bioRxiv Channel: Babraham Institute https://biorxiv.org This feed contains articles for bioRxiv Channel "Babraham Institute " bioRxiv bioRxiv https://biorxiv.org <![CDATA[ A Comparison of Peak Callers Used for DNase-seq Data ]]> https://biorxiv.org/cgi/content/short/003608v1?rss=1" Hashem Koohy Thomas Down Mikhail Spivakov Tim Hubbard 2014-03-27 doi:10.1101/003608 Cold Spring Harbor Laboratory Press 2014-03-27 <![CDATA[ CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data ]]> https://biorxiv.org/cgi/content/short/028068v1?rss=1" Jonathan Cairns Paula Freire-Pritchett Steven W. Wingett Csilla Várnai Andrew Dimond Vincent Plagnol Daniel Zerbino Stefan Schoenfelder Biola-Maria Javierre Cameron Osborne Peter Fraser Mikhail Spivakov 2015-10-01 doi:10.1101/028068 Cold Spring Harbor Laboratory Press 2015-10-01 <![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[ SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks ]]> https://biorxiv.org/cgi/content/short/107250v1?rss=1" Dalle Pezze, P. Le Novere, N. 2017-02-09 doi:10.1101/107250 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ Multi-Tissue DNA Methylation Age Predictor In Mouse ]]> https://biorxiv.org/cgi/content/short/119206v1?rss=1" Stubbs, T. M. Bonder, M. J. Stark, A.-K. Krueger, F. BI Ageing Clock Team, von Meyenn, F. Stegle, O. Reik, W. 2017-03-22 doi:10.1101/119206 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ A non-catalytic role of TET3 promotes open chromatin and enhances global transcription ]]> https://biorxiv.org/cgi/content/short/177626v1?rss=1" Krueger, C. Peat, J. R. Eckersley-Maslin, M. A. Hore, T. A. Mohammed, H. Andrews, S. R. Dean, W. Reik, W. 2017-08-17 doi:10.1101/177626 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates ]]> https://biorxiv.org/cgi/content/short/196147v1?rss=1" Morf, J. Wingett, S. W. Farabella, I. Cairns, J. Furlan-Magaril, M. Liu, X. Craig, F. F. Andrews, S. Marti-Renom, M. A. Fraser, P. 2017-09-29 doi:10.1101/196147 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Tri-methylation of Histone H3 Lysine 4 Facilitates Gene Expression in Ageing Cells ]]> https://biorxiv.org/cgi/content/short/238048v1?rss=1" Cruz, C. Della Rosa, M. Krueger, C. Gao, Q. Field, L. Houseley, J. 2017-12-22 doi:10.1101/238048 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Joint Profiling Of Chromatin Accessibility, DNA Methylation And Transcription In Single Cells ]]> https://biorxiv.org/cgi/content/short/138685v1?rss=1" Clark, S. J. Argelaguet, R. Kapourani, C.-A. Stubbs, T. M. Lee, H. J. Krueger, F. Sanguinetti, G. Kelsey, G. Marioni, J. C. Stegle, O. Reik, W. 2017-05-17 doi:10.1101/138685 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data ]]> https://biorxiv.org/cgi/content/short/165449v1?rss=1" Olova, N. Krueger, F. Andrews, S. Oxley, D. O. Branco, M. R. Reik, W. 2017-07-18 doi:10.1101/165449 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Nucleosome remodelling at origins of Global Genome-Nucleotide Excision Repair occurs at the boundaries of higher-order chromatin structure ]]> https://biorxiv.org/cgi/content/short/283747v1?rss=1" van Eijk, P. Nandi, S. P. Yu, S. Bennett, M. Leadbitter, M. Teng, Y. Reed, S. 2018-03-16 doi:10.1101/283747 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ PI3Kδ hyper-activation promotes the development of B cells that exacerbate Streptococcus pneumoniae infection in an antibody-independent manner ]]> https://biorxiv.org/cgi/content/short/280651v1?rss=1" Stark, A.