symmons, O. Cote, A. Raj, A. 2017-11-21 doi:10.1101/222794 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Dynamic reorganization of nuclear architecture during human cardiogenesis ]]> https://biorxiv.org/cgi/content/short/222877v1?rss=1" Fields, P. A. Ramani, V. Bonora, G. Yardimci, G. G. Bertero, A. Reinecke, H. Pabon, L. Noble, W. S. Shendure, J. Murry, C. 2017-11-21 doi:10.1101/222877 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ GITAR: An open source tool for analysis and visualization of Hi-C data ]]> https://biorxiv.org/cgi/content/short/259515v1?rss=1" Calandrelli, R. Wu, Q. Guan, J. Zhong, S. 2018-02-04 doi:10.1101/259515 Cold Spring Harbor Laboratory Press 2018-02-04 <![CDATA[ A quantitative map of human Condensins provides new insights into mitotic chromosome architecture ]]> https://biorxiv.org/cgi/content/short/237834v1?rss=1" Walther, N. Hossain, M. J. Politi, A. Z. Koch, B. Kueblbeck, M. Oedegaard-Fougner, O. Lampe, M. Ellenberg, J. 2018-01-09 doi:10.1101/237834 Cold Spring Harbor Laboratory Press 2018-01-09 <![CDATA[ Heterochromatin drives organization of conventional and inverted nuclei ]]> https://biorxiv.org/cgi/content/short/244038v1?rss=1" Falk, M. Feodorova, Y. Naumova, N. Imakaev, M. Lajoie, B. R. Leonhardt, H. Joffe, B. Dekker, J. Fudenberg, G. Solovei, I. Mirny, L. 2018-01-09 doi:10.1101/244038 Cold Spring Harbor Laboratory Press 2018-01-09 <![CDATA[ Emerging Evidence of Chromosome Folding by Loop Extrusion ]]> https://biorxiv.org/cgi/content/short/264648v1?rss=1" Fudenberg, G. Abdennur, N. Imakaev, M. Goloborodko, A. Mirny, L. 2018-02-16 doi:10.1101/264648 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ Multiplex Chromatin Interaction Analysis with Single-Molecule Precision ]]> https://biorxiv.org/cgi/content/short/252049v1?rss=1" Zheng, M. Tian, S. Z. Maurya, R. Lee, B. Kim, M. Capurso, D. Piecuch, E. Gong, L. Zhu, J. J. Wong, C. H. Ngan, C. Y. Wang, P. Ruan, X. Wei, C.-L. Ruan, Y. 2018-01-25 doi:10.1101/252049 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Chromatin interaction data visualization in the WashU Epigenome Browser ]]> https://biorxiv.org/cgi/content/short/239368v1?rss=1" Li, D. Hsu, S. Purushotham, D. Wang, T. 2017-12-24 doi:10.1101/239368 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 ]]> https://biorxiv.org/cgi/content/short/254797v1?rss=1" Dudchenko, O. Shamim, M. S. Batra, S. Durand, N. C. Musial, N. T. Mostofa, R. Pham, M. Glenn St Hilaire, B. Yao, W. Stamenova, E. Hoeger, M. Nyquist, S. K. Korchina, V. Pletch, K. Flanagan, J. P. Tomaszewicz, A. McAloose, D. Perez Estrada, C. Novak, B. J. Omer, A. D. Aiden, E. L. 2018-01-28 doi:10.1101/254797 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control ]]> https://biorxiv.org/cgi/content/short/240747v1?rss=1" Matthews, B. J. Dudchenko, O. Kingan, S. Koren, S. Antoshechkin, I. Crawford, J. E. Glassford, W. J. Herre, M. Redmond, S. N. Rose, N. H. Weedall, G. D. Wu, Y. Batra, S. S. Brito-Sierra, C. A. Buckingham, S. D. Campbell, C. L. Chan, S. Cox, E. Evans, B. R. Fansiri, T. Filipovic, I. Fontaine, A. Gloria-Soria, A. Hall, R. Joardar, V. S. Jones, A. K. Kay, R. G. G. Kodali, V. Lee, J. Lycett, G. J. Mitchell, S. N. Muehling, J. Murphy, M. R. Omer, A. Partridge, F. A. Peluso, P. Aiden, A. P. Ramasamy, V. Rasic, G. Roy, S. Saavedra-Rodriguez, K. Sharan, S. Sha 2017-12-29 doi:10.1101/240747 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome ]]> https://biorxiv.org/cgi/content/short/300483v1?rss=1" Chen, W. Yan, Z. Li, S. Huang, N. Huang, X. Zhang, J. Zhong, S. 2018-04-12 doi:10.1101/300483 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Pattern-Driven Navigation in 2D Multiscale Visual Spaces with Scalable Insets ]]> https://biorxiv.org/cgi/content/short/301036v1?rss=1" Lekschas, F. Behrisch, M. Bach, B. Kerpedjiev, P. Gehlenborg, N. Pfister, H. 2018-04-15 doi:10.1101/301036 Cold Spring Harbor Laboratory Press 2018-04-15 <![CDATA[ TSA-Seq Mapping of Nuclear Genome Organization ]]> https://biorxiv.org/cgi/content/short/307892v1?rss=1" Chen, Y. Zhang, Y. Wang, Y. Zhang, L. Brinkman, E. K. Adam, S. A. Goldman, R. van Steensel, B. Ma, J. Belmont, A. S. 2018-04-25 doi:10.1101/307892 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles ]]> https://biorxiv.org/cgi/content/short/347955v1?rss=1" Kim, J. Han, K. Y. Khanna, N. Ha, T. Belmont, A. S. 2018-06-15 doi:10.1101/347955 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ LADL: Light-activated dynamic looping for endogenous gene expression control ]]> https://biorxiv.org/cgi/content/short/349340v1?rss=1" Rege, M. Kim, J. H. Valeri, J. Dunagin, M. Metzger, A. Gong, W. Beagan, J. Raj, A. Phillips-Cremins, J. E. 2018-06-18 doi:10.1101/349340 Cold Spring Harbor Laboratory Press 2018-06-18 <![CDATA[ A combination of transcription factors mediates inducible interchromosomal pairing ]]> https://biorxiv.org/cgi/content/short/385047v1?rss=1" Kim, S. Dunham, M. Shendure, J. 2018-08-05 doi:10.1101/385047 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ Photon count estimation in single-molecule localization microscopy ]]> https://biorxiv.org/cgi/content/short/396424v1?rss=1" Rieger, B. Stallinga, S. Hulleman, C. N. Thorsen, R. O. Grunwald, D. Hammer, M. 2018-08-20 doi:10.1101/396424 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population Scale ]]> https://biorxiv.org/cgi/content/short/266981v1?rss=1" Sadowski, M. Kraft, A. Szalaj, P. Wlasnowolski, M. Tang, Z. Ruan, Y. Plewczynski, D. 2018-09-14 doi:10.1101/266981 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs ]]> https://biorxiv.org/cgi/content/short/472019v1?rss=1" Yan, Z. Huang, N. Wu, W. Chen, W. Jiang, Y. Chen, J. Huang, X. Wen, X. Xu, J. Jin, Q. Zhang, K. Chen, Z. Chien, S. Zhong, S. 2018-11-19 doi:10.1101/472019 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Feasibility of constructing multi-dimensional genomic maps of juvenile idiopathic arthritis ]]> https://biorxiv.org/cgi/content/short/349811v1?rss=1" Jarvis, J. N. Zhu, L. Jiang, K. Wong, L. Buck, M. J. Chen, Y. Moncrief, H. Macintosh, L. A. Liu, T. Sing, X. Li, D. Wang, T. O'Neil, K. M. 2018-06-18 doi:10.1101/349811 Cold Spring Harbor Laboratory Press 2018-06-18 <![CDATA[ An inter-chromosomal transcription hub activates the unfolded protein response in plasma cells ]]> https://biorxiv.org/cgi/content/short/295915v1?rss=1" Bortnick, A. He, Z. Aubrey, M. Chandra, V. Denholtz, M. Chen, K. Lin, Y. C. Murre, C. 2018-04-06 doi:10.1101/295915 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Mapping local and global liquid-liquid phase behavior in living cells using light-activated multivalent seeds ]]> https://biorxiv.org/cgi/content/short/283655v1?rss=1" Bracha, D. Walls, M. T. Wei, M.-T. Zhu, L. Kurian, M. Toettcher, J. E. Brangwynne, C. P. 2018-03-16 doi:10.1101/283655 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cells ]]> https://biorxiv.org/cgi/content/short/470963v1?rss=1" Ren, B. Li, G. Liu, Y. Fang, R. Kellis, M. Zhang, Y. 2018-11-14 doi:10.1101/470963 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Highly Structured Homolog Pairing Reflects Functional Organization of the Drosophila Genome ]]> https://biorxiv.org/cgi/content/short/443887v1?rss=1" AlHaj Abed, J. Erceg, J. Goloborodko, A. Nguyen, S. C. McCole, R. B. Saylor, W. Fudenberg, G. Lajoie, B. R. Dekker, J. Mirny, L. A. Wu, T. 2018-10-17 doi:10.1101/443887 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting ]]> https://biorxiv.org/cgi/content/short/386359v1?rss=1" Symmons, O. Chang, M. Mellis, I. Kalish, J. M. Bartolomei, M. S. Raj, A. 2018-08-07 doi:10.1101/386359 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Tibanna: software for scalable execution of portable pipelines on the cloud ]]> https://biorxiv.org/cgi/content/short/440974v1?rss=1" Lee, S. Johnson, J. Vitzthum, C. Kırlı, K. Alver, B. H. Park, P. J. 2018-10-11 doi:10.1101/440974 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Antigen receptor locus dynamics is orchestrated near the sol-gel phase transition to enforce stepwise VDJ gene rearrangement ]]> https://biorxiv.org/cgi/content/short/441444v1?rss=1" Khanna, N. Zhang, J. Dudko, O. Murre, C. 2018-10-12 doi:10.1101/441444 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ Satb1 integrates DNA sequence, shape, motif density and torsional stress to differentially bind targets in nucleosome-dense regions. ]]> https://biorxiv.org/cgi/content/short/450262v1?rss=1" GHOSH, R. P. SHI, Q. YANG, L. REDDICK, M. P. NIKITINA, T. ZHURKIN, V. B. FORDYCE, P. STASEVICH, T. J. CHANG, H. Y. GREENLEAF, W. J. LIPHARDT, J. T. 2018-10-26 doi:10.1101/450262 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum ]]> https://biorxiv.org/cgi/content/short/473553v1?rss=1" Dudchenko, O. Pham, M. Lui, C. Batra, S. S. Hoeger, M. Nyquist, S. K. Durand, N. C. Shamim, M. S. Machol, I. Erskine, W. Aiden, E. L. Kaur, P. 2018-11-20 doi:10.1101/473553 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors ]]> https://biorxiv.org/cgi/content/short/379016v1?rss=1" Shaffer, S. M. Emert, B. L. Sizemore, A. E. Gupte, R. Torre, E. Bassett, D. S. Raj, A. 2018-07-27 doi:10.1101/379016 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and function ]]> https://biorxiv.org/cgi/content/short/399139v1?rss=1" Lawlor, N. Marquez, E. J. Orchard, P. Narisu, N. Shamim, M. S. Thibodeau, A. Varshney, A. Kursawe, R. Erdos, M. R. Kanke, M. Gu, H. Pak, E. Dutra, A. Russell, S. Li, X. Piecuch, E. Luo, O. Chines, P. S. Fuchbserger, C. Sethupathy, P. Aiden, A. P. Ruan, Y. Aiden, E. L. Collins, F. S. Ucar, D. Parker, S. C. J. Stitzel, M. L. 2018-08-23 doi:10.1101/399139 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid mice ]]> https://biorxiv.org/cgi/content/short/338053v1?rss=1" Yin, Y. Jiang, Y. Berletch, J. B. Disteche, C. M. Noble, W. S. Steemers, F. J. Adey, A. C. Shendure, J. A. 2018-06-04 doi:10.1101/338053 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling ]]> https://biorxiv.org/cgi/content/short/374058v1?rss=1" Nir, G. Farabella, I. Perez Estrada, C. Ebeling, C. G. Beliveau, B. J. Sasaki, H. M. Lee, S. H. Nguyen, S. C. McCole, R. B. Chattoraj, S. Erceg, J. AlHaj Abed, J. Martins, N. M. C. Nguyen, H. Q. Hannan, M. A. Russell, S. Durand, N. C. Rao, S. S. P. Kishi, J. Y. Soler-Vila, P. Di Pierro, M. Onuchic, J. N. Callahan, S. Schreiner, J. Stuckey, J. Yin, P. Lieberman Aiden, E. Marti-Renom, M. A. Wu, C.- t. 2018-07-28 doi:10.1101/374058 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments ]]> https://biorxiv.org/cgi/content/short/411835v1?rss=1" Juric, I. Yu, M. Abnousi, A. Raviram, R. Fang, R. Zhao, Y. Zhang, Y. Yang, Y. Li, Y. Ren, B. Hu, M. 2018-09-08 doi:10.1101/411835 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning ]]> https://biorxiv.org/cgi/content/short/365866v1?rss=1" Oomen, M. E. Hansen, A. Liu, Y. Darzacq, X. Dekker, J. 2018-07-09 doi:10.1101/365866 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organization ]]> https://biorxiv.org/cgi/content/short/325209v1?rss=1" Kim, J.-S. He, X. Liu, J. Duan, Z. Kim, T. Gerard, J. Kim, B. Lane, W. S. Noble, W. S. Budnik, B. Waldman, T. 2018-05-17 doi:10.1101/325209 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Multi-scale deep tensor factorization learns a latent representation of the human epigenome ]]> https://biorxiv.org/cgi/content/short/364976v1?rss=1" Schreiber, J. Durham, T. J. Bilmes, J. Noble, W. S. 2018-07-08 doi:10.1101/364976 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos ]]> https://biorxiv.org/cgi/content/short/443028v1?rss=1" Erceg, J. AlHaj Abed, J. Goloborodko, A. Lajoie, B. R. Fudenberg, G. Abdennur, N. Imakaev, M. McCole, R. B. Nguyen, S. C. Saylor, W. Joyce, E. F. Senaratne, T. N. Hannan, M. A. Nir, G. Dekker, J. Mirny, L. A. Wu, C.-t. 2018-10-17 doi:10.1101/443028 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Limits of chromosome compaction by loop-extruding motors ]]> https://biorxiv.org/cgi/content/short/476424v1?rss=1" Banigan, E. J. Mirny, L. A. 2018-11-21 doi:10.1101/476424 Cold Spring Harbor Laboratory Press 2018-11-21 <![CDATA[ Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold ]]> https://biorxiv.org/cgi/content/short/384982v1?rss=1" Marko, J. Biggs, R. Sun, M. Hornick, J. 2018-08-04 doi:10.1101/384982 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Revealing Hi-C subcompartments by imputing high-resolution inter-chromosomal chromatin interactions ]]> https://biorxiv.org/cgi/content/short/505503v1?rss=1" Xiong, K. Ma, J. 2018-12-23 doi:10.1101/505503 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ An RNA-binding region regulates CTCF clustering and chromatin looping ]]> https://biorxiv.org/cgi/content/short/495432v1?rss=1" Hansen, A. S. Hsieh, T.-H. S. Cattoglio, C. Pustova, I. Darzacq, X. Tjian, R. 2018-12-13 doi:10.1101/495432 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Guided nuclear exploration increases CTCF target search efficiency ]]> https://biorxiv.org/cgi/content/short/495457v1?rss=1" Hansen, A. S. Amitai, A. Cattoglio, C. Tjian, R. Darzacq, X. 2018-12-13 doi:10.1101/495457 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase Separation ]]> https://biorxiv.org/cgi/content/short/375071v1?rss=1" McSwiggen, D. T. Hansen, A. S. Marie-Nelly, H. Teves, S. Heckert, A. B. Dugast-Darzacq, C. Hao, Y. Umemoto, K. K. Tjian, R. Darzacq, X. 2018-07-23 doi:10.1101/375071 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome ]]> https://biorxiv.org/cgi/content/short/542092v1?rss=1" Tian, D. Zhang, R. Zhang, Y. Zhu, X. Ma, J. 2019-02-07 doi:10.1101/542092 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Comparing 3D genome organization in multiple species using Phylo-HMRF ]]> https://biorxiv.org/cgi/content/short/552505v1?rss=1" Yang, Y. Zhang, Y. Ren, B. Dixon, J. Ma, J. 2019-02-19 doi:10.1101/552505 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy ]]> https://biorxiv.org/cgi/content/short/555250v1?rss=1" Bertero, A. Fields, P. A. Smith, A. S. Leonard, A. Beussman, K. Sniadecki, N. J. Kim, D.-H. Tse, H.-F. Pabon, L. Shendure, J. Noble, W. S. Murry, C. E. 2019-02-19 doi:10.1101/555250 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Localization microscopy at doubled precision with patterned illumination ]]> https://biorxiv.org/cgi/content/short/554337v1?rss=1" Cnossen, J. Hinsdale, T. Thorsen, R. Schueder, F. Jungmann, R. Smith, C. S. Rieger, B. Stallinga, S. 2019-02-20 doi:10.1101/554337 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Cooler: scalable storage for Hi-C data andother genomically-labeled arrays ]]> https://biorxiv.org/cgi/content/short/557660v1?rss=1" Abdennur, N. Mirny, L. 2019-02-22 doi:10.1101/557660 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Absolute quantification of cohesin, CTCF and their regulators in human cells ]]> https://biorxiv.org/cgi/content/short/560425v1?rss=1" Holzmann, J. Politi, A. Z. Nagasaka, K. Hantsche-Grininger, M. Walther, N. Koch, B. Fuchs, J. Dürnberger, G. Tang, W. Ladurner, R. Stocsits, R. R. Busslinger, G. A. Novak, B. Mechtler, K. Davidson, I. F. Ellenberg, J. Peters, J.-M. 2019-02-26 doi:10.1101/560425 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Architectural Features of 3D Genome Organization Revealed by Counting CTCF and Cohesin Molecules ]]> https://biorxiv.org/cgi/content/short/370650v1?rss=1" Cattoglio, C. Pustova, I. Ho, J. J. Inouye, C. J. Dailey, G. M. Darzacq, X. Tjian, R. Hansen, A. S. 2018-07-17 doi:10.1101/370650 Cold Spring Harbor Laboratory Press 2018-07-17 <![CDATA[ Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning ]]> https://biorxiv.org/cgi/content/short/597518v1?rss=1" Lekschas, F. Peterson, B. Haehn, D. Ma, E. Gehlenborg, N. Pfister, H. 2019-04-04 doi:10.1101/597518 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Common DNA sequence variation influences 3-dimensional conformation of the human genome ]]> https://biorxiv.org/cgi/content/short/592741v1?rss=1" Gorkin, D. Qiu, Y. Hu, M. Fletez-Brant, K. Liu, T. Schmitt, A. Noor, A. Chiou, J. Gaulton, K. Sebat, J. Li, Y. Hansen, K. Ren, B. 2019-03-30 doi:10.1101/592741 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Nuclear pores as versatile reference standards for quantitative superresolution microscopy ]]> https://biorxiv.org/cgi/content/short/582668v1?rss=1" Thevathasan, J. V. Kahnwald, M. Cieslinski, K. Hoess, P. Peneti, S. K. Reitberger, M. Heid, D. Kasuba, K. C. Hoerner, S. J. Li, Y. Wu, Y.