bioRxiv Channel: The Whitehead Institute https://biorxiv.org This feed contains articles for bioRxiv Channel "The Whitehead Institute" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data ]]> https://biorxiv.org/cgi/content/short/2022.02.17.480958v1?rss=1" Wang, P. Y. Bartel, D. P. 2022-02-19 doi:10.1101/2022.02.17.480958 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Pairing to the microRNA 3' region occurs through two alternative binding modes, with affinity shaped by nucleotide identity as well as pairing position ]]> https://biorxiv.org/cgi/content/short/2021.04.13.439700v1?rss=1" 1,000 3'-pairing architectures for each miRNA. In some cases, optimal 3' pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3'-pairing modes--one of which included additional nucleotides bridging seed and 3' pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3' pairing is determined for each miRNA. HIGHLIGHTSO_LIRNA bind-n-seq reveals relative affinities of >1,000 3'-pairing architectures C_LIO_LITwo distinct 3'-binding modes can enhance affinity, by >500-fold in some instances C_LIO_LIG and oligo(G/C) residues help define the miRNA 3' segment most critical for pairing C_LIO_LISeed mismatch identity can influence the contribution of compensatory 3' pairing C_LI ]]> McGeary, S. E. Bisaria, N. Bartel, D. P. 2021-04-14 doi:10.1101/2021.04.13.439700 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ The molecular basis of coupling between poly(A)-tail length and translational efficiency ]]> https://biorxiv.org/cgi/content/short/2021.01.18.427055v1?rss=1" Bartel, D. P. Xiang, K. 2021-01-19 doi:10.1101/2021.01.18.427055 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ A Golgi-localized peptide encoded by the CENP-R transcript provides a valuable tool for live cell imaging ]]> https://biorxiv.org/cgi/content/short/2020.12.13.422530v1?rss=1" Navarro, A. P. Cheeseman, I. M. 2020-12-13 doi:10.1101/2020.12.13.422530 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Dynamic cell cycle-dependent phosphorylation modulates CENP-L-CENP-N centromere recruitment ]]> https://biorxiv.org/cgi/content/short/2021.12.17.473210v1?rss=1" Navarro, A. P. Cheeseman, I. M. 2021-12-18 doi:10.1101/2021.12.17.473210 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ The phenotypic landscape of essential human genes ]]> https://biorxiv.org/cgi/content/short/2021.11.28.470116v1?rss=1" 31 million individual cells revealed measurable phenotypes for >90% of genes. Using multi-dimensional clustering based on hundreds of quantitative phenotypic parameters, we identified co-functional genes across diverse cellular activities, revealing novel gene functions and associations. Pooled live-cell screening of [~]450,000 cell division events for 239 genes further identified functional contributions to chromosome segregation. Our work creates a resource for the phenotypic analysis of core cellular processes and defines the functional landscape of essential human genes. ]]> Funk, L. Su, K.