-K. Chandra, A. Chakraborty, K. Alam, R. Carbonaro, V. Clark, J. Sriskantharajah, S. Bradley, G. Richter, A. G. Banham-Hall, E. Clatworthy, M. R. Nejentsev, S. Hamblin, J. N. Hessel, E. M. Condliffe, A. M. Okkenhaug, K. 2018-03-18 doi:10.1101/280651 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Genome-scale oscillations in DNA methylation during exit from pluripotency ]]> https://biorxiv.org/cgi/content/short/338822v1?rss=1" Rulands, S. Lee, H. J. Clark, S. J. Angermueller, C. Smallwood, S. A. Krueger, F. Mohammed, H. Dean, W. Nichols, J. Rugg-Gunn, P. Kelsey, G. Stegle, O. Simons, B. D. Reik, W. 2018-06-05 doi:10.1101/338822 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional programme ]]> https://biorxiv.org/cgi/content/short/431890v1?rss=1" Eckersley-Maslin, M. A. Alda-Catalinas, C. Blotenburg, M. Kreibich, E. Krueger, C. Reik, W. 2018-10-01 doi:10.1101/431890 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in muscle stem cells ]]> https://biorxiv.org/cgi/content/short/500900v1?rss=1" Hernando-Herraez, I. Evano, B. Stubbs, T. Commere, P.-H. Clark, S. Andrews, S. Tajbakhsh, S. Reik, W. 2018-12-19 doi:10.1101/500900 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Microglia-dependent presynaptic disruption in an organotypic hippocampal slice culture model of neuroinflammation ]]> https://biorxiv.org/cgi/content/short/502559v1?rss=1" Sheppard, O. Coleman, M. P. Durrant, C. S. 2018-12-20 doi:10.1101/502559 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification ]]> https://biorxiv.org/cgi/content/short/519207v1?rss=1" Argelaguet, R. Mohammed, H. Clark, S. Stapel, C. Krueger, C. Kapourani, C. A. Xiang, Y. Hanna, C. Smallwood, S. Ibarra Soria, X. Buettner, F. Sanguinetti, G. Krueger, F. Xie, W. Rugg-Gunn, P. Kelsey, G. Dean, W. Nichols, J. Stegle, O. Marioni, J. C. Reik, W. 2019-01-13 doi:10.1101/519207 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data ]]> https://biorxiv.org/cgi/content/short/526269v1?rss=1" Cairns, J. Orchard, W. R. Malysheva, V. Spivakov, M. 2019-01-22 doi:10.1101/526269 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1 ]]> https://biorxiv.org/cgi/content/short/545830v1?rss=1" Martin-Herranz, D. E. Aref-Eshghi, E. Bonder, M. J. Stubbs, T. M. Stegle, O. Sadikovic, B. Reik, W. Thornton, J. M. 2019-02-10 doi:10.1101/545830 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Beta secretase 1-dependent amyloid precursor protein processing promotes excessive vascular sprouting through NOTCH3 signaling ]]> https://biorxiv.org/cgi/content/short/585489v1?rss=1" Durrant, C. S. Ruscher, K. Sheppard, O. Coleman, M. P. Özen, I. 2019-03-21 doi:10.1101/585489 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters ]]> https://biorxiv.org/cgi/content/short/620062v1?rss=1" Mitchelmore, J. Grinberg, N. Wallace, C. Spivakov, M. 2019-04-29 doi:10.1101/620062 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain ]]> https://biorxiv.org/cgi/content/short/639807v1?rss=1" Debrand, E. Chakalova, L. Miles, J. Dai, Y.-F. Goyenechea, B. Dye, S. Osborne, C. Harju-Baker, S. Pink, R. Caley, D. Carter, D. Peterson, K. R. Fraser, P. 2019-05-15 doi:10.1101/639807 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Follicular regulatory T cells can access the germinal centre independently of CXCR5 ]]> https://biorxiv.org/cgi/content/short/641589v1?rss=1" Vanderleyden, I. Fra-Bido, S. Innocentin, S. Okkenhaug, H. Evans-Bailey, N. Pierson, W. Linterman, M. 2019-05-17 doi:10.1101/641589 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation ]]> https://biorxiv.org/cgi/content/short/741371v1?rss=1" Alda-Catalinas, C. Bredikhin, D. Hernando-Herraez, I. Kubinyecz, O. Santos, F. Eckersley-Maslin, M. A. Stegle, O. Reik, W. 2019-08-21 doi:10.1101/741371 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Transcription-induced formation of extrachromosomal DNA during yeast ageing ]]> https://biorxiv.org/cgi/content/short/744896v1?rss=1" Hull, R. King, M. Pizza, G. Krueger, F. Vergara, X. Houseley, J. 2019-08-22 doi:10.1101/744896 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy ]]> https://biorxiv.org/cgi/content/short/370114v1?rss=1" Dalle Pezze, P. Karanasios, E. Kandia, V. Walker, S. Ktistakis, N. Le Novere, N. 2018-07-16 doi:10.1101/370114 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Dppa2/4 target chromatin bivalency enabling multi-lineage commitment ]]> https://biorxiv.org/cgi/content/short/832873v1?rss=1" Eckersley-Maslin, M. A. Parry, A. J. Blotenburg, M. Krueger, C. Franklin, V. N. R. Clark, S. D'Santos, C. S. Reik, W. 2019-11-06 doi:10.1101/832873 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Polypyrimidine Tract Binding Proteins are essential for B cell development ]]> https://biorxiv.org/cgi/content/short/769141v1?rss=1" Monzon-Casanova, E. Matheson, L. S. Tabbada, K. Zarnack, K. Smith, C. W. J. Turner, M. 2019-09-14 doi:10.1101/769141 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Network analysis of promoter interactions reveals the hierarchical differences in genome organisation between human pluripotent states ]]> https://biorxiv.org/cgi/content/short/2019.12.13.875286v1?rss=1" Chovanec, P. Collier, A. Krueger, C. Varnai, C. Schoenfelder, S. Corcoran, A. Rugg-Gunn, P. 2019-12-13 doi:10.1101/2019.12.13.875286 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ A neuronal thermostat controls membrane fluidity in C. elegans ]]> https://biorxiv.org/cgi/content/short/2019.12.20.882514v1?rss=1" Casanueva, O. Chauve, L. Murdoch, S. Masoudzadeh, F. Hodge, F. Lopez-Clavijo, A. Okkenhaug, H. Wingett, S. Wakelam, M. Kleigrewe, K. 2019-12-20 doi:10.1101/2019.12.20.882514 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Leptin resistance establishment in the ovary of diet-induced obese mice and its relationship with cumulus cells transcriptome ]]> https://biorxiv.org/cgi/content/short/729657v1?rss=1" Wolodko, K. Walewska, E. Castillo-Fernandez, J. Kelsey, G. D. Galvao, A. 2019-08-15 doi:10.1101/729657 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers ]]> https://biorxiv.org/cgi/content/short/2020.02.10.941989v1?rss=1" Thiecke, M. J. Wutz, G. Muhar, M. Tang, W. Bevan, S. Malysheva, V. Stocsits, R. R. Neumann, T. Zuber, J. Fraser, P. Schoenfelder, S. Peters, J.-M. Spivakov, M. 2020-02-11 doi:10.1101/2020.02.10.941989 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Causes of death in newborn C57BL/6J mice ]]> https://biorxiv.org/cgi/content/short/2020.02.25.964551v1?rss=1" Peneda, S. C. Morello, G. M. Lamas, S. Olsson, A. Gilbert, C. 2020-02-26 doi:10.1101/2020.02.25.964551 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ High laboratory mouse pre-weaning mortality associated with litter overlap, advanced mother age, small and large litters ]]> https://biorxiv.org/cgi/content/short/2020.02.25.953067v1?rss=1" Morello, G. M. Hultgren, J. Peneda, S. C. Whiltshire, M. Thomas, A. Wardle-Jones, H. Brajon, S. Gilbert, C. Olsson, A. 2020-02-26 doi:10.1101/2020.02.25.953067 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions ]]> https://biorxiv.org/cgi/content/short/2020.03.21.000042v1?rss=1" Klobucar, T. Kreibich, E. Krueger, F. Arez, M. Polvora-Brandao, D. von