-L. Mund, M. Matti, U. Pereira, P. M. Henriques, R. Nijmeijer-Winter, B. Kueblbeck, M. Jimenez Sabinina, V. Ellenberg, J. Ries, J. 2019-03-20 doi:10.1101/582668 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINT ]]> https://biorxiv.org/cgi/content/short/579961v1?rss=1" Schlichthaerle, T. Strauss, M. T. Schueder, F. Auer, A. Nijmeijer, B. Kueblbeck, M. Jimenez Sabinina, V. Ries, J. Ellenberg, J. Jungmann, R. 2019-03-19 doi:10.1101/579961 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Transcription amplification by nuclear speckle association ]]> https://biorxiv.org/cgi/content/short/604298v1?rss=1" Kim, J. Khanna, N. Belmont, A. 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Gerace, L. 2018-12-03 doi:10.1101/486415 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Spring Model - chromatin modeling tool based on OpenMM ]]> https://biorxiv.org/cgi/content/short/642322v1?rss=1" Kadlof, M. Rozycka, J. Plewczynski, D. 2019-05-20 doi:10.1101/642322 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells ]]> https://biorxiv.org/cgi/content/short/621920v1?rss=1" Ruan, Y. Plewczynski, D. Zhu, J. J. Parteka, Z. Lee, B. Szalaj, P. Wang, P. Jodkowska, K. Arron, J. Chew, T. L. 2019-04-29 doi:10.1101/621920 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ HiNT: a computational method for detecting copy number variations and translocations from Hi-C data ]]> https://biorxiv.org/cgi/content/short/657080v1?rss=1" Wang, S. Lee, S. Chu, C. Jain, D. Nelson, G. Walsh, J. M. Alver, B. H. Park, P. J. 2019-06-03 doi:10.1101/657080 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Inferring diploid 3D chromatin structures from Hi-C data ]]> https://biorxiv.org/cgi/content/short/644294v1?rss=1" Cauer, A. Yardimci, G. G. Vert, J.-P. Varoquaux, N. Noble, W. 2019-05-21 doi:10.1101/644294 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Jointly embedding multiple single-cell omics measurements ]]> https://biorxiv.org/cgi/content/short/644310v1?rss=1" Liu, J. Huang, Y. Singh, R. Yardimci, G. G. Noble, W. 2019-05-21 doi:10.1101/644310 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome ]]> https://biorxiv.org/cgi/content/short/687236v1?rss=1" FANG, H. Bonora, G. Lewandowski, J. Thakur, J. Filippova, G. N. Henikoff, S. Shendure, J. Duan, Z. Rinn, J. Deng, X. Noble, W. S. Disteche, C. M. 2019-06-30 doi:10.1101/687236 Cold Spring Harbor Laboratory Press 2019-06-30 <![CDATA[ Photoactivation of silicon rhodamines via a light-induced protonation ]]> https://biorxiv.org/cgi/content/short/626853v1?rss=1" Frei, M. S. Hoess, P. Lampe, M. Nijmeijer, B. Kueblbeck, M. Ellenberg, J. Ries, J. Pitsch, S. Reymond, L. Johnsson, K. 2019-05-04 doi:10.1101/626853 Cold Spring Harbor Laboratory Press 2019-05-04 <![CDATA[ Chemogenetic control of nanobodies ]]> https://biorxiv.org/cgi/content/short/683557v1?rss=1" Farrants, H. Tarnawski, M. Müller, T. G. Otsuka, S. Hiblot, J. Koch, B. Kueblbeck, M. Kräusslich, H.-G. Ellenberg, J. Johnsson, K. 2019-06-27 doi:10.1101/683557 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC ]]> https://biorxiv.org/cgi/content/short/708024v1?rss=1" Zhao, B. Chaturvedi, P. Zimmerman, D. L. Belmont, A. S. 2019-07-19 doi:10.1101/708024 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction ]]> https://biorxiv.org/cgi/content/short/712950v1?rss=1" Calandrelli, R. Xu, L. Luo, Y. Wu, W. Fan, X. Nguyen, T. Chen, C. Sriram, K. Natarajan, R. Chen, Z. Zhong, S. 2019-07-24 doi:10.1101/712950 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C ]]> https://biorxiv.org/cgi/content/short/704957v1?rss=1" Belaghzal, H. Borrman, T. Stephens, A. D. Lafontaine, D. L. Venev, S. V. Marko, J. F. Weng, Z. Dekker, J. 2019-07-16 doi:10.1101/704957 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ A chromosome folding intermediate at the condensin-to-cohesin transition during telophase ]]> https://biorxiv.org/cgi/content/short/678474v1?rss=1" Abramo, K. Valton, A.-L. Venev, S. V. Ozadam, H. Fox, A. N. Dekker, J. 2019-06-21 doi:10.1101/678474 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Measuring significant changes in chromatin conformation with ACCOST ]]> https://biorxiv.org/cgi/content/short/727768v1?rss=1" Cook, K. B. Le Roch, K. G. Vert, J.-P. Noble, W. 2019-08-06 doi:10.1101/727768 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear speckles ]]> https://biorxiv.org/cgi/content/short/824433v1?rss=1" Zhang, L. Zhang, Y. Chen, Y. Gholamalamdari, O. Ma, J. Belmont, A. S. 2019-10-30 doi:10.1101/824433 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Direct, sensitive and specific detection of individual single- or double-strand DNA breaks by fluorescence microscopy ]]> https://biorxiv.org/cgi/content/short/772269v1?rss=1" Kordon, M. Zarebski, M. Solarczyk, K. Ma, H. Pederson, T. Dobrucki, J. W. 2019-09-18 doi:10.1101/772269 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells ]]> https://biorxiv.org/cgi/content/short/579573v1?rss=1" Ramani, V. Deng, X. Qiu, R. Lee, C. Disteche, C. M. Noble, W. S. Duan, Z. Shendure, J. 2019-03-15 doi:10.1101/579573 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ Chromosome organization by one-sided and two-sided loop extrusion ]]> https://biorxiv.org/cgi/content/short/815340v1?rss=1" Banigan, E. J. van den Berg, A. A. Brandao, H. B. Marko, J. F. Mirny, L. A. 2019-10-22 doi:10.1101/815340 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded Cells ]]> https://biorxiv.org/cgi/content/short/749754v1?rss=1" Yang, L. Ghosh, R. P. Franklin, J. M. You, C. Liphardt, J. 2019-08-28 doi:10.1101/749754 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Spatial genome re-organization between fetal and adult hematopoietic stem cells ]]> https://biorxiv.org/cgi/content/short/628214v1?rss=1" Chen, C. Yu, W. Tober, J. Gao, P. He, B. Lee, K. Trieu, T. Blobel, G. Speck, N. Tan, K. 2019-05-05 doi:10.1101/628214 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecture ]]> https://biorxiv.org/cgi/content/short/816611v1?rss=1" Cremer, M. Brandstetter, K. Maiser, A. Rao, S. S. Schmid, V. Mitra, N. Mamberti, S. Klein, K. N. Gilbert, D. M. Leonhardt, H. Cardoso, M. C. Lieberman Aiden, E. Harz, H. Cremer, T. 2019-10-24 doi:10.1101/816611 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Multiplex chromatin interaction analysis by signal processing and statistical algorithms ]]> https://biorxiv.org/cgi/content/short/665232v1?rss=1" Kim, M. Zheng, M. Tian, S. Z. Capurso, D. Lee, B. Chuang, J. H. Ruan, Y. 2019-06-10 doi:10.1101/665232 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Co-opted transposons help perpetuate conserved higher-order chromosomal structures ]]> https://biorxiv.org/cgi/content/short/485342v1?rss=1" Choudhary, M. N. Friedman, R. Z. Wang, J. T. Jang, H. S. Zhuo, X. Wang, T. 2018-12-05 doi:10.1101/485342 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL ]]> https://biorxiv.org/cgi/content/short/779058v1?rss=1" Wutz, G. St. Hilaire, B. T. G. Ladurner, R. Stocsits, R. Nagasaka, K. Pignard, B. Sanborn, A. Tang, W. Varnai, C. Ivanov, M. Schoenfelder, S. van der Lelij, P. Huang, X. Duernberger, G. Roitinger, E. Mechtler, K. Davidson, I. F. Fraser, P. Aiden, E. L. Peters, J. M. 2019-09-23 doi:10.1101/779058 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ A supervised learning framework for chromatin loop detection in genome-wide contact maps ]]> https://biorxiv.org/cgi/content/short/739698v1?rss=1" Salameh, T. J. Wang, X. Song, F. Zhang, B. Wright, S. M. Khunsriraksakul, C. Yue, F. 2019-08-20 doi:10.1101/739698 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Distinct features of nucleolus-associated domains in mouse embryonic stem cells ]]> https://biorxiv.org/cgi/content/short/740480v1?rss=1" Bizhanova, A. Yan, A. Yu, J. Zhu, L. J. Kaufman, P. D. 2019-08-20 doi:10.1101/740480 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ FIREcaller: an R package for detecting frequently interacting regions from Hi-C data ]]> https://biorxiv.org/cgi/content/short/619288v1?rss=1" Crowley, C. Yang, Y. Qiu, Y. Hu, B. Won, H. Ren, B. Hu, M. Li, Y. 2019-04-29 doi:10.1101/619288 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Composition dependent phase separation underlies directional flux through the nucleolus ]]> https://biorxiv.org/cgi/content/short/809210v1?rss=1" Riback, J. A. Zhu, L. Ferrolino, M. C. Tolbert, M. Mitrea, D. M. Sanders, D. W. Wei, M.-T. Kriwacki, R. W. Brangwynne, C. P. 2019-10-22 doi:10.1101/809210 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Supervised classification enables rapid annotation of cell atlases ]]> https://biorxiv.org/cgi/content/short/538652v1?rss=1" Pliner, H. A. Shendure, J. Trapnell, C. 2019-02-04 doi:10.1101/538652 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Genetic screening for single-cell variability modulators driving therapy resistance ]]> https://biorxiv.org/cgi/content/short/638809v1?rss=1" Torre, E. A. Arai, E. Bayatpour, S. Beck, L. E. Emert, B. L. Shaffer, S. M. Mellis, I. A. Budinich, K. A. Weeraratna, A. Shi, J. Raj, A. 2019-05-15 doi:10.1101/638809 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples ]]> https://biorxiv.org/cgi/content/short/533273v1?rss=1" Schreiber, J. Bilmes, J. Noble, W. 2019-01-29 doi:10.1101/533273 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data ]]> https://biorxiv.org/cgi/content/short/534800v1?rss=1" Kim, H.-J. Yardimici, G. G. Bonora, G. Ramani, V. Liu, J. Qiu, R. Lee, C. Hesson, J. Ware, C. B. Shendure, J. Duan, Z. Noble, W. S. 2019-01-30 doi:10.1101/534800 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition ]]> https://biorxiv.org/cgi/content/short/604355v1?rss=1" Zhang, H. Emerson, D. Gilgenast, T. Titus, K. Lan, Y. Huang, P. Zhang, D. Wang, H. Keller, C. Giardine, B. Hardison, R. Phillips-Cremins, J. Blobel, G. 2019-04-11 doi:10.1101/604355 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin ]]> https://biorxiv.org/cgi/content/short/484568v1?rss=1" Vertii, A. Ou, J. Yu, J. Yan, A. Pages, H. Liu, H. Zhu, L. J. Kaufman, P. D. 2018-12-03 doi:10.1101/484568 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Ultrastructural details of mammalian chromosome architecture ]]> https://biorxiv.org/cgi/content/short/639922v1?rss=1" Krietenstein, N. Abraham, S. Venev, S. Abdennur, N. Gibcus, J. Hsieh, T.-H. Parsi, K. M. Yang, L. Maehr, R. Mirny, L. Dekker, J. Rando, O. 2019-05-17 doi:10.1101/639922 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Nucleated transcriptional condensates amplify gene expression ]]> https://biorxiv.org/cgi/content/short/737387v1?rss=1" Wei, M.-T. Chang, Y.-C. Shimobayashi, S. F. Shin, Y. Brangwynne, C. P. 2019-08-16 doi:10.1101/737387 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks ]]> https://biorxiv.org/cgi/content/short/709683v1?rss=1" Zhang, H. B. Kim, M. Chuang, J. H. Ruan, Y. 2019-07-20 doi:10.1101/709683 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Spatial resets modulate YAP-dependent transcription ]]> https://biorxiv.org/cgi/content/short/539049v1?rss=1" Franklin, J. M. Ghosh, R. P. Shi, Q. Liphardt, J. T. 2019-02-03 doi:10.1101/539049 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ EpiAlignment: alignment with both DNA sequence and epigenomic data ]]> https://biorxiv.org/cgi/content/short/562199v1?rss=1" Lu, J. Cao, X. Zhong, S. 2019-02-27 doi:10.1101/562199 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancer ]]> https://biorxiv.org/cgi/content/short/704247v1?rss=1" Schuh, L. Saint-Antoine, M. Sanford, E. Emert, B. Singh, A. Marr, C. Goyal, Y. Raj, A. 2019-07-16 doi:10.1101/704247 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Chromatin is frequently unknotted at the megabase scale ]]> https://biorxiv.org/cgi/content/short/762872v1?rss=1" Goundaroulis, D. Aiden, E. L. Stasiak, A. 2019-09-09 doi:10.1101/762872 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells ]]> https://biorxiv.org/cgi/content/short/734483v1?rss=1" Wang, H. Nakamura, M. Zhao, D. Nguyen, C. M. Yu, C. Lo, A. Daley, T. La Russa, M. Liu, Y. Qi, L. S. 2019-08-13 doi:10.1101/734483 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization ]]> https://biorxiv.org/cgi/content/short/506683v1?rss=1" Capurso, D. Wang, J. Tian, S. Z. Cai, L. Namburi, S. Lee, B. Tjong, H. Tang, Z. Wang, P. Wei, C.-L. Ruan, Y. Li, S. 2018-12-27 doi:10.1101/506683 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Effects of altering histone post-translational modifications on mitotic chromosome structure and mechanics ]]> https://biorxiv.org/cgi/content/short/423541v1?rss=1" Biggs, R. Stephens, A. D. Liu, P. Marko, J. F. 2018-09-22 doi:10.1101/423541 Cold Spring Harbor Laboratory Press 2018-09-22 <![CDATA[ The accessible chromatin landscape of the hippocampus at single-cell resolution ]]> https://biorxiv.org/cgi/content/short/407668v1?rss=1" Sinnamon, J. R. Torkenczy, K. A. Linhoff, M. W. Vitak, S. A. Pliner, H. A. Trapnell, C. Steemers, F. J. Mandel, G. Adey, A. C. 2018-09-04 doi:10.1101/407668 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Predicting CTCF-mediated chromatin loops using CTCF-MP ]]> https://biorxiv.org/cgi/content/short/259416v1?rss=1" Zhang, R. Wang, Y. Yang, Y. Zhang, Y. Ma, J. 2018-02-02 doi:10.1101/259416 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ RTFBSDB: an integrated framework for transcription factor binding site analysis ]]> https://biorxiv.org/cgi/content/short/036053v1?rss=1" Zhong Wang Andre L Martins Charles G Danko 2016-01-06 doi:10.1101/036053 Cold Spring Harbor Laboratory Press 2016-01-06 <![CDATA[ Promoter-intrinsic and local chromatin features determine gene repression in lamina-associated domains ]]> https://biorxiv.org/cgi/content/short/464081v1?rss=1" Leemans, C. van der Zwalm, M. Brueckner, L. Comoglio, F. van Schaik, T. Pagie, L. van Arensbergen, J. van Steensel, B. 2018-11-06 doi:10.1101/464081 Cold Spring Harbor Laboratory Press 2018-11-06 <![CDATA[ Architectural RNA is required for heterochromatin organization ]]> https://biorxiv.org/cgi/content/short/784835v1?rss=1" Thakur, J. Fang, H. Llagas, T. Disteche, C. M. Henikoff, S. 2019-09-27 doi:10.1101/784835 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures ]]> https://biorxiv.org/cgi/content/short/616102v1?rss=1" Brahmachari, S. Marko, J. F. 2019-04-26 doi:10.1101/616102 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Receptor-ligand rebinding kinetics in confinement ]]> https://biorxiv.org/cgi/content/short/370395v1?rss=1" Erbas, A. Olvera de la Cruz, M. Marko, J. 2018-07-16 doi:10.1101/370395 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ A cost-efficient open source laser engine for microscopy ]]> https://biorxiv.org/cgi/content/short/796482v1?rss=1" Schroeder, D. Deschamps, J. Dasgupta, A. Matti, U. Ries, J. 2019-10-15 doi:10.1101/796482 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Resolving the 3D landscape of transcription-linked mammalian chromatin folding ]]> https://biorxiv.org/cgi/content/short/638775v1?rss=1" Hsieh, T.