-C. Feldman, D. Singh, A. Moodie, B. Blainey, P. Cheeseman, I. M. 2021-11-28 doi:10.1101/2021.11.28.470116 Cold Spring Harbor Laboratory Press 2021-11-28 <![CDATA[ Alternative Cdc20 translational isoforms bypass the spindle assembly checkpoint to control mitotic arrest duration ]]> https://biorxiv.org/cgi/content/short/2021.10.24.465552v1?rss=1" Tsang, M. J. Cheeseman, I. M. 2021-10-24 doi:10.1101/2021.10.24.465552 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Polarized Dishevelled dissolution and condensation drives embryonic axis specification in oocytes ]]> https://biorxiv.org/cgi/content/short/2021.05.17.444558v1?rss=1" Swartz, Z. Tan, T. H. Perillo, M. Fakhri, N. Wessel, G. M. Wikramanayake, A. Cheeseman, I. M. 2021-05-18 doi:10.1101/2021.05.17.444558 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Convergence of case-specific epigenetic alterations identify a confluence of genetic vulnerabilities tied to opioid dependence ]]> https://biorxiv.org/cgi/content/short/2021.06.15.447736v1?rss=1" Corradin, O. Sallari, R. Hoang, A. T. Kassim, B. S. Ben Hutta, G. Cuoto, L. Quach, B. C. Lovrenert, K. Hays, C. Gryder, B. E. Iskhakova, M. Cates, H. Song, Y. Bartels, C. F. Hancock, D. B. Mash, D. C. Johnson, E. O. Akbarian, S. Scacheri, P. C. 2021-06-16 doi:10.1101/2021.06.15.447736 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ RNA Pol IV has antagonistic parent-of-origin effects on Arabidopsis endosperm ]]> https://biorxiv.org/cgi/content/short/2021.03.24.436774v1?rss=1" Satyaki, P. R. V. Gehring, M. 2021-03-24 doi:10.1101/2021.03.24.436774 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time ]]> https://biorxiv.org/cgi/content/short/2021.03.29.437569v1?rss=1" Williams, B. P. Bechen, L. A. Pohlmann, D. A. Gehring, M. 2021-03-29 doi:10.1101/2021.03.29.437569 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Flanking sequences regulate the toxicity, non-ATG translation, and aggregation of RNA with tandem CAG Repeats ]]> https://biorxiv.org/cgi/content/short/2021.08.30.458106v1?rss=1" Das, M. R. Chang, Y. Saunders, R. Zhang, N. Tomberlin, C. Vale, R. D. Jain, A. 2021-08-31 doi:10.1101/2021.08.30.458106 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C ]]> https://biorxiv.org/cgi/content/short/2021.09.25.461797v1?rss=1" Hartooni, N. Sung, J. Jain, A. Morgan, D. O. 2021-09-26 doi:10.1101/2021.09.25.461797 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ A phosphoregulated RhoGEF feedback loop tunes cortical flow driven amoeboid migration in vivo ]]> https://biorxiv.org/cgi/content/short/2021.10.29.466358v1?rss=1" Lin, B. Luo, J. Lehmann, R. 2021-10-29 doi:10.1101/2021.10.29.466358 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Bioactive isoprenoids guide migrating germ cells to the embryonic gonad ]]> https://biorxiv.org/cgi/content/short/2021.09.30.462471v1?rss=1" Barton, L. Sanny, J. Dawson, E. P. Nouzova, M. Noriega, F. G. Stadtfeld, M. Lehmann, R. 2021-10-01 doi:10.1101/2021.09.30.462471 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A single cell atlas reveals unanticipated cell type complexity in Drosophila ovaries ]]> https://biorxiv.org/cgi/content/short/2021.01.21.427703v1?rss=1" Slaidina, M. Gupta, S. Lehmann, R. 2021-01-22 doi:10.1101/2021.01.21.427703 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ High-throughput functionalization of the Toxoplasma kinome uncovers a novel regulator of invasion and egress ]]> https://biorxiv.org/cgi/content/short/2021.09.23.461611v1?rss=1" Smith, T. A. Lopez-Perez, G. S. Shortt, E. Lourido, S. 2021-09-24 doi:10.1101/2021.09.23.461611 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Toxoplasma gondii subverts the host ESCRT machinery for parasite uptake of host cytosolic proteins ]]> https://biorxiv.org/cgi/content/short/2021.07.21.453261v1?rss=1" Rivera-Cuevas, Y. Mayoral, J. Di Cristina, M. Lawrence, A.