Meyenn, F. da Rocha, S. T. Eckersley-Maslin, M. A. 2020-03-23 doi:10.1101/2020.03.21.000042 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Specialisation and plasticity in a primitively social insect ]]> https://biorxiv.org/cgi/content/short/2020.03.31.007492v1?rss=1" Patalano, S. Alsina, A. Gregorio-Rodriguez, C. Bachman, M. Dreier, S. Hernando-Herraez, I. Nana, P. Balasubramanian, S. Sumner, S. Reik, W. Rulands, S. 2020-03-31 doi:10.1101/2020.03.31.007492 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Intrinsic defects in lymph node stromal cells underpin poor germinal center responses during aging ]]> https://biorxiv.org/cgi/content/short/2020.05.07.082255v1?rss=1" Denton, A. E. Silva-Cayetano, A. Dooley, J. Hill, D. L. Carr, E. J. Robert, P. Meyer-Hermann, M. Liston, A. Linterman, M. A. 2020-05-07 doi:10.1101/2020.05.07.082255 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine ]]> https://biorxiv.org/cgi/content/short/2020.05.14.096115v1?rss=1" Durgan, J. Lystad, A. H. Sloan, K. Carlsson, S. R. Wilson, M. I. Marcassa, E. Ulferts, R. Webster, J. Lopez-Clavijo, A. F. Wakelam, M. J. Beale, R. Simonsen, A. Oxley, D. Florey, O. 2020-05-15 doi:10.1101/2020.05.14.096115 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation ]]> https://biorxiv.org/cgi/content/short/2020.05.20.107219v1?rss=1" Evano, B. Gill, D. Hernando-Herraez, I. Comai, G. Stubbs, T. Commere, P.-H. Reik, W. Tajbakhsh, S. 2020-05-22 doi:10.1101/2020.05.20.107219 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells ]]> https://biorxiv.org/cgi/content/short/2020.06.08.139642v1?rss=1" Novo, C. L. Wong, E. Hockings, C. Poudel, C. Sheekey, E. Walker, S. Kaminski Schierle, G. S. Narlikar, G. Rugg-Gunn, P. 2020-06-08 doi:10.1101/2020.06.08.139642 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Protein citrullination was introduced into animals by horizontal gene transfer from cyanobacteria ]]> https://biorxiv.org/cgi/content/short/2020.06.13.150037v1?rss=1" Cummings, T. F. Gori, K. Sanchez-Pulido, L. Gavriilidis, G. Moi, D. Wilson, A. R. Murchison, E. P. Dessimoz, C. Ponting, C. Christophorou, M. A. 2020-06-15 doi:10.1101/2020.06.13.150037 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle ]]> https://biorxiv.org/cgi/content/short/2020.07.23.217992v1?rss=1" Furlan-Magaril, M. Ando-Kuri, M. Arzate-Mejia, R. G. Morf, J. Cairns, J. Poot- Hernandez, C. A. Andrews, S. Varnai, C. Virk, B. Wingett, S. W. Fraser, P. 2020-07-24 doi:10.1101/2020.07.23.217992 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ AutoSpill: a method for calculating spillover coefficients in high-parameter flow cytometry ]]> https://biorxiv.org/cgi/content/short/2020.06.29.177196v1?rss=1" Roca, C. P. Burton, O. T. Prezzemolo, T. Whyte, C. E. Halpert, R. Kreft, Łukasz Collier, J. Botzki, A. Spidlen, J. Humblet-Baron, S. Liston, A. 2020-06-29 doi:10.1101/2020.06.29.177196 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Genome-wide analysis of DNA replication and DNA double strand breaks by TrAEL-seq ]]> https://biorxiv.org/cgi/content/short/2020.08.10.243931v1?rss=1" Kara, N. Krueger, F. Rugg-Gunn, P. Houseley, J. 2020-08-10 doi:10.1101/2020.08.10.243931 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications ]]> https://biorxiv.org/cgi/content/short/2020.08.16.250878v1?rss=1" Alvarez-Jarreta, J. Rodrigues, P. Fahy, E. O'Connor, A. Price, A. Gaud, C. Andrews, S. Benton, P. Siuzdak, G. Hawksworth, J. Valdivia, M. Allen, S. O'Donnell, V. 2020-08-17 