-H. S. Slobodyanyuk, E. Hansen, A. S. Cattoglio, C. Rando, O. J. Tjian, R. Darzacq, X. 2019-05-17 doi:10.1101/638775 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation ]]> https://biorxiv.org/cgi/content/short/423442v1?rss=1" Stephens, A. D. Liu, P. Z. Kandula, V. Chen, H. Almassalha, L. M. Backman, V. O'Halloran, T. Adam, S. A. Goldman, R. D. Banigan, E. J. Marko, J. F. 2018-09-21 doi:10.1101/423442 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ CUT&Tag for efficient epigenomic profiling of small samples and single cells ]]> https://biorxiv.org/cgi/content/short/568915v1?rss=1" Kaya-Okur, H. S. Wu, S. J. Codomo, C. A. Pledger, E. S. Bryson, T. D. Henikoff, J. G. Ahmad, K. Henikoff, S. 2019-03-06 doi:10.1101/568915 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Developmental and conditional dynamics of gene expression in single root cells of A. thaliana ]]> https://biorxiv.org/cgi/content/short/448514v1?rss=1" Jean-Baptiste, K. McFaline-Figueroa, J. L. Alexandre, C. M. Dorrity, M. W. Saunders, L. Bubb, K. L. Trapnell, C. Fields, S. Queitsch, C. Cuperus, J. T. 2018-10-22 doi:10.1101/448514 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ Identification of cis elements for spatio-temporal control of DNA replication ]]> https://biorxiv.org/cgi/content/short/285650v1?rss=1" Sima, J. Chakraborty, A. Dileep, V. Michalski, M. Rivera-Mulia, J. C. Trevilla-Garcia, C. Klein, K. N. Bartlett, D. Washburn, B. K. Paulsen, M. T. Vera, D. Nora, E. P. Kraft, K. Mundlos, S. Bruneau, B. G. Ljungman, M. Fraser, P. Ay, F. Gilbert, D. M. 2018-03-21 doi:10.1101/285650 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution ]]> https://biorxiv.org/cgi/content/short/054031v1?rss=1" Amit Blumberg Edward J. Rice Anshul Kundaje Charles G. Danko Dan Mishmar 2016-05-18 doi:10.1101/054031 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Complementary chromosome folding by transcription factors and cohesin ]]> https://biorxiv.org/cgi/content/short/305359v1?rss=1" Pereira, M. C. F. Brackley, C. A. Michieletto, D. Annunziatella, C. Bianco, S. Chiariello, A. M. Nicodemi, M. Marenduzzo, D. 2018-04-23 doi:10.1101/305359 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Local rewiring of genome - nuclear lamina interactions by transcription. ]]> https://biorxiv.org/cgi/content/short/685255v1?rss=1" Brueckner, L. Zhao, P. A. van Schaik, T. Leemans, C. Sima, J. Peric-Hupkes, D. Gilbert, D. M. van Steensel, B. 2019-06-27 doi:10.1101/685255 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ 3D Single-Molecule Super-Resolution Microscopy With A Tilted Light Sheet ]]> https://biorxiv.org/cgi/content/short/135699v1?rss=1" Gustavsson, A.-K. Petrov, P. N. Lee, M. Y. Shechtman, Y. Moerner, W. E. 2017-05-09 doi:10.1101/135699 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Defect-Facilitated Buckling in Supercoiled Double-Helix DNA ]]> https://biorxiv.org/cgi/content/short/259689v1?rss=1" Brahmachari, S. Dittmore, A. Takagi, Y. Neuman, K. C. Marko, J. F. 2018-02-04 doi:10.1101/259689 Cold Spring Harbor Laboratory Press 2018-02-04 <![CDATA[ A streamlined protocol and analysis pipeline for CUT&RUN chromatin profiling ]]> https://biorxiv.org/cgi/content/short/569129v1?rss=1" Meers, M. P. Bryson, T. D. Henikoff, S. 2019-03-06 doi:10.1101/569129 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond ]]> https://biorxiv.org/cgi/content/short/422683v1?rss=1" Nomidis, S. K. Skoruppa, E. Carlon, E. Marko, J. F. 2018-09-20 doi:10.1101/422683 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation ]]> https://biorxiv.org/cgi/content/short/275354v1?rss=1" Bartman, C. R. Keller, C. A. Giardine, B. Hardison, R. C. Blobel, G. A. Raj, A. 2018-03-02 doi:10.1101/275354 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ Continuous-trait probabilistic model for comparing multi-species functional genomic data ]]> https://biorxiv.org/cgi/content/short/283093v1?rss=1" Yang, Y. Gu, Q. Zhang, Y. Sasaki, T. Crivello, J. O'Neill, R. J. Gilbert, D. M. Ma, J. 2018-03-16 doi:10.1101/283093 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes ]]> https://biorxiv.org/cgi/content/short/325373v1?rss=1" Marko, J. F. De Los Rios, P. Barducci, A. Gruber, S. 2018-05-17 doi:10.1101/325373 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development ]]> https://biorxiv.org/cgi/content/short/528877v1?rss=1" Paliou, C. Guckelberger, P. Schöpflin, R. Heinrich, V. Esposito, A. Chiariello, A. M. M. Bianco, S. Annunziatella, C. Helmuth, J. Haas, S. Jerkovic, I. Brieske, N. Wittler, L. Timmermann, B. Nicodemi, M. Vingron, M. Mundlos, S. Andrey, G. 2019-01-23 doi:10.1101/528877 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Bend-Induced Twist Waves and the Structure of Nucleosomal DNA ]]> https://biorxiv.org/cgi/content/short/256818v1?rss=1" Skoruppa, E. Nomidis, S. K. Marko, J. F. Carlon, E. 2018-01-30 doi:10.1101/256818 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ RNA polymerase II clustering through CTD phase separation ]]> https://biorxiv.org/cgi/content/short/316372v1?rss=1" Boehning, M. Dugast-Darzacq, C. Rankovic, M. Hansen, A. S. Yu, T.-K. Marie-Nelly, H. Kokic, G. Dailey, G. M. Cramer, P. Darzacq, X. Zweckstetter, M. 2018-05-07 doi:10.1101/316372 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ MS2-TRIBE evaluates protein-RNA interactions and nuclear organization of transcription by RNA editing ]]> https://biorxiv.org/cgi/content/short/829606v1?rss=1" Biswas, J. Rahman, R. Gupta, V. Rosbash, M. Singer, R. 2019-11-04 doi:10.1101/829606 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Probing multi-way chromatin interaction with hypergraph representation learning ]]> https://biorxiv.org/cgi/content/short/2020.01.22.916171v1?rss=1" Zhang, R. Ma, J. 2020-01-23 doi:10.1101/2020.01.22.916171 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos ]]> https://biorxiv.org/cgi/content/short/377812v1?rss=1" Mir, M. Stadler, M. R. Ortiz, S. A. Harrison, M. M. Darzacq, X. Eisen, M. B. 2018-07-26 doi:10.1101/377812 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ High-Resolution 3D Fluorescent Imaging of Intact Tissues ]]> https://biorxiv.org/cgi/content/short/855254v1?rss=1" 100 {micro}m) and resolution (<0.012 {micro}m3 voxel size) that has previously been limited to whole-mount in vitro organoid systems, embryos, and small model organisms. Confocal images of adult human and rodent organs, including heart, kidney, and liver, were generated for several chemical and antibody stains in cleared tissue sections >100 {micro}m thick. This method can be readily adopted by any lab performing routine histology and takes 3 days from the start of tissue preparation to 3D images. ]]> El-Nachef, D. Martinson, A. M. Yang, X. Murry, C. E. MacLellan, W. R. 2019-11-26 doi:10.1101/855254 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus ]]> https://biorxiv.org/cgi/content/short/2020.01.16.909333v1?rss=1" Ma, J. Do, M. Le Gros, M. A. Peskin, C. S. Larabell, C. A. Mori, Y. Isaacson, S. A. 2020-01-17 doi:10.1101/2020.01.16.909333 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild ]]> https://biorxiv.org/cgi/content/short/867341v1?rss=1" Humble, E. Dobrynin, P. Senn, H. Chuven, J. Scott, A. F. Mohr, D. W. Dudchenko, O. Omer, A. D. Colaric, Z. Lieberman Aiden, E. Wildt, D. Oliagi, S. Tamazian, G. Pukazhenthi, B. Ogden, R. Koepfli, K.-P. 2019-12-08 doi:10.1101/867341 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Schizophrenia and a high-resolution map of the three-dimensional chromatin interactome of adult and fetal cortex ]]> https://biorxiv.org/cgi/content/short/406330v1?rss=1" Giusti-Rodriguez, P. M. Sullivan, P. F. 2018-08-31 doi:10.1101/406330 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Cell cycle dynamics of lamina associated DNA ]]> https://biorxiv.org/cgi/content/short/2019.12.19.881979v1?rss=1" van Schaik, T. Vos, M. Peric-Hupkes, D. van Steensel, B. 2019-12-19 doi:10.1101/2019.12.19.881979 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies ]]> https://biorxiv.org/cgi/content/short/392662v1?rss=1" Sun, Z. Chen, L. Xin, H. Huang, Q. Cillo, A. Tabib, T. Ding, Y. Kolls, J. Bruno, T. Lafyatis, R. Vignali, D. Chen, K. Hu, M. Chen, W. 2018-08-16 doi:10.1101/392662 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data ]]> https://biorxiv.org/cgi/content/short/2020.01.30.927061v1?rss=1" Markowski, J. Kempfer, R. Kukalev, A. Irastorza-Azcarate, I. Loof, G. Pombo, A. Schwarz, R. F. 2020-01-31 doi:10.1101/2020.01.30.927061 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ An Improved 4'-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNA ]]> https://biorxiv.org/cgi/content/short/2020.02.29.971317v1?rss=1" Wielenberg, K. Wang, M. Yang, M. Ozer, A. Lis, J. Lin, H. 2020-02-29 doi:10.1101/2020.02.29.971317 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Condensin II inactivation in interphase does not affect chromatin folding or gene expression ]]> https://biorxiv.org/cgi/content/short/437459v1?rss=1" Abdennur, N. Schwarzer, W. Pekowska, A. Shaltiel, I. A. Huber, W. Haering, C. H. Mirny, L. Spitz, F. 2018-10-07 doi:10.1101/437459 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture Mapping ]]> https://biorxiv.org/cgi/content/short/2020.02.10.941047v1?rss=1" Welch, L. R. Baugher, C. Zhang, Y. Davis, T. Marzluff, W. F. Welch, J. D. Pombo, A. 2020-02-12 doi:10.1101/2020.02.10.941047 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ SPIN reveals genome-wide landscape of nuclear compartmentalization ]]> https://biorxiv.org/cgi/content/short/2020.03.09.982967v1?rss=1" Wang, Y. Zhang, Y. Zhang, R. van Schaik, T. Zhang, L. Sasaki, T. Peric-Hupkes, D. Chen, Y. Gilbert, D. M. van Steensel, B. Belmont, A. S. Ma, J. 2020-03-10 doi:10.1101/2020.03.09.982967 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Cell-type specialization in the brain is encoded by specific long-range chromatin topologies ]]> https://biorxiv.org/cgi/content/short/2020.04.02.020990v1?rss=1" 400 kb) when they are highly transcribed. We find many neuron-specific contacts which contain accessible chromatin regions enriched for putative binding sites for multiple neuronal transcription factors, and which connect cell-type specific genes that are associated with neurodegenerative disorders such as Parkinsons disease, or specialized functions such as synaptic plasticity and memory. Lastly, sensory receptor genes exhibit increased membership in heterochromatic compartments that establish strong contacts in brain cells. However, their silencing is compromised in a subpopulation of PGNs with molecular signatures of long-term potentiation. Overall, our work shows that the 3D organization of the genome is highly cell-type specific, and essential to better understand mechanisms of gene regulation in highly specialized tissues such as the brain. ]]> Winick-Ng, W. Kukalev, A. Harabula, I. Zea Redondo, L. Meijer, M. Serebreni, L. Bianco, S. Szabo, D. Chiariello, A. M. Irastorza Azcarate, I. Fiorillo, L. Musella, F. Thieme, C. Irani, E. Torlai Triglia, E. Kolodziejczyk, A. A. Abentung, A. Apostolova, G. Paul, E. J. Franke, V. Kempfer, R. Akalin, A. Teichmann, S. Dechant, G. Ungless, M. A. Nicodemi, M. Castelo-Branco, G. Pombo, A. 2020-04-02 doi:10.1101/2020.04.02.020990 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin ]]> https://biorxiv.org/cgi/content/short/2020.04.24.059915v1?rss=1" Fiorillo, L. Musella, F. Kempfer, R. Chiariello, A. M. Bianco, S. Kukalev, A. Irastorza-Azcarate, I. Esposito, A. Conte, M. Prisco, A. Pombo, A. Nicodemi, M. 2020-04-25 doi:10.1101/2020.04.24.059915 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells ]]> https://biorxiv.org/cgi/content/short/2020.03.21.001693v1?rss=1" Kubo, N. Ishii, H. Xiong, X. Bianco, S. Meitinger, F. Hu, R. Hocker, J. D. Conte, M. Gorkin, D. Yu, M. Li, B. Dixon, J. Hu, M. Nicodemi, M. Zhao, H. Ren, B. 2020-03-23 doi:10.1101/2020.03.21.001693 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data ]]> https://biorxiv.org/cgi/content/short/2020.04.27.060145v1?rss=1" Jain, D. Chu, C. Alver, B. H. Lee, S. Lee, E. A. Park, P. J. 2020-04-28 doi:10.1101/2020.04.27.060145 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Retrospective identification of rare cell populations underlying drug resistance connects molecular variability with cell fate ]]> https://biorxiv.org/cgi/content/short/2020.03.18.996660v1?rss=1" Emert, B. Cote, C. Torre, E. A. Dardani, I. P. Jiang, C. Jain, N. Shaffer, S. M. Raj, A. 2020-03-19 doi:10.1101/2020.03.18.996660 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments ]]> https://biorxiv.org/cgi/content/short/2020.04.10.036442v1?rss=1" Chen, Z. Shaw, A. Wilson, H. Woringer, M. Darzacq, X. Marqusee, S. Wang, Q. Bustamante, C. 2020-04-11 doi:10.1101/2020.04.10.036442 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell Lines ]]> https://biorxiv.org/cgi/content/short/2020.03.21.001917v1?rss=1" Cheng, R. R. Contessoto, V. Aiden, E. L. Wolynes, P. G. Di Pierro, M. Onuchic, J. N. 2020-03-22 doi:10.1101/2020.03.21.001917 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ EMU: reconfigurable graphical user interfaces for Micro-Manager ]]> https://biorxiv.org/cgi/content/short/2020.03.18.997494v1?rss=1" Deschamps, J. Ries, J. 2020-03-19 doi:10.1101/2020.03.18.997494 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Regulation of gene expression by repression condensates during development ]]> https://biorxiv.org/cgi/content/short/2020.03.03.975680v1?rss=1" Treen, N. Shimobayashi, S. F. Eeftens, J. Brangwynne, C. P. Levine, M. 2020-03-04 doi:10.1101/2020.03.03.975680 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH) ]]> https://biorxiv.org/cgi/content/short/2020.02.05.935106v1?rss=1" Trzaskoma, P. Ruszczycki, B. Lee, B. Pels, K. K. Krawczyk, K. Bokota, G. Szczepankiewicz, A. A. Aaron, J. Walczak, A. Sliwinska, M. Magalska, A. Kadloff, M. Wolny, A. Parteka, Z. Arabasz, S. Kiss- Arabasz, M. Plewczynski, D. Ruan, Y. Wilczynski, G. M. 2020-02-06 doi:10.1101/2020.02.05.935106 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Fluorophore-labelled RNA aptamers to common protein tags as super-resolution imaging reagents. ]]> https://biorxiv.org/cgi/content/short/2020.02.27.968578v1?rss=1" Wang, J. Singh, A. Ozer, A. Zipfel, W. R. 2020-02-28 doi:10.1101/2020.02.27.968578 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia ]]> https://biorxiv.org/cgi/content/short/2020.03.05.979070v1?rss=1" Ruan, Y. 2020-03-06 doi:10.1101/2020.03.05.979070 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia ]]> https://biorxiv.org/cgi/content/short/2020.02.23.961672v1?rss=1" Yang, H. Zhang, H. Luan, Y. Liu, T. Roberts, K. G. Qian, M.-x. Zhang, B. Yang, W. Perez-Andreu, V. Xu, J. Iyyanki, S. Kuang, D. Reshmi, S. C. Gastier-Foster, J. Smith, C. Pui, C.-H. Evans, W. E. Hunger, S. P. Platanias, L. C. Relling, M. V. Mullighan, C. G. Loh, M. L. Yue, F. Yang, J. J. 2020-02-25 doi:10.1101/2020.02.23.961672 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genes ]]> https://biorxiv.org/cgi/content/short/2020.04.06.028092v1?rss=1" Cote, A. J. Cote, C. J. Bayatpour, S. Drexler, H. L. Alexander, K. A. Chen, F. Wassie, A. T. Boyden, E. S. Berger, S. Churchman, L. S. Raj, A. 2020-04-07 doi:10.1101/2020.04.06.028092 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer ]]> https://biorxiv.org/cgi/content/short/2020.02.26.966697v1?rss=1" Iyyanki, T. S. Zhang, B. Jin, Q. Yang, H. Liu, T. Wang, X. Song, F. Luan, Y. Yamashita, H. Wang, L. Warrick, J. Raman, J. Meeks, J. DeGraff, D. J. Yue, F. 2020-02-29 doi:10.1101/2020.02.26.966697 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Accurate 4Pi single-molecule localization using an experimental PSF model ]]> https://biorxiv.org/cgi/content/short/2020.03.18.997163v1?rss=1" Li, Y. Buglakova, E. Zhang, Y. Thevathasan, J. V. Bewersdorf, J. Ries, J. 2020-03-19 doi:10.1101/2020.03.18.997163 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Exploring the coronavirus epidemic using the new WashU Virus Genome Browser ]]> https://biorxiv.org/cgi/content/short/2020.02.07.939124v1?rss=1" Flynn, J. Purushotham, D. Choudhary, M. N. Zhuo, X. Fan, C. Matt, G. Li, D. Wang, T. 2020-02-11 doi:10.1101/2020.02.07.939124 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization ]]> https://biorxiv.org/cgi/content/short/2020.02.18.954610v1?rss=1" Feng, Y. Wang, Y. Yang, C. Naseri, A. Pederson, T. Zheng, J. Xiao, X. Zhang, S. Xie, W. Ma, H. 2020-02-19 doi:10.1101/2020.02.18.954610 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Efficient Homology-directed Repair with Circular ssDNA Donors ]]> https://biorxiv.org/cgi/content/short/864199v1?rss=1" Iyer, S. Mir, A. Ibraheim, R. Lee, J. VegaBadillo, J. Roscoe, B. Zhu, L. J. Liu, P. Luk, K. Mintzer, E. de Brito, J. S. Zamore, P. Sontheimer, E. J. Wolfe, S. 2019-12-05 doi:10.1101/864199 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ The qBED track: a novel genome browser visualization for point processes ]]> https://biorxiv.org/cgi/content/short/2020.04.27.060061v1?rss=1" Moudgil, A. Li, D. Hsu, S. Purushotham, D. Wang, T. Mitra, R. D. 2020-04-29 doi:10.1101/2020.04.27.060061 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance ]]> https://biorxiv.org/cgi/content/short/2020.05.05.078436v1?rss=1" 1,000 genomic locations. This revealed that NHEJ is broadly biased towards euchromatin, while microhomology-mediated end-joining (MMEJ) is more efficient in specific heterochromatin contexts. In H3K27me3-marked heterochromatin, inhibition of the H3K27 methyltransferase EZH2 shifts the balance towards NHEJ. Single-strand templated repair (SSTR), often used