-L. E. Olafsson, E. B. Thornhill, D. Waldman, B. S. Ono, A. Sexton, J. Lourido, S. Weiss, L. M. Carruthers, V. B. 2021-07-21 doi:10.1101/2021.07.21.453261 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ A gene-by-gene mosaic of dosage compensation strategies on the human X chromosome ]]> https://biorxiv.org/cgi/content/short/2021.08.09.455676v1?rss=1" San Roman, A. K. Godfrey, A. K. Skaletsky, H. Bellott, D. W. Groff, A. F. Blanton, L. V. Hughes, J. F. Brown, L. Phou, S. Buscetta, A. Kruszka, P. Banks, N. Dutra, A. Pak, E. Lasutschinkow, P. C. Keen, C. Davis, S. M. Tartaglia, N. R. Samango-Sprouse, C. Muenke, M. Page, D. C. 2021-08-09 doi:10.1101/2021.08.09.455676 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ GC-biased gene conversion in X-Chromosome palindromes conserved in human, chimpanzee, and rhesus macaque ]]> https://biorxiv.org/cgi/content/short/2021.04.21.440828v1?rss=1" Jackson, E. K. Bellott, D. W. Skaletsky, H. Page, D. C. 2021-04-21 doi:10.1101/2021.04.21.440828 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Krüppel-like factor 4 is required for development and regeneration of germline and yolk cells from somatic stem cells in planarians ]]> https://biorxiv.org/cgi/content/short/2021.11.08.467675v1?rss=1" Issigonis, M. Redkar, A. Rozario, T. Khan, U. Mejia-Sanchez, R. Lapan, S. Reddien, P. Newmark, P. A. 2021-11-08 doi:10.1101/2021.11.08.467675 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ m6A is required for resolving progenitor identity during planarian stem cell differentiation ]]> https://biorxiv.org/cgi/content/short/2021.07.27.453979v1?rss=1" 20,000 cells following perturbation of the pathway, we discovered that m6A negatively regulates transcription of histone variants, and that inhibition of the pathway resulted in accumulation of undifferentiated cells throughout the animal in an abnormal transcriptional state. Analysis of >1000 planarian gene expression datasets revealed that the inhibition of the chromatin modifying complex NuRD had almost indistinguishable consequences, unraveling an unappreciated link between m6A and chromatin modifications. Our findings reveal that m6A is critical for planarian stem cell homeostasis and gene regulation in regeneration. ]]> Dagan, Y. Yesharim, Y. Bonneau, A. R. Schwartz, S. Reddien, P. W. Wurtzel, O. 2021-07-28 doi:10.1101/2021.07.27.453979 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution ]]> https://biorxiv.org/cgi/content/short/2021.10.12.464111v1?rss=1" Yang, D. Jones, M. G. Naranjo, S. Rideout, W. M. Min, K. H. J. Ho, R. Wu, W. Replogle, J. M. Page, J. L. Quinn, J. J. Horns, F. Qiu, X. Chen, M. Z. Freed-Pastor, W. A. McGinnis, C. S. Patterson, D. M. Gartner, Z. J. Chow, E. D. Bivona, T. G. Chan, M. M. Yosef, N. Jacks, T. Weissman, J. S. 2021-10-13 doi:10.1101/2021.10.12.464111 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq ]]> https://biorxiv.org/cgi/content/short/2021.12.16.473013v1?rss=1" 2.5 million human cells and present a framework to power biological discovery with the resulting genotype-phenotype map. We use transcriptional phenotypes to predict the function of poorly-characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena - from RNA processing to differentiation. We leverage this ability to systematically identify the genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene function and cellular behavior. ]]> Replogle, J. M. Saunders, R. A. Pogson, A. N. Hussmann, J. A. Lenail, A. Guna, A. Mascibroda, L. Wagner, E. J. Adelman, K. Bonnar, J. L. Jost, M. Norman, T. M. Weissman, J. S. 2021-12-17 doi:10.1101/2021.12.16.473013 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Coupled protein quality control during nonsense