doi:10.1101/2020.08.16.250878 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ IL-7R signalling activates widespread VH and DH gene usage to drive antibody diversity in bone marrow B cells ]]> https://biorxiv.org/cgi/content/short/2020.09.24.298000v1?rss=1" Baizan Edge, A. Stubbs, B. A. Stubbington, M. J. T. Bolland, D. J. Tabbada, K. Andrews, S. Corcoran, A. E. 2020-09-25 doi:10.1101/2020.09.24.298000 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry ]]> https://biorxiv.org/cgi/content/short/2020.10.05.326082v1?rss=1" Channathodiyil, P. Houseley, J. 2020-10-05 doi:10.1101/2020.10.05.326082 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ A booster dose enhances immunogenicity of the COVID-19 vaccine candidate ChAdOx1 nCoV-19 in aged mice ]]> https://biorxiv.org/cgi/content/short/2020.10.27.357426v1?rss=1" Silva-Cayetano, A. Foster, W. S. Innocentin, S. Belij-Rammerstorfer, S. Spencer, A. J. Burton, O. T. Fra-Bido, S. Lee, J. L. Thakur, N. Conceicao, C. Wright, D. Barrett, J. Evans-Bailey, N. Noble, C. Bailey, D. Liston, A. Gilbert, S. C. Lambe, T. Linterman, M. A. 2020-10-27 doi:10.1101/2020.10.27.357426 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis ]]> https://biorxiv.org/cgi/content/short/2020.11.20.391896v1?rss=1" Lohoff, T. Ghazanfar, S. Missarova, A. Koulena, N. Pierson, N. Griffiths, J. A. Bardot, E. S. Eng, C.-H. L. Tyser, R. C. V. Argelaguet, R. Guibentif, C. Srinivas, S. Briscoe, J. Simons, B. D. Hadjantonakis, A.-K. Gottgens, B. Reik, W. Nichols, J. Cai, L. Marioni, J. C. 2020-11-21 doi:10.1101/2020.11.20.391896 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ BAP1/ASXL complex modulation regulates Epithelial-Mesenchymal Transition during trophoblast differentiation and invasion ]]> https://biorxiv.org/cgi/content/short/2020.12.01.405902v1?rss=1" Perez-Garcia, V. Lopez-Jimenez, P. Burton, G. J. Moffett, A. Turco, M. Y. Hemberger, M. 2020-12-02 doi:10.1101/2020.12.01.405902 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Context-dependent effects of IL-2 rewire immunity into distinct cellular circuits ]]> https://biorxiv.org/cgi/content/short/2020.12.18.423431v1?rss=1" Whyte, C. E. Singh, K. Burton, O. T. Aloulou, M. Moudra, A. Roca, C. P. Naranjo, F. J. Lombard-Vadnais, F. Kouser, L. Hochepied, T. Halim, T. Y. F. Schlenner, S. Lesage, S. Dooley, J. Liston, A. 2020-12-20 doi:10.1101/2020.12.18.423431 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Multi-omic rejuvenation of human cells by maturation phase transient reprogramming ]]> https://biorxiv.org/cgi/content/short/2021.01.15.426786v1?rss=1" Gill, D. Parry, A. Santos, F. Hernando-Herraez, I. Stubbs, T. M. Milagre, I. Reik, W. 2021-01-17 doi:10.1101/2021.01.15.426786 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ ORFLine: a bioinformatic pipeline to prioritise small open reading frames identifies candidate secreted small proteins from lymphocytes ]]> https://biorxiv.org/cgi/content/short/2021.01.21.426789v1?rss=1" Hu, F. Lu, J. Munoz, M. D. Saveliev, A. Turner, M. 2021-01-21 doi:10.1101/2021.01.21.426789 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Stimulation of adaptive gene amplification by origin firing under replication fork constraint ]]> https://biorxiv.org/cgi/content/short/2021.03.04.433911v1?rss=1" Whale, A. J. King, M. Hull, R. M. Krueger, F. Houseley, J. 2021-03-04 doi:10.1101/2021.03.04.433911 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte ]]> https://biorxiv.org/cgi/content/short/2021.03.11.434836v1?rss=1" Hanna, C. W. Huang, J. Belton, C. Reinhardt, S. Dahl, A. Andrews, S. Stewart, A. F. Kranz, A. Kelsey, G. 