for precise CRISPR editing, competes with MMEJ, and this competition is weakly associated with chromatin context. These results provide insight into the impact of chromatin on DSB repair pathway balance, and guidance for the design of Cas9-mediated genome editing experiments. ]]> Schep, R. Brinkman, E. K. Leemans, C. Vergara, X. Morris, B. van Schaik, T. Manzo, S. G. Peric Hupkes, D. van den Berg, J. Beijersbergen, R. Medema, R. H. van Steensel, B. 2020-05-05 doi:10.1101/2020.05.05.078436 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Chromatin folding variability across single-cells results from state degeneracy in phase-separation ]]> https://biorxiv.org/cgi/content/short/2020.05.16.099275v1?rss=1" Conte, M. Fiorillo, L. Bianco, S. Chiariello, A. M. Esposito, A. Nicodemi, M. 2020-05-16 doi:10.1101/2020.05.16.099275 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals ]]> https://biorxiv.org/cgi/content/short/2020.05.26.116962v1?rss=1" Sanford, E. M. Emert, B. L. Cote, A. Raj, A. 2020-05-27 doi:10.1101/2020.05.26.116962 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Unsupervised manifold alignment for single-cell multi-omics data ]]> https://biorxiv.org/cgi/content/short/2020.06.13.149195v1?rss=1" Singh, R. Demetci, P. Bonora, G. Ramani, V. Lee, C. Fang, H. Duan, Z. Deng, X. Shendure, J. Disteche, C. Noble, W. S. 2020-06-15 doi:10.1101/2020.06.13.149195 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity ]]> https://biorxiv.org/cgi/content/short/2020.06.11.147207v1?rss=1" Mellis, I. A. Edelstein, H. I. Truitt, R. Beck, L. E. Symmons, O. Goyal, Y. Dunagin, M. C. Linares Saldana, R. A. Shah, P. P. Yang, W. Jain, R. Raj, A. 2020-06-12 doi:10.1101/2020.06.11.147207 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Chromatin Mechanics Dictates Subdiffusion and Coarsening Dynamics of Embedded Condensates ]]> https://biorxiv.org/cgi/content/short/2020.06.03.128561v1?rss=1" Lee, D. S. W. Wingreen, N. S. Brangwynne, C. P. 2020-06-04 doi:10.1101/2020.06.03.128561 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Gromov-Wasserstein optimal transport to align single-cell multi-omics data ]]> https://biorxiv.org/cgi/content/short/2020.04.28.066787v1?rss=1" Demetci, P. Santorella, R. Sandstede, B. Noble, W. S. Singh, R. 2020-04-29 doi:10.1101/2020.04.28.066787 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains ]]> https://biorxiv.org/cgi/content/short/2020.07.07.192526v1?rss=1" Hui Huang Quan Zhu Adam Jussila Yuanyuan Han Bogdan Bintu Colin Kern Mattia Conte Yanxiao Zhang Simona Bianco Andrea Chiariello Miao Yu Rong Hu Ivan Juric Ming Hu Mario Nicodemi Xiaowei Zhuang Bing Ren 2020-07-08 doi:10.1101/2020.07.07.192526 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies ]]> https://biorxiv.org/cgi/content/short/2020.07.16.206789v1?rss=1" Bokota, G. Sroka, J. Basu, S. Das, N. Trzaskoma, P. Yushkevich, Y. Grabowska, A. Magalska, A. Plewczynski, D. 2020-07-17 doi:10.1101/2020.07.16.206789 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Simultaneous Epigenetic Perturbation and Genome Imaging Reveal Distinct Roles of H3K9me3 in Chromatin Architecture and Transcription ]]> https://biorxiv.org/cgi/content/short/2020.07.15.204719v1?rss=1" Feng, Y. Wang, Y. Wang, X. He, X. Yang, C. Naseri, A. Pederson, T. Zheng, J. Zhang, S. Xiao, X. Xie, W. Ma, H. 2020-07-16 doi:10.1101/2020.07.15.204719 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C ]]> https://biorxiv.org/cgi/content/short/2020.07.31.230284v1?rss=1" Beagrie, R. A. Thieme, C. J. Annunziatella, C. Baugher, C. Zhang, Y. Schueler, M. Kramer, D. C. Chiariello, A. M. Bianco, S. Kukalev, A. Li, Y. Kempfer, R. Scialdone, A. Welch, L. A. Nicodemi, M. Pombo, A. 2020-07-31 doi:10.1101/2020.07.31.230284 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells ]]> https://biorxiv.org/cgi/content/short/2020.08.11.242081v1?rss=1" Arrastia, M. V. Jachowicz, J. W. Ollikainen, N. Curtis, M. S. Lai, C. Quinodoz, S. Selck, D. A. Guttman, M. Ismagilov, R. F. 2020-08-12 doi:10.1101/2020.08.11.242081 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ RNA promotes the formation of spatial compartments in the nucleus ]]> https://biorxiv.org/cgi/content/short/2020.08.25.267435v1?rss=1" Quinodoz, S. A. Bhat, P. Ollikainen, N. Jachowicz, J. W. Banerjee, A. K. Chovanec, P. Blanco, M. R. Chow, A. Markaki, Y. Plath, K. Guttman, M. 2020-08-25 doi:10.1101/2020.08.25.267435 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Single-Molecule Micromanipulation Studies Of Methylated DNA ]]> https://biorxiv.org/cgi/content/short/2020.07.29.227199v1?rss=1" Zaichuk, T. Marko, J. 2020-07-30 doi:10.1101/2020.07.29.227199 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Epigenetic memory as a time integral over prior history of Polycomb phase separation ]]> https://biorxiv.org/cgi/content/short/2020.08.19.254706v1?rss=1" Eeftens, J. M. Kapoor, M. Brangwynne, C. P. 2020-08-19 doi:10.1101/2020.08.19.254706 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Transcript assembly improves expression quantification of transposable elements in single cell RNA-seq data ]]> https://biorxiv.org/cgi/content/short/2020.07.31.231027v1?rss=1" Shao, W. Wang, T. 2020-07-31 doi:10.1101/2020.07.31.231027 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization ]]> https://biorxiv.org/cgi/content/short/2020.08.31.276402v1?rss=1" Marko, J. F. Qiao, H. Liu, N. Biggs, R. J. Peng, Y. 2020-09-01 doi:10.1101/2020.08.31.276402 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization ]]> https://biorxiv.org/cgi/content/short/2020.08.30.274035v1?rss=1" 1000 olfactory receptor (OR) genes is stochastic but, yet, spatially organized in stereotypic anatomical segments, or "zones", along the dorsoventral axis of the mouse olfactory epithelium. We discovered that zonal OR expression is specified by OR chromatin structure and genome architecture during olfactory neuron differentiation. Specifically, across every zone dorsally expressed ORs have higher levels of heterochromatic marks and long-range contacts than ORs expressed ventrally. However, OR heterochromatin levels and frequency of genomic contacts between ORs gradually increase towards ventral zones. Consequently, ORs from dorsal indexes accumulate high H3K9me3/H3K79me3 enrichment and become silenced in ventral zones, while ORs from ventral indexes lack activating long-range genomic interactions and, thus, cannot be chosen in dorsal segments. This process is regulated by NFIA, B, and X gradients along the dorsoventral axis, triple deletion of which causes homeotic transformations on zonal OR expression, heterochromatin formation, and genomic compartmentalization. ]]> Bashkirova, E. Monahan, K. Campbell, C. E. Osinski, J. M. Tan, L. Schieren, I. Barnea, G. Xie, S. Gronostajski, R. M. Lomvardas, S. 2020-08-30 doi:10.1101/2020.08.30.274035 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates ]]> https://biorxiv.org/cgi/content/short/2020.08.28.263020v1?rss=1" Geusz, R. J. Wang, A. Lam, D. K. Vinckier, N. K. Alysandratos, K.-D. Roberts, D. A. Wang, J. Kefalopoulou, S. Qiu, Y. Chiou, J. Gaulton, K. J. Ren, B. Kotton, D. N. Sander, M. 2020-08-29 doi:10.1101/2020.08.28.263020 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ MCM complexes are barriers that restrict cohesin-mediated loop extrusion ]]> https://biorxiv.org/cgi/content/short/2020.10.15.340356v1?rss=1" Dequeker, B. J. H. Brandao, H. B. Scherr, M. J. Gassler, J. Powell, S. Gaspar, I. Flyamer, I. M. Tang, W. Stocsits, R. Davidson, I. F. Peters, J.-M. Duderstadt, K. E. Mirny, L. A. Tachibana, K. 2020-10-15 doi:10.1101/2020.10.15.340356 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ DNA-loop extruding SMC complexes can traverse one another in vivo ]]> https://biorxiv.org/cgi/content/short/2020.10.26.356329v1?rss=1" Brandão, H. B. Ren, Z. Karaboja, X. Mirny, L. A. Wang, X. 2020-10-27 doi:10.1101/2020.10.26.356329 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Deep learning enables fast and dense single-molecule localization with high accuracy ]]> https://biorxiv.org/cgi/content/short/2020.10.26.355164v1?rss=1" Speiser, A. Müller, L.-R. Matti, U. Obara, C. J. Legant, W. R. Kreshuk, A. Macke, J. H. Ries, J. Turaga, S. C. 2020-10-26 doi:10.1101/2020.10.26.355164 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ HiCRep.py: Fast comparison of Hi-C contact matrices in Python ]]> https://biorxiv.org/cgi/content/short/2020.10.27.357756v1?rss=1" Lin, D. Sanders, J. Noble, W. S. 2020-10-28 doi:10.1101/2020.10.27.357756 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics ]]> https://biorxiv.org/cgi/content/short/2020.10.09.331900v1?rss=1" Strom, A. R. Biggs, R. J. Banigan, E. J. Wang, X. Chiu, K. Herman, C. Collado, J. Yue, F. Ritland Politz, J. C. Tait, L. J. Scalzo, D. Telling, A. Groudine, M. Brangwynne, C. P. Marko, J. Stephens, A. D. 2020-10-09 doi:10.1101/2020.10.09.331900 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ PYMEVisualize: an open-source tool for exploring 3D super-resolution data ]]> https://biorxiv.org/cgi/content/short/2020.09.29.315671v1?rss=1" Marin, Z. Graff, M. Barentine, A. E. S. Soeller, C. Chung, K. K. H. Fuentes, L. A. Baddeley, D. 2020-09-30 doi:10.1101/2020.09.29.315671 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches ]]> https://biorxiv.org/cgi/content/short/2019.12.20.885533v1?rss=1" 2 pN) and high salt concentration (> 0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail. ]]> Desai, P. R. Brahmachari, S. Marko, J. F. Das, S. Neuman, K. C. 2019-12-21 doi:10.1101/2019.12.20.885533 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia ]]> https://biorxiv.org/cgi/content/short/2020.10.06.328948v1?rss=1" Janssens, D. Meers, M. P. Wu, S. J. Babaeva, E. Meshinchi, S. Sarthy, J. F. Ahmad, K. Henikoff, S. 2020-10-08 doi:10.1101/2020.10.06.328948 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells ]]> https://biorxiv.org/cgi/content/short/2020.11.24.396713v1?rss=1" Swygert, S. G. Lin, D. Portillo-Ledesma, S. Lin, P.-Y. Hunt, D. R. Kao, C.-F. Schlick, T. Noble, W. S. Tsukiyama, T. 2020-11-24 doi:10.1101/2020.11.24.396713 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors ]]> https://biorxiv.org/cgi/content/short/2020.11.03.366914v1?rss=1" Ypsilanti, A. R. Pattabiraman, K. Catta-Preta, R. Golonzhka, O. Lindtner, S. Tang, K. Jones, I. Abnousi, A. Juric, I. Hu, M. Shen, Y. Dickel, D. E. Visel, A. Pennachio, L. A. Hawrylycz, M. Thompson, C. Zeng, H. Barozzi, I. Nord, A. S. Rubenstein, J. L. R. 2020-11-04 doi:10.1101/2020.11.03.366914 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation ]]> https://biorxiv.org/cgi/content/short/2020.11.20.390765v1?rss=1" Bonora, G. Ramani, V. Singh, R. Fang, H. Jackson, D. Srivatsan, S. Qiu, R. Lee, C. Trapnell, C. Shendure, J. Duan, Z. Deng, X. Noble, W. S. Disteche, C. M. 2020-11-20 doi:10.1101/2020.11.20.390765 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test ]]> https://biorxiv.org/cgi/content/short/2020.10.28.359869v1?rss=1" Lagler, T. M. Yang, Y. Abnousi, A. Hu, M. Li, Y. 2020-10-29 doi:10.1101/2020.10.28.359869 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ DANGO: Predicting higher-order genetic interactions ]]> https://biorxiv.org/cgi/content/short/2020.11.26.400739v1?rss=1" Zhang, R. Ma, J. Ma, J. 2020-11-27 doi:10.1101/2020.11.26.400739 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity ]]> https://biorxiv.org/cgi/content/short/2020.11.29.383067v1?rss=1" Chidester, B. Zhou, T. Ma, J. 2020-11-30 doi:10.1101/2020.11.29.383067 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ DMA-tudor interaction modules control the specificity of in vivo condensates ]]> https://biorxiv.org/cgi/content/short/2020.09.15.297994v1?rss=1" Courchaine, E. M. Barentine, A. E. S. Straube, K. Bewersdorf, J. Neugebauer, K. M. 2020-09-16 doi:10.1101/2020.09.15.297994 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Multiscale and integrative single-cell Hi-C analysis with Higashi ]]> https://biorxiv.org/cgi/content/short/2020.12.13.422537v1?rss=1" Zhang, R. Zhou, T. Ma, J. 2020-12-15 doi:10.1101/2020.12.13.422537 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data ]]> https://biorxiv.org/cgi/content/short/2020.12.13.422543v1?rss=1" Yu, M. Abnousi, A. Zhang, Y. Li, G. Lee, L. Chen, Z. Fang, R. Wen, J. Sun, Q. Li, Y. Ren, B. Hu, M. 2020-12-15 doi:10.1101/2020.12.13.422543 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator ]]> https://biorxiv.org/cgi/content/short/2020.12.18.423551v1?rss=1" Sanborn, A. L. Yeh, B. T. Feigerle, J. T. Hao, C. V. Townshend, R. J. L. Aiden, E. L. Dror, R. O. Kornberg, R. D. 2020-12-18 doi:10.1101/2020.12.18.423551 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ 3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex ]]> https://biorxiv.org/cgi/content/short/2020.11.27.386599v1?rss=1" Jimenez Sabinina, V. Hossain, M. J. Heriche, J.-K. Hoess, P. Nijmeijer, B. Mosalaganti, S. Kueblbeck, M. Callegari, A. Szymborska, A. Beck, M. Ries, J. Ellenberg, J. 2020-11-27 doi:10.1101/2020.11.27.386599 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ HiCAR: a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility, and cis-regulatory chromatin contacts ]]> https://biorxiv.org/cgi/content/short/2020.11.02.366062v1?rss=1" Wei, X. Xiang, Y. Abnousi, A. Sun, T. Lin, X. Li, W. Hu, M. Diao, Y. 2020-11-04 doi:10.1101/2020.11.02.366062 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Systematic evaluation of chromosome conformation capture assays ]]> https://biorxiv.org/cgi/content/short/2020.12.26.424448v1?rss=1" Akgol Oksuz, B. Yang, L. Abraham, S. Venev, S. V. Krietenstein, N. Parsi, K. M. Ozadam, H. Oomen, M. E. Nand, A. Mao, H. Genga, R. M. J. Maehr, R. Rando, O. Mirny, L. Gibcus, J. H. Dekker, J. 2020-12-27 doi:10.1101/2020.12.26.424448 Cold Spring Harbor Laboratory Press 2020-12-27 <![CDATA[ Cohesin-mediated loop anchors confine the location of human replication origins ]]> https://biorxiv.org/cgi/content/short/2021.01.05.425437v1?rss=1" Emerson, D. J. Zhao, P. A. Klein, K. Ge, C. Zhou, L. Sasaki, T. Yang, L. Venvev, S. V. Gibcus, J. H. Dekker, J. Gilbert, D. M. Phillips-Cremins, J. E. 2021-01-06 doi:10.1101/2021.01.05.425437 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Mechanical frustration of phase separation in the cell nucleus by chromatin ]]> https://biorxiv.org/cgi/content/short/2020.12.24.424222v1?rss=1" Zhang, Y. Lee, D. S. W. Meir, Y. Brangwynne, C. P. Wingreen, N. S. 2020-12-24 doi:10.1101/2020.12.24.424222 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Disruption of nuclear architecture as a cause of COVID-19 induced anosmia ]]> https://biorxiv.org/cgi/content/short/2021.02.09.430314v1?rss=1" Zazhytska, M. Kodra, A. Hoagland, D. A. Fullard, J. Shayya, H. J. Omer, A. Firestein, S. Gong, Q. Canoll, P. Goldman, J. E. Roussos, P. tenOever, B. R. Overdevest, J. B. Lomvardas, S. 2021-02-09 doi:10.1101/2021.02.09.430314 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Genome-wide variability in recombination activity is associated with meiotic chromatin organization ]]> https://biorxiv.org/cgi/content/short/2021.01.06.425599v1?rss=1" Jin, X. Fudenberg, G. Pollard, K. S. 2021-01-07 doi:10.1101/2021.01.06.425599 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Polymer physics and machine learning reveal a combinatorial code linking chromatin 3D architecture to 1D epigenetics ]]> https://biorxiv.org/cgi/content/short/2021.03.01.433416v1?rss=1" Esposito, A. Bianco, S. Chiariello, A. M. Abraham, A. Fiorillo, L. Conte, M. Campanile, R. Nicodemi, M. 2021-03-01 doi:10.1101/2021.03.01.433416 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Stripenn detects architectural stripes from chromatin conformation data using computer vision ]]> https://biorxiv.org/cgi/content/short/2021.04.16.440239v1?rss=1" Yoon, S. Vahedi, G. 2021-04-18 doi:10.1101/2021.04.16.440239 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model ]]> https://biorxiv.org/cgi/content/short/2021.04.25.441198v1?rss=1" Hammer, M. Huisman, M. Rigano, A. Boehm, U. Chambers, J. J. Gaudreault, N. North, A. J. Pimentel, J. A. Sudar, D. Bajcsy, P. Brown, C. M. Corbett, A. D. Faklaris, O. Lacoste, J. Laude, A. Nelson, G. Nitschke, R. Farzam, F. Smith, C. Grunwald, D. Strambio-De-Castillia, C. 2021-04-26 doi:10.1101/2021.04.25.441198 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture ]]> https://biorxiv.org/cgi/content/short/2021.04.26.441547v1?rss=1" Takei, Y. Zheng, S. Yun, J. Shah, S. Pierson, N. White, J. Schindler, S. Tischbirek, C. Yuan, G.