mediated mRNA decay ]]> https://biorxiv.org/cgi/content/short/2021.12.22.473893v1?rss=1" Inglis, A. J. Guna, A. Merchan, A. G. Pal, A. Esantsi, T. K. Keys, H. R. Frenkel, E. M. Oania, R. Weissman, J. S. Voorhees, R. M. 2021-12-23 doi:10.1101/2021.12.22.473893 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Mechanistic basis for the emergence of EPS1 as a catalyst in plant salicylic acid biosynthesis ]]> https://biorxiv.org/cgi/content/short/2021.08.21.457228v1?rss=1" Torrens-Spence, M. P. Li, T. Wang, Z. Glinkerman, C. M. Matos, J. O. Wang, Y. Weng, J.-K. 2021-08-22 doi:10.1101/2021.08.21.457228 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ Structural basis for independent origins of new catalytic machineries in plant AAAD proteins ]]> https://biorxiv.org/cgi/content/short/404970v1?rss=1" Torrens-Spence, M. P. Chiang, Y.-C. Smith, T. Vicent, M. A. Wang, Y. Weng, J.-K. 2018-08-31 doi:10.1101/404970 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence ]]> https://biorxiv.org/cgi/content/short/708065v1?rss=1" Goodheart, J. A. Minsky, G. Brynjegard-Bialik, M. N. Drummond, M. S. Munoz, J. D. Fallon, T. R. Schultz, D. T. Weng, J.-K. Torres, E. Oakley, T. H. 2019-07-21 doi:10.1101/708065 Cold Spring Harbor Laboratory Press 2019-07-21 <![CDATA[ PBS3 and EPS1 complete salicylic acid biosynthesis from isochorismate in Arabidopsis ]]> https://biorxiv.org/cgi/content/short/601948v1?rss=1" Torrens-Spence, M. P. Bobokalonova, A. Carballo, V. Glinkerman, C. M. Pluskal, T. Shen, A. Weng, J.-K. 2019-04-07 doi:10.1101/601948 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Ribosomal DNA and the rDNA-binding protein Indra mediate non-random sister chromatid segregation in Drosophila male germline stem cells ]]> https://biorxiv.org/cgi/content/short/498352v1?rss=1" Watase, G. Yamashita, Y. 2018-12-16 doi:10.1101/498352 Cold Spring Harbor Laboratory Press 2018-12-16 <![CDATA[ The retrotransposon R2 maintains Drosophila ribosomal DNA repeats ]]> https://biorxiv.org/cgi/content/short/2021.07.12.451825v1?rss=1" Nelson, J. O. Slicko, A. Yamashita, Y. M. 2021-07-12 doi:10.1101/2021.07.12.451825 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Defective satellite DNA clustering into chromocenters underlies hybrid incompatibility in Drosophila ]]> https://biorxiv.org/cgi/content/short/2021.04.16.440167v1?rss=1" Jagannathan, M. Yamashita, Y. M. 2021-04-16 doi:10.1101/2021.04.16.440167 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ me31B regulates stem cell homeostasis by preventing excess dedifferentiation in the Drosophila male germline. ]]> https://biorxiv.org/cgi/content/short/2021.04.07.438888v1?rss=1" Jensen, L. Venkei, Z. Watase, G. Bisai, B. Pletcher, S. Lee, C.-Y. Yamashita, Y. M. 2021-04-09 doi:10.1101/2021.04.07.438888 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Long Noncoding RNA RROL Provides Chromatin Scaffold for MYC-WDR82 Interaction to Impact Lipid Metabolism and Tumor Cell Growth in Multiple Myeloma ]]> https://biorxiv.org/cgi/content/short/2021.12.08.471297v1?rss=1" Morelli, E. Fulciniti, M. Samur, M. K. Ribeiro, C. F. Wert-Lamas, L. Henninger, J. E. Gulla, A. Aktas-Samur, A. Todoerti, K. Talluri, S. Park, W. D. Federico, C. Scionti, F. Amodio, N. Bianchi, G. Johnstone, M. Liu, N. Gramegna, D. Russo, N. A. Lin, C. Tai, Y.-T. Neri, A. Chauhan, D. Hideshima, T. Shammas, M. Tassone, P. Gryaznov, S. Young, R. Anderson, K. C. Novina, C. Loda, M. Munshi, N. C. 2021-12-09 doi:10.1101/2021.12.08.471297 Cold Spring Harbor Laboratory Press 2021-12-09