2021-03-11 doi:10.1101/2021.03.11.434836 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ DNA replication during acute MEK inhibition drives acquisition of resistance through amplification of the BRAF oncogene ]]> https://biorxiv.org/cgi/content/short/2021.03.23.436572v1?rss=1" Channathodiyil, P. Segonds-Pichon, A. Smith, P. D. Cook, S. J. Houseley, J. 2021-03-23 doi:10.1101/2021.03.23.436572 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Peptidylarginine deiminase IV (PADI4) is not essential for cell-autonomous HSC maintenance and normal haematopoiesis ]]> https://biorxiv.org/cgi/content/short/2021.04.13.439513v1?rss=1" Young, C. Russell, J. P. Lawson, H. Mapperley, C. Kranc, K. R. Christophorou, M. A. 2021-04-14 doi:10.1101/2021.04.13.439513 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ V-ATPase is a universal regulator of LC3 associated phagocytosis and non-canonical autophagy ]]> https://biorxiv.org/cgi/content/short/2021.05.20.444917v1?rss=1" Hooper, K. M. Jacquin, E. Li, T. Goodwin, J. M. Brumell, J. H. Durgan, J. Florey, O. 2021-05-20 doi:10.1101/2021.05.20.444917 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ The timing of differentiation and potency of CD8 effector function is set by RNA binding proteins ]]> https://biorxiv.org/cgi/content/short/2021.06.03.446738v1?rss=1" Petkau, G. Mitchell, T. J. Chakraborty, K. Bell, S. E. DAngeli, V. Matheson, L. Turner, D. J. Salerno, F. Katsikis, P. D. Turner, M. 2021-06-03 doi:10.1101/2021.06.03.446738 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells ]]> https://biorxiv.org/cgi/content/short/2021.07.10.451887v1?rss=1" Osnato, A. Brown, S. Krueger, C. Andrews, S. Collier, A. J. Nakanoh, S. Quiroga Londono, M. Wesley, B. T. Muraro, D. Brumm, S. Niakan, K. Vallier, L. Ortmann, D. Rugg-Gunn, P. J. 2021-07-11 doi:10.1101/2021.07.10.451887 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ The RNA m6A binding protein YTHDF2 promotes the B cell to plasma cell transition. ]]> https://biorxiv.org/cgi/content/short/2021.07.21.453193v1?rss=1" Turner, D. Saveliev, A. Salerno, F. Matheson, L. S. Screen, M. Lawson, H. Wotherspoon, D. Kranc, K. Turner, M. 2021-07-21 doi:10.1101/2021.07.21.453193 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Replicative aging is associated with loss of genetic heterogeneity from extrachromosomal circular DNA in Saccharomyces cerevisiae ]]> https://biorxiv.org/cgi/content/short/2020.02.11.943357v1?rss=1" 95% of all circular DNA. We discovered circles had flexible inherence patterns. Glucose limited conditions selected for cells with glucose-transporter gene circles, [HXT6/7circle], and up to 50% of cells in a population carried them. [HXT6/7circle] cells were eventually substituted by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting circular DNA were intermediates in chromosomal amplifications. In conclusion, DNA circles can offer a flexible adaptive solution but cells lose genetic heterogeneity from circular DNA as they undergo replicative aging. ]]> Prada-Luengo, I. Moller, H. D. Henriksen, R. A. Gao, Q. Larsen, C. E. Alizadeh, S. Maretty, L. Houseley, J. Regenberg, B. 2020-02-12 doi:10.1101/2020.02.11.943357 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Leptin Signalling in the Ovary of Diet-Induced Obese Mice Regulates Activation of Nod-Like Receptor Protein 3 Inflammasome ]]> https://biorxiv.org/cgi/content/short/2021.08.16.456479v1?rss=1" Adamowski, M. Wolodko, K. Oliveira, J. Castillo-Fernandez, J. Murta, D. Kelsey, G. D. Galvao, A. 