-C. Cai, L. 2021-04-27 doi:10.1101/2021.04.26.441547 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Quantification of durable CRISPR-based gene silencing activity ]]> https://biorxiv.org/cgi/content/short/2021.03.31.436355v1?rss=1" Nakamura, M. Ivec, A. Gao, Y. Qi, L. S. 2021-03-31 doi:10.1101/2021.03.31.436355 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications ]]> https://biorxiv.org/cgi/content/short/2021.05.31.446382v1?rss=1" Rigano, A. Ehmsen, S. Ozturk, S. U. Ryan, J. Balashov, A. Hammer, M. Kirli, K. Bellve, K. Boehm, U. Brown, C. M. Chambers, J. J. Coleman, R. A. Cosolo, A. Faklaris, O. Fogarty, K. Guilbert, T. Hamacher, A. B. Itano, M. S. Keeley, D. P. Kunis, S. Lacoste, J. Laude, A. Ma, W. Marcello, M. Montero-Llopis, P. Nelson, G. Nitschke, R. Pimentel, J. A. Weidtkamp-Peters, S. Park, P. J. Alver, B. Grunwald, D. Strambio-De-Castillia, C. 2021-05-31 doi:10.1101/2021.05.31.446382 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells ]]> https://biorxiv.org/cgi/content/short/2021.06.10.447969v1?rss=1" Calandrelli, R. Wen, X. Nguyen, T. C. Chen, C.-J. Qi, Z. Chen, W. Yan, Z. Wu, W. Zaleta-Rivera, K. Hu, R. Yu, M. Wang, Y. Ma, J. Ren, B. Zhong, S. 2021-06-11 doi:10.1101/2021.06.10.447969 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Systematic reconstruction of the cellular trajectories of mammalian embryogenesis ]]> https://biorxiv.org/cgi/content/short/2021.06.08.447626v1?rss=1" Qiu, C. Cao, J. Li, T. Srivatsan, S. Huang, X. Calderon, D. Noble, W. S. Disteche, C. M. Spielmann, M. Moens, C. B. Trapnell, C. Shendure, J. 2021-06-09 doi:10.1101/2021.06.08.447626 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Interrogation of the Dynamic Properties of Higher-Order Heterochromatin Using CRISPR/dCas9 ]]> https://biorxiv.org/cgi/content/short/2021.06.06.447300v1?rss=1" Gao, Y. Han, M. Shang, S. Wang, H. Qi, L. S. 2021-06-07 doi:10.1101/2021.06.06.447300 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection ]]> https://biorxiv.org/cgi/content/short/2021.06.09.447760v1?rss=1" Wang, J. Han, M. Wang, H. Moeckl, L. Zeng, L. Moerner, W. E. Qi, L. S. 2021-06-09 doi:10.1101/2021.06.09.447760 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state ]]> https://biorxiv.org/cgi/content/short/2021.06.24.449850v1?rss=1" Daniel, B. Belk, J. A. Meier, S. L. Chen, A. Y. Sandor, K. Qi, Y. Kitano, H. Wheeler, J. R. Foster, D. S. Januszyk, M. S. Longaker, M. T. Chang, H. Y. Satpathy, A. T. 2021-06-25 doi:10.1101/2021.06.24.449850 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Mapping the nuclear microenvironment of genes at agenome-wide scale ]]> https://biorxiv.org/cgi/content/short/2021.07.11.451976v1?rss=1" Yildirim, A. Hua, N. Boninsegna, L. Polles, G. Gong, K. Hao, S. Li, W. Zhou, X. J. Alber, F. 2021-07-12 doi:10.1101/2021.07.11.451976 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR ]]> https://biorxiv.org/cgi/content/short/2021.06.21.449316v1?rss=1" Sharma, A. Akshay, A. Rogne, M. Eskeland, R. 2021-06-22 doi:10.1101/2021.06.21.449316 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ SARS-CoV-2 Restructures the Host Chromatin Architecture ]]> https://biorxiv.org/cgi/content/short/2021.07.20.453146v1?rss=1" 190-million infections worldwide, thus it is pivotal to understand the viral impacts on host cells. Many viruses can significantly alter host chromatin1, but such roles of SARS-CoV-2 are largely unknown. Here, we characterized the three-dimensional (3D) genome architecture and epigenome landscapes in human cells after SARS-CoV-2 infection, revealing remarkable restructuring of host chromatin architecture. High-resolution Hi-C 3.0 uncovered widespread A compartmental weakening and A-B mixing, together with a global reduction of intra-TAD chromatin contacts. The cohesin complex, a central organizer of the 3D genome, was significantly depleted from intra-TAD regions, supporting that SARS-CoV-2 disrupts cohesin loop extrusion. Calibrated ChIP-Seq verified chromatin restructuring by SARS-CoV-2 that is particularly manifested by a pervasive reduction of euchromatin modifications. Built on the rewired 3D genome/epigenome maps, a modified activity-by-contact model2 highlights the transcriptional weakening of antiviral interferon response genes or virus sensors (e.g., DDX58) incurred by SARS-CoV-2. In contrast, pro-inflammatory genes (e.g. IL-6) high in severe infections were uniquely regulated by augmented H3K4me3 at their promoters. These findings illustrate how SARS-CoV-2 rewires host chromatin architecture to confer immunological gene deregulation, laying a foundation to characterize the long-term epigenomic impacts of this virus. ]]> Wang, R. Lee, J.-H. Xiong, F. Kim, J. Al Hasani, L. Yuan, X. Shivshankar, P. Krakowiak, J. Qi, C. Wang, Y. Eltzschig, H. K. Li, W. 2021-07-21 doi:10.1101/2021.07.20.453146 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers ]]> https://biorxiv.org/cgi/content/short/2021.08.05.455340v1?rss=1" Spracklin, G. Abdennur, N. A. Imakaev, M. Chowdhury, N. Pradhan, S. Mirny, L. Dekker, J. 2021-08-06 doi:10.1101/2021.08.05.455340 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Cell type determination for cardiac differentiation occurs soon after seeding of human induced pluripotent stem cells ]]> https://biorxiv.org/cgi/content/short/2021.08.08.455532v1?rss=1" Jiang, C. L. Goyal, Y. Jain, N. Wang, Q. Truitt, R. E. Cote, A. J. Emert, B. Mellis, I. A. Kiani, K. Yang, W. Jain, R. Raj, A. 2021-08-08 doi:10.1101/2021.08.08.455532 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen ]]> https://biorxiv.org/cgi/content/short/2021.08.06.455141v1?rss=1" Xia, Y. Sandor, K. Pai, J. A. Daniel, B. Raju, S. Wu, R. Hsiung, S. Qi, Y. Yangdon, T. Okamoto, M. Schreiber, R. D. Murphy, K. M. Satpathy, A. T. Egawa, T. 2021-08-09 doi:10.1101/2021.08.06.455141 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Biochemically distinct cohesin complexes mediate positioned loops between CTCF sites and dynamic loops within chromatin domains ]]> https://biorxiv.org/cgi/content/short/2021.08.24.457555v1?rss=1" Liu, Y. Dekker, J. 2021-08-26 doi:10.1101/2021.08.24.457555 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs ]]> https://biorxiv.org/cgi/content/short/2021.08.24.457552v1?rss=1" Lee, S. Vitzthum, C. Alver, B. H. Park, P. J. 2021-08-26 doi:10.1101/2021.08.24.457552 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer ]]> https://biorxiv.org/cgi/content/short/2021.09.27.461866v1?rss=1" View larger version (65K): org.highwire.dtl.DTLVardef@1fb1c4aorg.highwire.dtl.DTLVardef@fe4571org.highwire.dtl.DTLVardef@1812f76org.highwire.dtl.DTLVardef@5317d5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kersten, K. Hu, K. H. Combes, A. J. Samad, B. Harwin, T. Ray, A. Rao, A. A. Cai, E. Marchuk, K. Artichoker, J. Courau, T. Shi, Q. Belk, J. Satpathy, A. T. Krummel, M. F. 2021-09-28 doi:10.1101/2021.09.27.461866 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Regional and clonal T cell dynamics at single cell resolution in immune checkpoint blockade ]]> https://biorxiv.org/cgi/content/short/2021.09.27.461389v1?rss=1" Pai, J. A. Chow, A. Sauter, J. Mattar, M. Rizvi, H. Woo, H. J. Shah, N. Uddin, F. Quintanal-Villalonga, A. Chan, J. M. Manoj, P. Allaj, V. Baine, M. Chaft, J. E. Plodkowski, A. J. Won, H. Wells, D. Donoghue, M. T. A. de Stanchina, E. Sen, T. Wolchok, J. D. Houck-Loomis, B. Merghoub, T. Rudin, C. M. Satpathy, A. T. Hellmann, M. D. 2021-09-27 doi:10.1101/2021.09.27.461389 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data ]]> https://biorxiv.org/cgi/content/short/2021.10.14.464435v1?rss=1" Reiff, S. B. Schroeder, A. J. Kirli, K. Cosolo, A. Bakker, C. Mercado, L. Lee, S. B. Veit, A. D. Balashov, A. K. Vitzthum, C. Ronchetti, W. Pitman, K. M. Johnson, J. Ehmsen, S. R. Kerpedjiev, P. Abdennur, N. A. Imakaev, M. Ozturk, S. U. Camoglu, U. Mirny, L. Gehlenborg, N. Alver, B. H. Park, P. J. 2021-10-15 doi:10.1101/2021.10.14.464435 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Kinetic principles underlying pioneer function of GAGA transcription factor in live cells ]]> https://biorxiv.org/cgi/content/short/2021.10.21.465351v1?rss=1" Wu, C. Tang, X. Li, T. Liu, S. Wisniewski, J. Zheng, Q. Lavis, L. Rong, Y. 2021-10-23 doi:10.1101/2021.10.21.465351 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding ]]> https://biorxiv.org/cgi/content/short/2021.11.02.466589v1?rss=1" Conte, M. Irani, E. Chiariello, A. M. Abraham, A. Bianco, S. Esposito, A. Nicodemi, M. 2021-11-02 doi:10.1101/2021.11.02.466589 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ CTCF blocks anti-sense transcription initiation at divergent gene promoters ]]> https://biorxiv.org/cgi/content/short/2021.10.30.465508v1?rss=1" Luan, J. Syrett, C. M. Vermunt, M. W. Cote, A. Tome, J. M. Zhang, H. Huang, A. Luppino, J. M. Keller, C. A. Giardine, B. M. Zhang, S. Dunagin, M. C. Zhang, Z. Joyce, E. F. Lis, J. T. Raj, A. Hardison, R. C. Blobel, G. A. 2021-10-30 doi:10.1101/2021.10.30.465508 Cold Spring Harbor Laboratory Press 2021-10-30 <![CDATA[ Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation ]]> https://biorxiv.org/cgi/content/short/2021.10.13.464280v1?rss=1" Singh, A. P. Wu, P. Ryabichko, S. Raimundo, J. Swan, M. Wieschaus, E. Gregor, T. Toettcher, J. E. 2021-10-14 doi:10.1101/2021.10.13.464280 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Allelic correlation is a marker of tradeoffs between barriers to transmission of expression variability and signal responsiveness in genetic networks ]]> https://biorxiv.org/cgi/content/short/2021.11.26.470134v1?rss=1" Boe, R. H. Ayyappan, V. Schuh, L. Raj, A. 2021-11-26 doi:10.1101/2021.11.26.470134 Cold Spring Harbor Laboratory Press 2021-11-26 <![CDATA[ Single-Cell Multiomics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium ]]> https://biorxiv.org/cgi/content/short/2021.11.05.467513v1?rss=1" Wang, J. Lareau, C. A. Bautista, J. L. Gupta, A. R. Sandor, K. Germino, J. Yin, Y. Arvedson, M. P. Reeder, G. C. Cramer, N. T. Xie, F. Ntranos, V. Satpathy, A. T. Anderson, M. S. Gardner, J. M. 2021-11-06 doi:10.1101/2021.11.05.467513 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ Divergent clonal differentiation trajectories of T cell exhaustion ]]> https://biorxiv.org/cgi/content/short/2021.12.16.472900v1?rss=1" Daniel, B. Yost, K. E. Sandor, K. Xia, Y. Qi, Y. Hiam-Galvez, K. J. Meier, S. L. Belk, J. Giles, J. R. Wherry, E. J. Chang, H. Egawa, T. Satpathy, A. 2021-12-17 doi:10.1101/2021.12.16.472900 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ CRISPR Cas13-based tools to track and manipulate endogenous telomeric repeat-containing RNAs in living cells ]]> https://biorxiv.org/cgi/content/short/2021.12.03.471109v1?rss=1" Xu, M. Chigumira, T. Chen, Z. Tones, J. Zhao, R. Dahl, K. N. Chenoweth, D. M. Zhang, H. 2021-12-04 doi:10.1101/2021.12.03.471109 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ Chromatin interaction aware gene regulatory modeling with graph attention networks ]]> https://biorxiv.org/cgi/content/short/2021.03.31.437978v1?rss=1" Karbalayghareh, A. Sahin, M. Leslie, C. S. 2021-04-02 doi:10.1101/2021.03.31.437978 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Single-fiber nucleosome density shapes the regulatory output of a mammalian chromatin remodeling enzyme ]]> https://biorxiv.org/cgi/content/short/2021.12.10.472156v1?rss=1" Abdulhay, N. J. Hsieh, L. J. McNally, C. P. Ketavarapu, M. Kasinathan, S. Nanda, A. S. Ostrowski, M. S. Wu, K. Moore, C. M. Goodarzi, H. Narlikar, G. J. Ramani, V. 2021-12-11 doi:10.1101/2021.12.10.472156 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Massively parallel genomic perturbations with multi-target CRISPR reveal new insights on Cas9 activity and DNA damage responses at endogenous sites ]]> https://biorxiv.org/cgi/content/short/2022.01.18.476836v1?rss=1" Zou, R. S. Marin-Gonzalez, A. Liu, Y. Liu, H. B. Shen, L. Dveirin, R. Luo, J. X. J. Kalhor, R. Ha, T. 2022-01-20 doi:10.1101/2022.01.18.476836 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Activity-induced gene expression and long-range enhancer-promoter contacts in cohesin-deficient neurons ]]> https://biorxiv.org/cgi/content/short/2021.02.24.432639v1?rss=1" Calderon, L. Weiss, F. D. Beagan, J. A. Oliveira, M. S. Wang, Y.-F. Carroll, T. Dharmalingam, G. Gong, W. Tossell, K. de Paola, V. Whilding, C. Ungless, M. A. Fisher, A. G. Phillips-Cremins, J. E. Merkenschlager, M. 2021-02-24 doi:10.1101/2021.02.24.432639 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser ]]> https://biorxiv.org/cgi/content/short/2022.01.18.476849v1?rss=1" Li, D. Purushotham, D. Harrison, J. K. Wang, T. 2022-01-21 doi:10.1101/2022.01.18.476849 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes and gene regulation ]]> https://biorxiv.org/cgi/content/short/2022.02.01.475239v1?rss=1" Choudhary, M. N. Quaid, K. Xing, X. Schmidt, H. Wang, T. 2022-02-03 doi:10.1101/2022.02.01.475239 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding ]]> https://biorxiv.org/cgi/content/short/2022.02.13.480215v1?rss=1" Fang, W. Bell, C. M. Sapirstein, A. Asami, S. Leeper, K. Zack, D. J. Ji, H. Kalhor, R. 2022-02-14 doi:10.1101/2022.02.13.480215 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome ]]> https://biorxiv.org/cgi/content/short/2022.02.21.481225v1?rss=1" Zhu, X. Zhang, Y. Wang, Y. Tian, D. Belmont, A. S. Swedlow, J. R. Ma, J. 2022-02-22 doi:10.1101/2022.02.21.481225 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Cas9-Mediated Knockout of Ndrg2 Enhances the Regenerative Potential of Dendritic Cells for Wound Healing ]]> https://biorxiv.org/cgi/content/short/2022.03.14.484360v1?rss=1" Henn, D. Zhao, D. Chen, K. Trotsyuk, A. Bonham, C. A. Fischer, K. S. Kehl, T. Fehlmann, T. Sivaraj, D. Greco, A. H. Moortgat Illouz, S. E. Padmanabhan, J. Barrera, J. A. Kneser, U. Lenhof, H.-P. Januszyk, M. Levi, B. Keller, A. Longaker, M. T. Qi, L. S. Gurtner, G. C. 2022-03-15 doi:10.1101/2022.03.14.484360 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ ]]> https://biorxiv.org/cgi/content/short/2022.03.16.484659v1?rss=1" Dardani, I. Emert, B. L. Goyal, Y. Jiang, C. L. Kaur, A. Lee, J. Rouhanifard, S. H. Alicea, G. M. Fane, M. E. Xiao, M. Herlyn, M. Weeraratna, A. T. Raj, A. 2022-03-17 doi:10.1101/2022.03.16.484659 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ A spatial genome aligner for multiplexed DNA-FISH ]]> https://biorxiv.org/cgi/content/short/2022.03.25.485845v1?rss=1" Jia, B. B. Jussila, A. P. Kern, J. C. Zhu, Q. Ren, B. 2022-03-27 doi:10.1101/2022.03.25.485845 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation ]]> https://biorxiv.org/cgi/content/short/2022.04.15.488491v1?rss=1" Alavattam, K. G. Mitzelfelt, K. A. Bonora, G. Fields, P. A. Yang, X. Chiu, H. S. Pabon, L. Bertero, A. Palpant, N. J. Noble, W. S. Murry, C. E. 2022-04-16 doi:10.1101/2022.04.15.488491 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi ]]> https://biorxiv.org/cgi/content/short/2022.04.18.488683v1?rss=1" Zhang, R. Zhou, T. Ma, J. 2022-04-19 doi:10.1101/2022.04.18.488683 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing ]]> https://biorxiv.org/cgi/content/short/2022.04.21.488684v1?rss=1" Yang, Y. Wang, Y. Zhang, Y. Ma, J. 2022-04-22 doi:10.1101/2022.04.21.488684 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence ]]> https://biorxiv.org/cgi/content/short/2022.04.20.488974v1?rss=1" Belk, J. Yao, W. Ly, N. Freitas, K. Chen, Y.-T. Shi, Q. Valencia, A. Shifrut, E. Kale, N. Yost, K. Duffy, C. Hwee, M. Miao, Z. Ashworth, A. Mackall, C. Marson, A. Carnevale, J. Vardhana, S. Satpathy, A. 2022-04-21 doi:10.1101/2022.04.20.488974 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ NIPBL and WAPL balance cohesin activity to regulate chromatin folding and gene expression ]]> https://biorxiv.org/cgi/content/short/2022.04.19.488785v1?rss=1" Luppino, J. M. Field, A. Nguyen, S. C. Park, D. S. Shah, P. P. Lan, Y. Yunker, R. Jain, R. Adelman, K. Joyce, E. F. 2022-04-19 doi:10.1101/2022.04.19.488785 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ High-throughput Oligopaint screen identifies druggable regulators of genome folding ]]> https://biorxiv.org/cgi/content/short/2022.04.08.487672v1?rss=1" 300 factors that regulate chromatin folding during interphase, including 43 validated hits that either increase or decrease interactions between topological associating domains (TADs). We discovered that genetic or chemical inhibition of the ubiquitous kinase GSK3A enhances long-range interactions by dysregulating cohesin-mediated chromatin looping. Collectively, these results highlight a noncanonical role for GSK3A signaling in nuclear architecture and underscore the broader utility of HiDRO-based screening to identify novel mechanisms that drive the spatial organization of the genome. ]]> Park, D. S. Nguyen, S. C. Isenhart, R. Shah, P. P. Kim, W. Barnett, R. J. Chandra, A. Luppino, J. M. Harke, J. Wai, M. Yang, R. Lan, Y. Yoon, S. Yunker, R. Vahedi, G. Phillips-Cremins, J. E. Jain, R. Joyce, E. F. 2022-04-10 doi:10.1101/2022.04.08.487672 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Reducing peptide sequence bias in quantitative mass spectrometry data with machine learning ]]> https://biorxiv.org/cgi/content/short/2022.04.11.487945v1?rss=1" Dincer, A. B. Lu, Y. Schweppe, D. Oh, S. Noble, W. S. 2022-04-12 doi:10.1101/2022.04.11.487945 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ A unique epigenomic landscape defines CD8+ tissue-resident memory T cells ]]> https://biorxiv.org/cgi/content/short/2022.05.04.490680v1?rss=1" View larger version (56K): org.highwire.dtl.DTLVardef@b03f1corg.highwire.dtl.DTLVardef@ff6871org.highwire.dtl.DTLVardef@220db2org.highwire.dtl.DTLVardef@1b15166_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIscATAC atlas reveals the epigenetic variance of memory CD8+ T cell subsets over the course of acute infection C_LIO_LIEarly bifurcation of memory precursors leads to circulating versus tissue-resident cell fates C_LIO_LIIntegrating transcriptional and epigenetic analyses identified organ-specific TRM cell regulators including HIC1 and BACH2 C_LIO_LIEpigenetic distinction of TRM cells and TEX cell subsets C_LI ]]> Buquicchio, F. A. Fonseca, R. Belk, J. A. Evrard, M. Obers, A. Qi, Y. Daniel, B. Yost, K. E. Satpathy, A. T. Mackay, L. K. 2022-05-06 doi:10.1101/2022.05.04.490680 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer ]]> https://biorxiv.org/cgi/content/short/2022.05.21.492846v1?rss=1" Rodrigues, A. MacQuarrie, K. L. Freeman, E. Willis, A. B. Xu, Z. Alvarez, A. A. Ma, Y. Perez White, B. E. Foltz, D. R. Huang, S. 2022-05-21 doi:10.1101/2022.05.21.492846 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ The association of MEG3 lncRNA with nuclear speckles in living cells ]]> https://biorxiv.org/cgi/content/short/2022.05.11.491451v1?rss=1" Hasenson, S. Alkalay, E. Atrash, M. K. Boocholez, A. Gershbaum, J. Hochberg-Laufer, H. Shav-Tal, Y. 2022-05-11 doi:10.1101/2022.05.11.491451 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution ]]> https://biorxiv.org/cgi/content/short/2022.05.26.493621v1?rss=1" Nair, S. Barrett, A. Li, D. Raney, B. J. Lee, B. T. Kerpedjiev, P. Ramalingam, V. Pampari, A. Lekschas, F. Wang, T. Haeussler, M. Kundaje, A. 2022-05-28 doi:10.1101/2022.05.26.493621 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Multi-scale phase separation by explosive percolation with single chromatin loop resolution ]]> https://biorxiv.org/cgi/content/short/2022.04.28.489670v1?rss=1" Sengupta, K. Denkiewicz, M. Chilinski, M. Szczepinska, T. Mollah, A. F. Korsak, S. D'Souza, R. Ruan, Y. Plewczynski, D. 2022-04-29 doi:10.1101/2022.04.28.489670 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Beyond TADs: microscopy reveals 2 axes of chromosome organization by CTCF and cohesin ]]> https://biorxiv.org/cgi/content/short/2022.07.13.499982v1?rss=1" Hafner, A. Park, M. Berger, S. E. Nora, E. Boettiger, A. N. 2022-07-13 doi:10.1101/2022.07.13.499982 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Phase separation of Myc differentially regulates gene transcription ]]> https://biorxiv.org/cgi/content/short/2022.06.28.498043v1?rss=1" 97% of N-myc-regulated genes are not affected by N-myc phase separation, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery. ]]> Yang, J. Chung, C.-I. Koach, J. Liu, H. Zhao, Q. Yang, X. Shen, Y. Weiss, W. A. Shu, X. 2022-06-29 doi:10.1101/2022.06.28.498043 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Development and application of an uncapped mRNA platform ]]> https://biorxiv.org/cgi/content/short/2022.06.05.494796v1?rss=1" Liu, B. Ni, P. Cai, L. Shi, X. Ji, S. Ke, Z. Zhang, S. Hu, B. Yang, B. Xu, Y. Long, W. Fang, Z. Hu, H. Wang, Y. Zhang, W. Geng, H. Xu, Y. Zheng, X. Wang, Z. Zhang, B. Pan, K. Zhou, K. Cui, Y. Wang, H. Liu, B. 2022-06-05 doi:10.1101/2022.06.05.494796 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut ]]> https://biorxiv.org/cgi/content/short/2022.07.26.501624v1?rss=1" Bara, A. M. Chen, L. Ma, C. Underwood, J. Moreci, R. S. Sumigray, K. Sun, T. Diao, Y. Verzi, M. Lechler, T. 2022-07-28 doi:10.1101/2022.07.26.501624 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ In silico discovery of repetitive elements as key sequence determinants of 3D genome folding ]]> https://biorxiv.org/cgi/content/short/2022.08.11.503410v1?rss=1" Gunsalus, L. M. Keiser, M. J. Pollard, K. S. 2022-08-12 doi:10.1101/2022.08.11.503410 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Identification of a self-renewing muscle satellite cell state by single-cell chromatin accessibility profiling ]]> https://biorxiv.org/cgi/content/short/2022.09.16.508339v1?rss=1" Okafor, A. E. Lin, X. Situ, C. Wei, X. Wei, X. Wu, Z. Diao, Y. 2022-09-17 doi:10.1101/2022.09.16.508339 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells ]]> https://biorxiv.org/cgi/content/short/2022.09.08.507172v1?rss=1" Sun, T. Xu, Y. Xiang, Y. Soderblom, E. J. Diao, Y. 2022-09-12 doi:10.1101/2022.09.08.507172 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Remodeling and compaction of the inactive X is regulated by Xist during female B cell activation ]]> https://biorxiv.org/cgi/content/short/2022.10.19.512821v1?rss=1" Anguera, M. Sierra, I. Nguyen, S. C. Barnett, R. J. Cook, A. Ryu, H.-S. Beethem, Z. Phillips-Cremins, J. E. Joyce, E. F. 2022-10-21 doi:10.1101/2022.10.19.512821 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Structural elements facilitate extreme long-range gene regulation at a human disease locus ]]> https://biorxiv.org/cgi/content/short/2022.10.20.513057v1?rss=1" Chen, L.-F. Long, H. K. Park, M. Swigut, T. Boettiger, A. N. Wysocka, J. 2022-10-21 doi:10.1101/2022.10.20.513057 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+ ]]> https://biorxiv.org/cgi/content/short/2022.10.29.514376v1?rss=1" Zou, R. S. Liu, Y. Reyes Gaido, O. E. Konig, M. F. Mog, B. J. Shen, L. L. Aviles-Vazquez, F. Marin-Gonzalez, A. Ha, T. 2022-10-30 doi:10.1101/2022.10.29.514376 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing ]]> https://biorxiv.org/cgi/content/short/2022.10.14.512199v1?rss=1" Murphy, S. E. Boettiger, A. 2022-10-14 doi:10.1101/2022.10.14.512199 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Chromosome decompaction and cohesin direct Topoisomerase II activity to establish and maintain an unentangled interphase genome ]]> https://biorxiv.org/cgi/content/short/2022.10.15.511838v1?rss=1" Hildebrand, E. M. Polovnikov, K. Dekker, B. Liu, Y. Lafontaine, D. L. Fox, A. N. Li, Y. Venev, S. V. Mirny, L. A. Dekker, J. 2022-10-16 doi:10.1101/2022.10.15.511838 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Programmable Drug Control of Receptor Valency Modulates the Potency of Cell Therapeutics ]]> https://biorxiv.org/cgi/content/short/2023.01.04.522664v1?rss=1" Finn, P. Chavez, M. Chen, X. Wang, H. Rane, D. A. Gurjar, J. Qi, L. S. 2023-01-04 doi:10.1101/2023.01.04.522664 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ 3D genome organization around nuclear speckles drives mRNA splicing efficiency ]]> https://biorxiv.org/cgi/content/short/2023.01.04.522632v1?rss=1" Bhat, P. Chow, A. Emert, B. Ettlin, O. Quinodoz, S. A. Takei, Y. Huang, W. Blanco, M. R. Guttman, M. 2023-01-04 doi:10.1101/2023.01.04.522632 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila ]]> https://biorxiv.org/cgi/content/short/2023.01.03.522592v1?rss=1" Singh, B. N. Tran, H. Kramer, J. Kirishenko, E. Changela, N. Wang, F. Feng, Y. Kumar, D. Tu, M. Liang, S. Lan, J. Bizet, M. Fuks, F. Steward, R. 2023-01-07 doi:10.1101/2023.01.03.522592 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Stochastic motion and transcriptional dynamicsof distal enhancer-promoter pairs on a compacted chromosome ]]> https://biorxiv.org/cgi/content/short/2023.01.18.524527v1?rss=1" Brueckner, D. B. Chen, H. Barinov, L. Zoller, B. Gregor, T. 2023-01-20 doi:10.1101/2023.01.18.524527 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells ]]> https://biorxiv.org/cgi/content/short/2023.02.10.527870v1?rss=1" Jain, N. Goyal, Y. Dunagin, M. C. Cote, C. J. Mellis, I. A. Emert, B. Jiang, C. L. Dardani, I. P. Reffsin, S. Raj, A. 2023-02-10 doi:10.1101/2023.02.10.527870 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Deep learning enables fast, gentle STED microscopy ]]> https://biorxiv.org/cgi/content/short/2023.01.26.525571v1?rss=1" Ebrahimi, V. Stephan, T. Kim, J. Carravilla, P. Eggeling, C. Jakobs, S. Han, K. Y. 2023-01-27 doi:10.1101/2023.01.26.525571 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity ]]> https://biorxiv.org/cgi/content/short/2023.02.22.529589v1?rss=1" Liu, Z. Lee, D.-S. Liang, Y. Zheng, Y. Dixon, J. 2023-02-23 doi:10.1101/2023.02.22.529589 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development ]]> https://biorxiv.org/cgi/content/short/2023.02.06.527380v1?rss=1" Hung, T.-C. Kingsley, D. M. Boettiger, A. N. 2023-02-06 doi:10.1101/2023.02.06.527380 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function ]]> https://biorxiv.org/cgi/content/short/2023.02.18.528138v1?rss=1" Zhan, Y. Yildirim, A. Boninsegna, L. Alber, F. 2023-02-19 doi:10.1101/2023.02.18.528138 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens ]]> https://biorxiv.org/cgi/content/short/2023.01.30.526264v1?rss=1" Attar, S. Browning, V. E. Liu, Y. Nichols, E. K. Tsue, A. F. Shechner, D. M. Shendure, J. Lieberman, J. A. Akilesh, S. Beliveau, B. J. 2023-02-01 doi:10.1101/2023.01.30.526264 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes ]]> https://biorxiv.org/cgi/content/short/2023.03.06.530899v1?rss=1" 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA. ]]> Aguilar, R. Camplisson, C. K. Lin, Q. Miga, K. H. Noble, W. S. Beliveau, B. J. 2023-03-07 doi:10.1101/2023.03.06.530899 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Nucleolar structure connects with global nuclear organization ]]> https://biorxiv.org/cgi/content/short/2023.03.30.534966v1?rss=1" Wang, C. Ma, H. Baserga, S. Pederson, T. Huang, S. 2023-03-31 doi:10.1101/2023.03.30.534966 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo ]]> https://biorxiv.org/cgi/content/short/2023.03.09.531972v1?rss=1" Ho, E. K. Oatman, H. R. McFann, S. E. Yang, L. Johnson, H. E. Shvartsman, S. Y. Toettcher, J. E. 2023-03-10 doi:10.1101/2023.03.09.531972 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions ]]> https://biorxiv.org/cgi/content/short/2023.03.07.531569v1?rss=1" Luo, R. Yan, J. Oh, J. W. Xi, W. Shigaki, D. Wong, W. Cho, H. Murphy, D. Cutler, R. Rosen, B. P. Pulecio, J. Yang, D. Glenn, R. Chen, T. Li, Q. V. Vierbuchen, T. Sidoli, S. Apostolou, E. Huangfu, D. Beer, M. A. 2023-03-09 doi:10.1101/2023.03.07.531569 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins ]]> https://biorxiv.org/cgi/content/short/2023.03.21.533670v1?rss=1" Faber, G. P. Hauschner, H. Atrash, M. K. Bilinsky, L. Shav-Tal, Y. 2023-03-24 doi:10.1101/2023.03.21.533670 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Comparing chromatin contact maps at scale: methods and insights ]]> https://biorxiv.org/cgi/content/short/2023.04.04.535480v1?rss=1" Gunsalus, L. M. McArthur, E. Gjoni, K. Kuang, S. Pittman, M. Capra, J. A. Pollard, K. S. 2023-04-04 doi:10.1101/2023.04.04.535480 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Pro-inflammatory macrophages impair skeletal muscle regeneration in ischemic-damaged limbs by inducing precocious differentiation of satellite cells ]]> https://biorxiv.org/cgi/content/short/2023.04.01.535211v1?rss=1" Southerland, K. W. Xu, Y. Peters, D. T. Wei, X. Lin, X. Xiang, Y. Fei, K. Olivere, L. A. Morowitz, J. M. Otto, J. Kontos, C. D. Diao, Y. 2023-04-03 doi:10.1101/2023.04.01.535211 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex ]]> https://biorxiv.org/cgi/content/short/2023.04.08.536119v1?rss=1" Zemke, N. R. Armand, E. J. Wang, W. Lee, S. Zhou, J. Li, Y. E. Liu, H. Tian, W. Nery, J. R. Castanon, R. G. Bartlett, A. Osteen, J. K. Li, D. Zhuo, X. Xu, V. Miller, M. Krienen, F. M. Zhang, Q. Taskin, N. Ting, J. Feng, G. McCarroll, S. A. Callaway, E. M. Wang, T. Behrens, M. Lein, E. S. Ecker, J. R. Ren, B. 2023-04-08 doi:10.1101/2023.04.08.536119 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions ]]> https://biorxiv.org/cgi/content/short/2023.04.06.535849v1?rss=1" Chilinski, M. Lipinski, J. Agarwal, A. Ruan, Y. Plewczynski, D. 2023-04-06 doi:10.1101/2023.04.06.535849 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ The temporal progression of immune remodeling during metastasis. ]]> https://biorxiv.org/cgi/content/short/2023.05.04.539153v1?rss=1" View larger version (27K): org.highwire.dtl.DTLVardef@1333376org.highwire.dtl.DTLVardef@77c937org.highwire.dtl.DTLVardef@3b78b1org.highwire.dtl.DTLVardef@70d497_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefMcGinnis et al. report a longitudinal scRNA-seq atlas of lung immune cells in mice bearing PyMT-driven metastatic breast tumors and identify immune cell transcriptional states, shifts in population structure, and rewiring of cell-cell signaling networks which correlate with metastatic progression. HighlightsO_LILongitudinal scRNA-seq reveals distinct stages of immune remodeling before, during, and after metastatic colonization in the lungs of PyMT mice. C_LIO_LITLR-NF{kappa}B inflammation correlates with pre-metastatic niche formation and involves both tissue-resident and bone marrow-derived myeloid cell populations. C_LIO_LIInflammatory lung myeloid cells mirror activated primary tumor MDSCs, suggesting that primary tumor-derived cues induce Cd14 expression and TLR-NF{kappa}B inflammation in the lung. C_LIO_LILymphocytes contribute to the inflammatory and immunosuppressive lung metastatic microenvironment, highlighted by enrichment of cytotoxic NK cells in the lung over time. C_LIO_LICell-cell signaling network modeling predicts cell type-specific Ccl6 regulation and IGF1-IGF1R signaling between neutrophils and interstitial macrophages. C_LI ]]> McGinnis, C. S. Mao, Z. Reticker-Flynn, N. E. Winkler, J. Satpathy, A. T. 2023-05-07 doi:10.1101/2023.05.04.539153 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ High-resolution spatial multi-omics reveals cell-type specific nuclear compartments ]]> https://biorxiv.org/cgi/content/short/2023.05.07.539762v1?rss=1" 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues. ]]> Takei, Y. Yang, Y. White, J. Yun, J. Prasad, M. Ombelets, L. J. Schindler, S. Cai, L. 2023-05-09 doi:10.1101/2023.05.07.539762 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation ]]> https://biorxiv.org/cgi/content/short/2023.05.04.539469v1?rss=1" Fang, H. Tronco, A. R. Bonora, G. Nguyen, T. Thakur, J. Berletch, J. B. Filippova, G. N. Henikoff, S. Shendure, J. Noble, W. S. Disteche, C. M. Deng, X. 2023-05-04 doi:10.1101/2023.05.04.539469 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ scGHOST: Identifying single-cell 3D genome subcompartments ]]> https://biorxiv.org/cgi/content/short/2023.05.24.542032v1?rss=1" Xiong, K. Zhang, R. Ma, J. 2023-05-25 doi:10.1101/2023.05.24.542032 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Recording morphogen signals reveals origins of gastruloid symmetry breaking ]]> https://biorxiv.org/cgi/content/short/2023.06.02.543474v1?rss=1" McNamara, H. M. Solley, S. C. Adamson, B. Chan, M. M. Toettcher, J. E. 2023-06-05 doi:10.1101/2023.06.02.543474 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain ]]> https://biorxiv.org/cgi/content/short/2023.06.28.546457v1?rss=1" Luo, Z. Wen, X. Zhao, W. Nguyen, T. Wan, X. Richard, J. L. C. Zhong, S. 2023-06-29 doi:10.1101/2023.06.28.546457 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells ]]> https://biorxiv.org/cgi/content/short/2023.06.14.544990v1?rss=1" Pulecio, J. Tayyebi, Z. Liu, D. Wong, W. Luo, R. Damodaran, J. R. Kaplan, S. Cho, H. Yan, J. Murphy, D. J. Rickert, R. Shukla, A. Zhong, A. Gonzalez, F. Yang, D. Li, W. Zhou, T. Apostolou, E. Leslie, C. Huangfu, D. 2023-06-14 doi:10.1101/2023.06.14.544990 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress ]]> https://biorxiv.org/cgi/content/short/2023.06.05.543769v1?rss=1" Wolin, E. Guo, J. K. Blanco, M. R. Perez, A. A. Goronzy, I. N. Abdou, A. A. Gorhe, D. Guttman, M. Jovanovic, M. 2023-06-07 doi:10.1101/2023.06.05.543769 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states ]]> https://biorxiv.org/cgi/content/short/2023.07.06.547955v1?rss=1" Reffsin, S. Miller, J. Ayyanathan, K. Dunagin, M. C. Jain, N. Schultz, D. C. Cherry, S. Raj, A. 2023-07-07 doi:10.1101/2023.07.06.547955 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells ]]> https://biorxiv.org/cgi/content/short/2023.07.20.549578v1?rss=1" Zhou, T. Zhang, R. Jia, D. Doty, R. T. Munday, A. D. Gao, D. Xin, L. Abkowitz, J. L. Duan, Z. Ma, J. 2023-07-25 doi:10.1101/2023.07.20.549578 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ A genome-wide single-cell 3D genome atlas of lung cancer progression ]]> https://biorxiv.org/cgi/content/short/2023.07.23.550157v1?rss=1" Liu, M. Jin, S. Agabiti, S. S. Jensen, T. B. Yang, T. Radda, J. S. D. Ruiz, C. F. Baldissera, G. Muzumdar, M. D. Wang, S. 2023-07-24 doi:10.1101/2023.07.23.550157 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression ]]> https://biorxiv.org/cgi/content/short/2023.07.19.549714v1?rss=1" Murphy, D. Salataj, E. Di Giammartino, D. C. Rodriguez-Hernaez, J. Kloetgen, A. Garg, V. Char, E. Uyehara, C. M. Ee, L.