2021-08-17 doi:10.1101/2021.08.16.456479 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ An improved iCLIP protocol ]]> https://biorxiv.org/cgi/content/short/2021.08.27.457890v1?rss=1" Lee, F. C. Y. Chakrabarti, A. M. Hänel, H. Monzon-Casanova, E. Hallegger, M. Militti, C. Capraro, F. Sadee, C. Toolan-Kerr, P. Wilkins, O. Turner, M. König, J. Sibley, C. Ule, J. 2021-08-27 doi:10.1101/2021.08.27.457890 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Zfp36l1 and Zfp36l2 balances proliferation and differentiation in the developing retina ]]> https://biorxiv.org/cgi/content/short/2020.12.15.422926v1?rss=1" Mu, X. Wu, F. Kaczynski, T. Matheson, L. Liu, T. Wang, J. Turner, M. 2020-12-15 doi:10.1101/2020.12.15.422926 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Human immunodeficiency reveals GIMAP5 as lymphocyte-specific regulator of senescence ]]> https://biorxiv.org/cgi/content/short/2021.02.22.432146v1?rss=1" Park, A. Y. Leney-Greene, M. Lynberg, M. Xu, X. Zheng, L. Zhang, Y. Matthews, H. Chao, B. Morawski, A. Jiang, P. Aluri, J. Aydine, E. K. Kiykim, A. Pascall, J. Barlan, I. Sari, S. Butcher, G. Rao, V. K. Lifton, R. P. Baris, S. Ozen, A. Vilarinho, S. Su, H. Lenardo, M. J. 2021-02-23 doi:10.1101/2021.02.22.432146 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Solvent Precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads ]]> https://biorxiv.org/cgi/content/short/2021.09.24.461247v1?rss=1" View larger version (49K): org.highwire.dtl.DTLVardef@1ba615corg.highwire.dtl.DTLVardef@14df25dorg.highwire.dtl.DTLVardef@62f0c1org.highwire.dtl.DTLVardef@1ac436a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Johnston, H. E. Yadav, K. Kirkpatrick, J. M. Biggs, G. S. Oxley, D. Kramer, H. B. Samant, R. S. 2021-09-24 doi:10.1101/2021.09.24.461247 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ The distinct effects of MEK and GSK3 inhibition upon the methylome and transcriptome of mouse embryonic stem cells ]]> https://biorxiv.org/cgi/content/short/2021.11.18.469000v1?rss=1" Spindel, J. Krueger, C. Krueger, F. Papachristou, E. K. Kishore, K. D'Santos, C. S. Reik, W. 2021-11-18 doi:10.1101/2021.11.18.469000 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Nucleosomal Asymmetry Shapes Histone Mark Binding and Promotes Poising at Bivalent Domains ]]> https://biorxiv.org/cgi/content/short/2021.02.08.430127v1?rss=1" Bryan, E. Warburton, M. Webb, K. M. McLaughlin, K. A. Spanos, C. Ambrosi, C. Major, V. Baubec, T. Rappsilber, J. Voigt, P. 2021-02-08 doi:10.1101/2021.02.08.430127 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ The TAZ2 domain of CBP/p300 directs acetylation towards H3K27 within chromatin ]]> https://biorxiv.org/cgi/content/short/2020.07.21.214338v1?rss=1" Sheahan, T. W. Major, V. Webb, K. M. Bryan, E. Voigt, P. 2020-07-21 doi:10.1101/2020.07.21.214338 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Molecular mechanism of Afadin substrate recruitment to the receptor phosphatase PTPRK via its pseudophosphatase domain ]]> https://biorxiv.org/cgi/content/short/2022.04.27.489754v1?rss=1" Hay, I. M. Mulholland, K. E. Graham, S. C. Sharpe, H. Deane, J. E. 2022-04-27 doi:10.1101/2022.04.27.489754 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ Senescence in yeast is associated with chromosome XII cleavage rather than ribosomal DNA circle accumulation ]]> https://biorxiv.org/cgi/content/short/2022.07.14.500009v1?rss=1" Zylstra, A. Horkai, D. Hadj-Moussa, H. Piguet, B. Houseley, J. 