-s. Lee, U. Stadtfeld, M. Hadjantonakis, A.-K. Tsirigos, A. Polyzos, A. Apostolou, E. 2023-07-19 doi:10.1101/2023.07.19.549714 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ High throughput PRIME editing screens identify functional DNA variants in the human genome ]]> https://biorxiv.org/cgi/content/short/2023.07.12.548736v1?rss=1" Ren, X. Yang, H. Nierenberg, J. L. Sun, Y. Chen, J. Beaman, C. Pham, T. Nobuhara, M. Takagi, M. A. Narayan, V. Li, Y. Ziv, E. Shen, Y. 2023-07-12 doi:10.1101/2023.07.12.548736 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ ChromaFold predicts the 3D contact map from single-cell chromatin accessibility ]]> https://biorxiv.org/cgi/content/short/2023.07.27.550836v1?rss=1" Gao, V. R. Yang, R. Das, A. Luo, R. Luo, H. McNally, D. R. Karagiannidis, I. Rivas, M. A. Wang, Z.-m. Barisic, D. Karbalayghareh, A. Wong, W. Zhan, Y. Chin, C. R. Noble, W. S. Bilmes, J. A. Apostolou, E. Kharas, M. Beguelin, W. Viny, A. D. Huangfu, D. Rudensky, A. Melnick, A. Leslie, C. S. 2023-07-28 doi:10.1101/2023.07.27.550836 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells ]]> https://biorxiv.org/cgi/content/short/2023.07.27.550709v1?rss=1" Chiariello, A. M. Abraham, A. Bianco, S. Esposito, A. Vercellone, F. Conte, M. Fontana, A. Nicodemi, M. 2023-07-28 doi:10.1101/2023.07.27.550709 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons ]]> https://biorxiv.org/cgi/content/short/2023.08.30.555359v1?rss=1" Yang, X. Jones, I. R. Chen, P. B. Yang, H. Ren, X. Zheng, L. Li, B. Li, Y. E. Sun, Q. Wen, J. Beaman, C. Cui, X. Li, Y. Wang, W. Hu, M. Ren, B. Shen, Y. 2023-08-30 doi:10.1101/2023.08.30.555359 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum ]]> https://biorxiv.org/cgi/content/short/2023.07.19.549737v1?rss=1" Zhao, Z. Parra, O. P. Muscella, F. Alber, F. Scrutton-Alvarado, N. Muscella, F. Yang, Y. Yamada, T. 2023-07-21 doi:10.1101/2023.07.19.549737 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation ]]> https://biorxiv.org/cgi/content/short/2023.10.13.562147v1?rss=1" Sinha, J. Nickels, J. F. Thurm, A. R. Ludwig, C. H. Archibald, B. N. Hinks, M. M. Wan, J. Fang, D. Bintu, L. 2023-10-14 doi:10.1101/2023.10.13.562147 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Single-cell chromatin state transitions during epigenetic memory formation ]]> https://biorxiv.org/cgi/content/short/2023.10.03.560616v1?rss=1" Fujimori, T. Rios-Martinez, C. Thurm, A. R. Hinks, M. M. Doughty, B. R. Sinha, J. Le, D. Hafner, A. Greenleaf, W. J. Boettiger, A. N. Bintu, L. 2023-10-05 doi:10.1101/2023.10.03.560616 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning ]]> https://biorxiv.org/cgi/content/short/2023.10.22.563498v1?rss=1" Kuang, S. Pollard, K. S. 2023-10-24 doi:10.1101/2023.10.22.563498 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ HybriSeq: Probe-based Device-free Single-cell RNA Profiling ]]> https://biorxiv.org/cgi/content/short/2023.09.27.559406v1?rss=1" Foyt, D. Brown, D. Zhou, S. Huang, B. 2023-09-29 doi:10.1101/2023.09.27.559406 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types ]]> https://biorxiv.org/cgi/content/short/2023.10.29.564613v1?rss=1" Kumar, P. Gholamalamdari, O. Zhang, Y. Zhang, L. Vertii, A. van Schaik, T. Peric-Hupkes, D. Sasaki, T. Gilbert, D. M. van Steensel, B. Ma, J. Kaufman, P. D. Belmont, A. S. 2023-11-01 doi:10.1101/2023.10.29.564613 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models ]]> https://biorxiv.org/cgi/content/short/2023.11.03.565556v1?rss=1" Gjoni, K. Pollard, K. S. 2023-11-05 doi:10.1101/2023.11.03.565556 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization ]]> https://biorxiv.org/cgi/content/short/2023.11.22.568268v1?rss=1" Gunsalus, L. M. Keiser, M. J. Pollard, K. S. 2023-11-22 doi:10.1101/2023.11.22.568268 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Genome folding principles revealed in condensin-depleted mitotic chromosomes ]]> https://biorxiv.org/cgi/content/short/2023.11.09.566494v1?rss=1" Zhao, H. Lin, Y. Lin, E. Liu, F. Shu, L. Jing, D. Wang, B. Wang, M. Shan, F. Zhang, L. Lam, J. Midla, S. Giardine, B. Keller, C. Hardison, R. Blobel, G. Zhang, H. 2023-11-13 doi:10.1101/2023.11.09.566494 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles ]]> https://biorxiv.org/cgi/content/short/2023.11.07.566110v1?rss=1" Andronov, L. Han, M. Zhu, Y. Roy, A. R. Barentine, A. E. S. Garhyan, J. Qi, L. S. Moerner, W. E. 2023-11-08 doi:10.1101/2023.11.07.566110 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression ]]> https://biorxiv.org/cgi/content/short/2023.12.14.571730v1?rss=1" Perez, A. A. Goronzy, I. N. Blanco, M. R. Guo, J. K. Guttman, M. 2023-12-18 doi:10.1101/2023.12.14.571730 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ Electrostatic encoding of genome organization principles within single native nucleosomes ]]> https://biorxiv.org/cgi/content/short/2023.12.08.570828v1?rss=1" Park, S. Athreya, A. Carrizo, G. Benning, N. Mitchener, M. Bhanu, N. Garcia, B. Zhang, B. Muir, T. W. Pearce, E. Ha, T. 2023-12-09 doi:10.1101/2023.12.08.570828 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation ]]> https://biorxiv.org/cgi/content/short/2023.12.04.569731v1?rss=1" 4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops, promoter-promoter loops, or unlooped. Genes transitioning from repression to RNAPolII initiation exhibit slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNAPolII-mediated elongation during neural cell fate transitions. HighlightsO_LIThousands of loops are decommissioned and gained upon human iPSC differentiation to NPCs/neurons C_LIO_LIGenes transitioning from initiated-to-elongated exhibit robust mRNA upregulation when connected in cell type-specific promoter-enhancer loops C_LIO_LIGenes transitioning from repressed-to-initiated exhibit slight increases in mRNA levels independent of loop status C_LIO_LIUpon short-term RNAPolII degradation, loops formed by elongated genes are more severely disrupted than those anchoring initiated genes C_LI ]]> Titus, K. R. Simandi, Z. Chandrashekar, H. Paquet, D. Phillips-Cremins, J. E. 2023-12-05 doi:10.1101/2023.12.04.569731 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Machine learning reveals the diversity of human 3D chromatin contact patterns ]]> https://biorxiv.org/cgi/content/short/2023.12.22.573104v1?rss=1" Gilbertson, E. N. Brand, C. M. McArthur, E. Rinker, D. C. Kuang, S. Pollard, K. S. Capra, J. A. 2023-12-23 doi:10.1101/2023.12.22.573104 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Understanding how genetically encoded tags affect phase separation by Heterochromatin Protein HP1α ]]> https://biorxiv.org/cgi/content/short/2023.12.04.569983v1?rss=1" Zhou, Z. Narlikar, G. J. 2023-12-05 doi:10.1101/2023.12.04.569983 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag ]]> https://biorxiv.org/cgi/content/short/2024.01.16.575860v1?rss=1" Brumbaugh-Reed, E. H. Aoki, K. Toettcher, J. E. 2024-01-17 doi:10.1101/2024.01.16.575860 Cold Spring Harbor Laboratory Press 2024-01-17 <![CDATA[ Pseudotime analysis for time-series single-cell sequencing and imaging data ]]> https://biorxiv.org/cgi/content/short/2023.11.03.565575v1?rss=1" Li, G. Kim, H.-J. Pendyala, S. Zhang, R. Disteche, C. M. Vert, J.-P. Deng, X. Fowler, D. Noble, W. S. 2023-11-05 doi:10.1101/2023.11.03.565575 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning ]]> https://biorxiv.org/cgi/content/short/2024.01.31.578123v1?rss=1" Niu, Z. O'Farrell, A. Li, J. Reffsin, S. Jain, N. Dardani, I. Goyal, Y. Raj, A. 2024-01-31 doi:10.1101/2024.01.31.578123 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations ]]> https://biorxiv.org/cgi/content/short/2024.02.27.582395v1?rss=1" Chandrashekar, H. Simandi, Z. Choi, H. Ryu, H.-S. Waldman, A. J. Nikish, A. Muppidi, S. S. Gong, W. Paquet, D. Phillips-Cremins, J. E. 2024-02-27 doi:10.1101/2024.02.27.582395 Cold Spring Harbor Laboratory Press 2024-02-27 <![CDATA[ HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences ]]> https://biorxiv.org/cgi/content/short/2024.02.01.578389v1?rss=1" Chilinski, M. Plewczynski, D. 2024-02-05 doi:10.1101/2024.02.01.578389 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ LoopSage: An Energy-Based Monte Carlo approach for the Loop Extrusion Modelling of Chromatin ]]> https://biorxiv.org/cgi/content/short/2024.01.10.574968v1?rss=1" Korsak, S. Plewczynski, D. 2024-01-12 doi:10.1101/2024.01.10.574968 Cold Spring Harbor Laboratory Press 2024-01-12 <![CDATA[ Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level ]]> https://biorxiv.org/cgi/content/short/2024.02.05.576943v1?rss=1" Stein, J. Ericsson, M. Nofal, M. Magni, L. Aufmkolk, S. McMillan, R. B. Breimann, L. Herlihy, C. P. Lee, S. D. Willemin, A. Wohlmann, J. Arguedas-Jimenez, L. Yin, P. Pombo, A. Church, G. M. Wu, C.-t. 2024-02-05 doi:10.1101/2024.02.05.576943 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types ]]> https://biorxiv.org/cgi/content/short/2024.02.10.579769v1?rss=1" Hamazaki, N. Yang, W. Kubo, C. Qiu, C. Martin, B. K. Garge, R. K. Regalado, S. G. Nichols, E. Lee, C. Daza, R. M. Srivatsan, S. Shendure, J. 2024-02-12 doi:10.1101/2024.02.10.579769 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML ]]> https://biorxiv.org/cgi/content/short/2024.02.29.582813v1?rss=1" Zhao, R. Xu, M. Wondisford, A. R. Lackner, R. M. Salsman, J. Dellaire, G. Chenoweth, D. M. O'Sullivan, R. J. Zhao, X. Zhang, H. 2024-02-29 doi:10.1101/2024.02.29.582813 Cold Spring Harbor Laboratory Press 2024-02-29 <![CDATA[ Regulation of immune signal integration and memory by inflammation-induced chromosome conformation ]]> https://biorxiv.org/cgi/content/short/2024.02.29.582872v1?rss=1" Daniel, B. Chen, A. Y. Sandor, K. Zhang, W. Miao, Z. Lareau, C. A. Yost, K. E. Chang, H. Satpathy, A. 2024-03-04 doi:10.1101/2024.02.29.582872 Cold Spring Harbor Laboratory Press 2024-03-04 <![CDATA[ Super-enhancer interactomes from single cells link clustering and transcription ]]> https://biorxiv.org/cgi/content/short/2024.05.08.593251v1?rss=1" Le, D. Hafner, A. Gaddam, S. Wang, K. Boettiger, A. N. 2024-05-10 doi:10.1101/2024.05.08.593251 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant ]]> https://biorxiv.org/cgi/content/short/2024.04.26.591412v1?rss=1" Kaplan, S. J. Wong, W. Yan, J. Pulecio, J. Cho, H. Leslie-Iyer, J. Kazakov, J. Zhao, J. Li, Q. Murphy, D. Luo, R. Dey, K. K. Apostolou, E. Lesie, C. S. Huangfu, D. 2024-04-29 doi:10.1101/2024.04.26.591412 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing ]]> https://biorxiv.org/cgi/content/short/2024.04.29.591790v1?rss=1" ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses. Key pointsO_LIWe provide a protocol for MASTR-seq: Multiplexed Analysis of Short Tandem Repeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. C_LIO_LIMASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease. C_LIO_LIMASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell. C_LI ]]> Chandradoss, K. R. Su, C. Malachowski, T. Boya, R. Ryu, H.-S. Brennand, K. Phillips-Cremins, J. E. 2024-05-02 doi:10.1101/2024.04.29.591790 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes ]]> https://biorxiv.org/cgi/content/short/2024.05.16.594268v1?rss=1" Jodkowska, K. Parteka-Tojek, Z. Agarwal, A. Denkiewicz, M. Korsak, S. Chilinski, M. Banecki, K. Plewczynski, D. 2024-05-20 doi:10.1101/2024.05.16.594268 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ HLH-30/TFEB rewires the chaperone network to promote proteostasis under conditions of Coenzyme A and Iron-Sulfur Cluster Deficiency ]]> https://biorxiv.org/cgi/content/short/2024.06.05.597553v1?rss=1" Shalash, R. Levi-Ferber, M. von Chrzanowski, H. Atrash, M. K. Shav-Tal, Y. Henis-Korenblit, S. 2024-06-06 doi:10.1101/2024.06.05.597553 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data ]]> https://biorxiv.org/cgi/content/short/2024.06.18.599627v1?rss=1" Patel, R. Pham, K. Chandrashekar, H. Phillips-Cremins, J. E. 2024-06-18 doi:10.1101/2024.06.18.599627 Cold Spring Harbor Laboratory Press 2024-06-18 <![CDATA[ Vcam1+ Fibro-adipogenic Progenitors Mark Fatty Infiltration in Chronic Limb Threatening Ischemia ]]> https://biorxiv.org/cgi/content/short/2024.07.08.602430v1?rss=1" Dai, Q. Wan, C. Xu, Y. Fei, K. Olivere, L. A. Garrett, B. Akers, L. Peters, D. Otto, J. C. Kontos, C. D. Ji, Z. Diao, Y. Southerland, K. W. 2024-07-11 doi:10.1101/2024.07.08.602430 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing ]]> https://biorxiv.org/cgi/content/short/2024.07.09.602710v1?rss=1" Nguyen, L. T. Rakestraw, N. R. Pizzano, B. L. Young, C. B. Huang, Y. Beerensson, K. T. Fang, A. Antal, S. G. Anamiss, K. V. Peggs, C. M. Yan, J. Jing, Y. Burdine, R. D. Adamson, B. Toettcher, J. E. Myhrvold, C. Jain, P. K. 2024-07-10 doi:10.1101/2024.07.09.602710 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance ]]> https://biorxiv.org/cgi/content/short/2024.06.30.601416v1?rss=1" Boe, R. H. Triandafillou, C. G. Lazcano, R. Wargo, J. A. Raj, A. 2024-07-02 doi:10.1101/2024.06.30.601416 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Long range regulation of transcription scales with genomic distance in a gene specific manner ]]> https://biorxiv.org/cgi/content/short/2024.07.19.604327v1?rss=1" Jensen, C. L. Chen, L.-F. Swigut, T. Crocker, O. J. Yao, D. Bassik, M. C. Ferrell, J. Boettiger, A. Wysocka, J. 2024-07-19 doi:10.1101/2024.07.19.604327 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Multiscale Molecular Modelling of Chromatin with MultiMM: From Nucleosomes to the Whole Genome ]]> https://biorxiv.org/cgi/content/short/2024.07.26.605260v1?rss=1" Korsak, S. Banecki, K. Plewczynski, D. 2024-07-26 doi:10.1101/2024.07.26.605260 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ ConsensuSV-ONT - a modern method for accurate structural variant calling ]]> https://biorxiv.org/cgi/content/short/2024.07.26.605267v1?rss=1" Pietryga, A. Chilinski, M. Gadakh, S. Plewczynski, D. 2024-07-26 doi:10.1101/2024.07.26.605267 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ LDB1 establishes multi-enhancer networks to regulate gene expression ]]> https://biorxiv.org/cgi/content/short/2024.08.23.609430v1?rss=1" Aboreden, N. G. Lam, J. C. Goel, V. Y. Wang, S. Wang, X. Midla, S. C. Quijano, A. Keller, C. A. Giardine, B. M. Hardison, R. C. Zhang, H. Hansen, A. S. Blobel, G. 2024-08-24 doi:10.1101/2024.08.23.609430 Cold Spring Harbor Laboratory Press 2024-08-24 <![CDATA[ YAP charge patterning mediates signal integration through transcriptional co-condensates ]]> https://biorxiv.org/cgi/content/short/2024.08.10.607443v1?rss=1" Meyer, K. Yserentant, K. Cheloor-Kovilakam, R. Ruff, K. M. Chung, C.-I. Shu, X. Huang, B. Weiner, O. D. 2024-08-10 doi:10.1101/2024.08.10.607443 Cold Spring Harbor Laboratory Press 2024-08-10 <![CDATA[ HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA ]]> https://biorxiv.org/cgi/content/short/2024.08.23.609244v1?rss=1" Saunders, H. S. Chio, U. S. Moore, C. M. Ramani, V. Cheng, Y. Narlikar, G. 2024-08-24 doi:10.1101/2024.08.23.609244 Cold Spring Harbor Laboratory Press 2024-08-24 <![CDATA[ Prediction of single-cell chromatin compartments from single-cell chromosome structures by MaxComp ]]> https://biorxiv.org/cgi/content/short/2024.07.02.600897v1?rss=1" Zhan, Y. Musella, F. Alber, F. 2024-07-04 doi:10.1101/2024.07.02.600897 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance ]]> https://biorxiv.org/cgi/content/short/2024.07.25.604999v1?rss=1" Li, J. Ravindran, P. T. O'Farrell, A. Busch, G. T. Boe, R. H. Niu, Z. Woo, S. Dunagin, M. C. Jain, N. Goyal, Y. Sarma, K. Herlyn, M. Raj, A. 2024-07-25 doi:10.1101/2024.07.25.604999 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues ]]> https://biorxiv.org/cgi/content/short/2024.09.24.614640v1?rss=1" Asami, S. Yin, C. Garza, L. A. Kalhor, R. 2024-09-24 doi:10.1101/2024.09.24.614640 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers ]]> https://biorxiv.org/cgi/content/short/2024.09.10.611504v1?rss=1" Moore, C. M. Kaur, U. Wong, E. Chio, U. S. M. Zhou, Z. Ostrowski, M. Wu, K. Irkliyenko, I. Wang, S. Ramani, V. Narlikar, G. 2024-09-10 doi:10.1101/2024.09.10.611504 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Dynamics of microcompartment formation at the mitosis-to-G1 transition ]]> https://biorxiv.org/cgi/content/short/2024.09.16.611917v1?rss=1" Goel, V. Y. Aboreden, N. G. Jusuf, J. M. Zhang, H. Mori, L. Mirny, L. A. Blobel, G. Banigan, E. J. Hansen, A. S. 2024-09-16 doi:10.1101/2024.09.16.611917 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/cgi/content/short/2024.09.17.613111v1?rss=1" The 4D Nucleome Consortium, Dekker, J. Oksuz, B. A. Zhang, Y. Wang, Y. Minsk, M. K. Kuang, S. Yang, L. Gibcus, J. H. Krietenstein, N. Rando, O. Xu, J. Janssens, D. H. Henikoff, S. Kukalev, A. Willemin, A. Winick-Ng, W. Kempfer, R. Pombo, A. Yu, M. Kumar, P. Zhang, L. Belmont, A. S. Sasaki, T. van Schaik, T. Brueckner, L. Peric-Hupkes, D. van Steensel, B. Wang, P. Chai, H. Kim, M. Ruan, Y. Zhang, R. Quinodoz, S. A. Bhat, P. Guttman, M. Zhao, W. Chien, S. Liu, Y. Venev, S. V. Plewczynski, D. Irastorza Azcarate, I. Szabo, D. Thieme, C. J. Szczepinska, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/cgi/content/short/2024.10.04.616668v1?rss=1" Sen, A. Xu, Z. Tyndale, S. Yasis, J. Cho, C. Y. Bump, R. Chandran, S. Luo, L. Fu, Y. Petersen, L. K. Shokhirev, M. Kuo, D. J. McVicker, G. P. Dixon, J. R. 2024-10-05 doi:10.1101/2024.10.04.616668 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Genome-wide in vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation ]]> https://biorxiv.org/cgi/content/short/2024.10.02.616323v1?rss=1" Popay, T. M. Pant, A. Munting, F. Black, M. E. Haghani, N. Dixon, J. 2024-10-02 doi:10.1101/2024.10.02.616323 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon ]]> https://biorxiv.org/cgi/content/short/2024.10.02.616241v1?rss=1" Kubica, J. Korsak, S. Clerkin, A. B. Kouril, D. Schirman, D. Yadavalli, A. D. Banecki, K. Kadlof, M. Busby, B. Plewczynski, D. 2024-10-03 doi:10.1101/2024.10.02.616241 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes ]]> https://biorxiv.org/cgi/content/short/2024.11.06.621353v1?rss=1" Gjoni, K. Ren, X. Everitt, A. Shen, Y. Pollard, K. S. 2024-11-07 doi:10.1101/2024.11.06.621353 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells ]]> https://biorxiv.org/cgi/content/short/2024.12.21.628413v1?rss=1" Yan, J. Luo, R. Rosen, B. P. Liu, D. Wong, W. Leslie, C. S. Huangfu, D. 2024-12-21 doi:10.1101/2024.12.21.628413 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Distinct Control of histone H1 expression within the Histone Locus body by CRAMP1 ]]> https://biorxiv.org/cgi/content/short/2025.01.07.631602v1?rss=1" Bodner, J. Vadlamani, P. Helmin, K. A. Liu, Q. Mendillo, M. L. Singer, B. D. Srivastava, S. Foltz, D. R. 2025-01-08 doi:10.1101/2025.01.07.631602 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Telomeric SUMO level influences the choices of APB formation pathways and ALT efficiency ]]> https://biorxiv.org/cgi/content/short/2025.01.16.633463v1?rss=1" Zhao, R. Wivagg, A. Lackner, R. M. Salsman, J. Dellaire, G. Matunis, M. J. Chenoweth, D. M. Zhao, X. Zhang, H. 2025-01-20 doi:10.1101/2025.01.16.633463 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers ]]> https://biorxiv.org/cgi/content/short/2025.01.17.633622v1?rss=1" 85% of nucleosomes surveyed displaying degrees of intranucleosomally accessible DNA. We observe epigenomic-domain-specific patterns of distorted nucleosome co-occupancy and positioning, including at enhancers, promoters, and mouse satellite repeat sequences. Nucleosome distortion is programmed by the presence of bound transcription factors (TFs) at cognate motifs; occupied TF binding sites are differentially decorated by distorted nucleosomes compared to unbound sites, and degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, we apply IDLI in the context of primary mouse hepatocytes, observing evidence for pervasive nucleosomal distortion in vivo. Further genetic experiments reveal a role for the hepatocyte master regulator FOXA2 in directly impacting nucleosome distortion at hepatocyte-specific regulatory elements in vivo. Our work suggests extreme--but regulated--plasticity in nucleosomal DNA accessibility at the single-molecule level. Further, our study offers an essential new framework to model transcription factor binding, nucleosome remodeling, and cell-type specific gene regulation across biological contexts. ]]> Yang, M. G. Richter, H. J. Wang, S. McNally, C. P. Harris, N. Dhillon, S. Maresca, M. de Wit, E. Willenbring, H. Maher, J. Goodarzi, H. Ramani, V. 2025-01-22 doi:10.1101/2025.01.17.633622 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ In vivo measurements of receptor tyrosine kinase activity reveal feedback regulation of a developmental gradient ]]> https://biorxiv.org/cgi/content/short/2025.01.06.631605v1?rss=1" Ho, E. K. Kim-Yip, R. P. Simpkins, A. G. Farahani, P. E. Oatman, H. R. Posfai, E. Shvartsman, S. Y. Toettcher, J. E. 2025-01-07 doi:10.1101/2025.01.06.631605 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor ]]> https://biorxiv.org/cgi/content/short/2025.01.09.632202v1?rss=1" Grant, Z. L. Kuang, S. Zhang, S. Horrillo, A. J. Rao, K. S. Kameswaran, V. Joubran, C. Lau, P. K. Dong, K. Yang, B. Bartosik, W. M. Zemke, N. R. Ren, B. Kathiriya, I. S. Pollard, K. S. Bruneau, B. G. 2025-01-12 doi:10.1101/2025.01.09.632202 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Innate Immune Memory is Stimulus Specific ]]> https://biorxiv.org/cgi/content/short/2025.01.22.634275v1?rss=1" O'Farrell, A. Niu, Z. Li, J. Van Eyndhoven, L. C. Sarma, K. Raj, A. 2025-01-24 doi:10.1101/2025.01.22.634275 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization ]]> https://biorxiv.org/cgi/content/short/2025.02.18.638941v1?rss=1" Sang, M. Johnson, M. E. 2025-02-23 doi:10.1101/2025.02.18.638941 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Cis-regulatory chromatin contacts form de novo in the absence of loop extrusion ]]> https://biorxiv.org/cgi/content/short/2025.01.12.632634v1?rss=1" Aboreden, N. Zhao, H. Shan, F. Liu, F. Zhang, H. Blobel, G. 2025-01-13 doi:10.1101/2025.01.12.632634 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade ]]> https://biorxiv.org/cgi/content/short/2025.02.10.637523v1?rss=1" Raposo, C. J. Yan, P. K. Chen, A. Y. Majidi, S. Hiam-Galvez, K. J. Satpathy, A. T. 2025-02-15 doi:10.1101/2025.02.10.637523 Cold Spring Harbor Laboratory Press 2025-02-15 <![CDATA[ Cohesin drives chromatin scanning during the RAD51-mediated homology search. ]]> https://biorxiv.org/cgi/content/short/2025.02.10.637451v1?rss=1" Marin-Gonzalez, A. Rybczynski, A. T. Nilavar, N. M. Nguyen, D. Karwacki- Neisius, V. Li, A. G. Zou, R. S. Aviles-Vazquez, F. J. Kanemaki, M. T. Scully, R. Ha, T. 2025-02-11 doi:10.1101/2025.02.10.637451 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ B cell stimulation changes the structure and higher-order organization of the inactive X chromosome ]]> https://biorxiv.org/cgi/content/short/2025.01.30.635789v1?rss=1" Toothacre, N. Anguera, M. Sierra, I. 2025-02-02 doi:10.1101/2025.01.30.635789 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ Rewired m6A methylation of promoter antisense RNAs in Alzheimer disease regulates global gene transcription in the 3D nucleome ]]> https://biorxiv.org/cgi/content/short/2025.03.22.644756v1?rss=1" LI, W. 2025-03-23 doi:10.1101/2025.03.22.644756 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue ]]> https://biorxiv.org/cgi/content/short/2025.03.06.641951v1?rss=1" Cheng, Y. Dang, S. Zhang, Y. Chen, Y. Yu, R. Liu, M. Jin, S. Han, A. Katz, S. Wang, S. 2025-03-11 doi:10.1101/2025.03.06.641951 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation ]]> https://biorxiv.org/cgi/content/short/2025.03.23.644697v1?rss=1" Zhou, J. Wu, Y. Liu, H. Tian, W. Castanon, R. G. Bartlett, A. Zhang, Z. Yao, G. Shi, D. Clock, B. Marcotte, S. Nery, J. R. Liem, M. Claffey, N. Boggeman, L. Barragan, C. eDrigo, R. A. Weimer, A. K. Shi, M. Cooper-Knock, J. Zhang, S. Snyder, M. P. Preissl, S. Ren, B. O'Connor, C. Chen, S. Luo, C. Dixon, J. R. Ecker, J. R. 2025-03-24 doi:10.1101/2025.03.23.644697 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity ]]> https://biorxiv.org/cgi/content/short/2025.03.19.644148v1?rss=1" 250 genes and exhibit patient-specific H3K9me3 variation. Using N=4 FXS iPSC lines and N=7 single-cell isogenic FXS iPSC subclones, we observe a strong correlation between inter-sample H3K9me3 variation and heterogeneous BREACH gene repression. We demonstrate improved prediction of cognitive metrics in FXS patients with an additive model of blood FMRP and mRNA levels of H3K9me3-mosaic, but not H3K9me3-invariant, BREACH genes. Our results highlight the utility of H3K9me3 variation at BREACHes for identifying genes associated with FXS clinical metrics. ]]> Pham, K. Malachowski, T. Zhou, L. Kim, J. H. Su, C. Phillips-Cremins, J. E. 2025-03-19 doi:10.1101/2025.03.19.644148 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Multimodal control of Cas13 activity through domain insertion at an allosteric hotspot ]]> https://biorxiv.org/cgi/content/short/2025.04.21.649818v1?rss=1" Zhu, L. Nguyen, L. T. Bell, A. G. Gillmann, K. M. Oatman, H. Hariri, J. Myhrvold, C. E. Toettcher, J. E. 2025-04-21 doi:10.1101/2025.04.21.649818 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Kinetic organization of the genome revealed by ultra-resolution, multiscale live imaging ]]> https://biorxiv.org/cgi/content/short/2025.03.27.645817v1?rss=1" Lee, J. Chen, L.-F. Gaudin, S. Gupta, K. Spakowitz, A. Boettiger, A. 2025-04-01 doi:10.1101/2025.03.27.645817 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Heterogeneous therapy-resistant cancer cells have distinct and exploitable drug sensitivity profiles ]]> https://biorxiv.org/cgi/content/short/2025.04.25.650475v1?rss=1" Busch, G. T. Boe, R. H. Li, J. Gruener, R. F. Arnett, M. J. Ravindran, P. T. Herlyn, M. Huang, R. S. Raj, A. 2025-04-25 doi:10.1101/2025.04.25.650475 Cold Spring Harbor Laboratory Press 2025-04-25 <![CDATA[ Oncogenic drivers shape the tumor microenvironment in human gliomas ]]> https://biorxiv.org/cgi/content/short/2025.05.16.654515v1?rss=1" Zhao, B. Cho, C. Y. Ye, L. Keal, T. Mitchell, T. J. Martin-Barrio, I. Weinberg, J. S. Huse, J. T. Dixon, J. R. Lang, F. F. Akdemir, K. C. 2025-05-21 doi:10.1101/2025.05.16.654515 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Rate Limiting Enzymes in Nucleotide Metabolism Synchronize Nucleotide Biosynthesis and Chromatin Formation ]]> https://biorxiv.org/cgi/content/short/2025.05.21.655426v1?rss=1" Srivastava, S. Samaniego-Castruita, D. Khurana, S. Shukla, V. Ben-Sahra, I. Foltz, D. R. 2025-05-24 doi:10.1101/2025.05.21.655426 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Nonrandom interchromatin trafficking through dynamic multiphase speckle connections ]]> https://biorxiv.org/cgi/content/short/2025.05.23.655761v1?rss=1" Kim, J. Gonzalez, G. A. H. Venkata, N. C. Han, K. Y. Belmont, A. S. 2025-05-23 doi:10.1101/2025.05.23.655761 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Lineage memory shapes viral resistance barriers in human skin ]]> https://biorxiv.org/cgi/content/short/2025.06.27.661951v1?rss=1" Van Eyndhoven, L. C. C. Kinsler, G. Zhang, J. O'Farrell, A. Abderrahim, R. Srivastav, A. Triandafillou, C. G. Greco, T. M. Zaret, K. S. Cristea, I. M. Orzalli, M. H. Drayman, N. Singh, A. Raj, A. 2025-06-27 doi:10.1101/2025.06.27.661951 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids ]]> https://biorxiv.org/cgi/content/short/2025.07.14.664617v1?rss=1" Triandafillou, C. G. Sompalle, P. Heyman, Y. Raj, A. 2025-07-14 doi:10.1101/2025.07.14.664617 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Gastruloid patterning reflects division of labor among biased stem cell clones ]]> https://biorxiv.org/cgi/content/short/2025.07.12.664536v1?rss=1" Ayyappan, V. Triandafillou, C. Sarma, K. Raj, A. 2025-07-14 doi:10.1101/2025.07.12.664536 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions ]]> https://biorxiv.org/cgi/content/short/2025.07.29.667515v1?rss=1" Smith, R. G. Fu, Y. Schiela, K. L. Dautle, M. Williams, R. Wilson, H. M. Azadegan, C. Whetstine, J. R. Dekker, J. Liu, Y. 2025-08-01 doi:10.1101/2025.07.29.667515 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data ]]> https://biorxiv.org/cgi/content/short/2025.08.11.666099v1?rss=1" Mohseni Ahooyi, T. Stear, B. Simmons, J. A. Metzger, V. T. Kumar, P. Evangelista, J. E. Clarke, D. J. B. Xie, Z. Kim, H. Jenkins, S. L. Maurya, M. R. Ramachandran, S. Fahy, E. Imam, F. T. Kokash, N. Roth, M. E. Fullem, R. Jevtic, D. Mihajlovic, A. Tiemeyer, M. Gillespie, T. H. Bakker, C. Schroeder, A. J. Markowski, J. Nedzel, J. Hill, D. D. Terry, J. Nemarich, C. Park, P. Ardlie, K. G. Vora, J. Mazumder, R. Ranzinger, R. de Bono, B. Subramaniam, S. Grethe, J. S. Yang, J. J. Lambert, C. G. Resnick, A. Milosavljevic, A. Ma'ayan, A. Silverstein, J. C. Tay 2025-08-15 doi:10.1101/2025.08.11.666099 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease ]]> https://biorxiv.org/cgi/content/short/2025.08.16.669546v1?rss=1" Kathiriya, I. S. Rao, K. S. Clark, A. P. Hu, K. M. Grant, Z. L. Matthews, M. N. Chen, Z. Saucerman, J. J. Hota, S. K. Bruneau, B. 2025-08-19 doi:10.1101/2025.08.16.669546 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation ]]> https://biorxiv.org/cgi/content/short/2025.08.07.669196v1?rss=1" Yan, J. Cho, H. S. Luo, R. Beer, M. A. Li, W. Huangfu, D. 2025-08-08 doi:10.1101/2025.08.07.669196 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells ]]> https://biorxiv.org/cgi/content/short/2025.08.15.670620v1?rss=1" Andronov, L. Han, M. Balaji, A. Zhu, Y. Qi, L. S. Moerner, W. E. 2025-08-18 doi:10.1101/2025.08.15.670620 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Genome-wide chromatin recording resolves dynamic cell state changes ]]> https://biorxiv.org/cgi/content/short/2025.08.05.668773v1?rss=1" Takei, Y. Lay, J. A. Linton, J. M. Chadly, D. M. Ochiai, Y. Hadas, R. Perez, A. A. Blanco, M. R. Laurino, P. Guttman, M. Elowitz, M. B. 2025-08-06 doi:10.1101/2025.08.05.668773 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space ]]> https://biorxiv.org/cgi/content/short/2025.08.23.671945v1?rss=1" Venkata, N. C. Kim, J. Faber, G. Misra, S. Bektash, A. Chaturvedi, P. Hernanadez, G. Dopie, J. Kanemaki, M. Han, K. Y. Shav-Tal, Y. Belmont, A. S. 2025-08-25 doi:10.1101/2025.08.23.671945 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development ]]> https://biorxiv.org/cgi/content/short/2025.08.07.669116v1?rss=1" Reimonn, T. Yilmaz, V. O. Tran, H. Ng, G. Liu, D. Abdennur, N. A. 2025-08-07 doi:10.1101/2025.08.07.669116 Cold Spring Harbor Laboratory Press 2025-08-07