2022-07-14 doi:10.1101/2022.07.14.500009 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Dietary change without caloric restriction maintains a youthful profile in ageing yeast ]]> https://biorxiv.org/cgi/content/short/2022.07.19.500645v1?rss=1" Horkai, D. Houseley, J. 2022-07-20 doi:10.1101/2022.07.19.500645 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Back to the Future: Unleashing your cytometers spectral potential ]]> https://biorxiv.org/cgi/content/short/2022.12.21.521417v1?rss=1" Walker, R. V. Hall, C. Ibrahim, H. Thompson, S. Hobson, P. Crofts, J.-A. Nobes, P. Lim, S. Burpee, T. 2022-12-22 doi:10.1101/2022.12.21.521417 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ An integrated proteome and transcriptome of B cell maturation defines poised activation states of transitional and mature B cells ]]> https://biorxiv.org/cgi/content/short/2022.12.22.521580v1?rss=1" Salerno, F. Howden, A. J. Matheson, L. S. Gizlenci, O. Screen, M. Lingel, H. Brunner-Weinzierl, M. Turner, M. 2022-12-22 doi:10.1101/2022.12.22.521580 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Lysosome damage triggers direct ATG8 conjugation and ATG2 engagement via CASM ]]> https://biorxiv.org/cgi/content/short/2023.03.22.533754v1?rss=1" Cross, J. Durgan, J. McEwan, D. G. Florey, O. 2023-03-22 doi:10.1101/2023.03.22.533754 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Zfp36l1 establishes the high affinity CD8 T cell response by directly linking TCR affinity to cytokine sensing ]]> https://biorxiv.org/cgi/content/short/2023.05.11.539978v1?rss=1" Petkau, G. Mitchell, T. Jones Evans, M. Matheson, L. S. Salerno, F. Turner, M. 2023-05-13 doi:10.1101/2023.05.11.539978 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ B cells from aged mice do not have intrinsic defects in affinity maturation ]]> https://biorxiv.org/cgi/content/short/2023.04.24.538044v1?rss=1" Lee, J. L. Innocentin, S. Silva-Cayetano, A. Guillaume, S. Linterman, M. A. 2023-04-25 doi:10.1101/2023.04.24.538044 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate ]]> https://biorxiv.org/cgi/content/short/2023.05.18.541123v1?rss=1" Chessa, T. A. M. Jung, P. Suire, S. Anwar, A. Anderson, K. E. Barneda, D. Kielkowska, A. Sadiq, B. A. Oxley, D. Felisbino, S. Spensberger, D. Segonds-Pichon, A. Wilson, M. Walker, S. Okkenhaug, H. Cosulich, S. Hawkins, P. T. Stephens, L. R. 2023-05-18 doi:10.1101/2023.05.18.541123 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Ubiquitination is a novel post-translational modification of VMP1 in autophagy of human tumor cells ]]> https://biorxiv.org/cgi/content/short/2023.02.13.528037v1?rss=1" View larger version (21K): org.highwire.dtl.DTLVardef@1a1538dorg.highwire.dtl.DTLVardef@74580corg.highwire.dtl.DTLVardef@409ef0org.highwire.dtl.DTLVardef@82b856_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Renna, F. J. Steinberg, J. H. E. Manifava, M. Gonzalez, C. D. Tadic, M. S. Orquera, T. Vecino, C. V. Ropolo, A. Rossi, M. Ktistakis, N. T. Vaccaro, M. I. 2023-02-13 doi:10.1101/2023.02.13.528037 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ MICA: A multi-omics method to predict gene regulatory networks in early human embryos ]]> https://biorxiv.org/cgi/content/short/2023.02.03.527081v1?rss=1" Alanis-Lobato, G. Bartlett, T. E. Huang, Q. Simon, C. McCarthy, A. Elder, K. Snell, P. Christie, L. Niakan, K. 2023-02-03 doi:10.1101/2023.02.03.527081 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Single cell DNA methylation ageing in mouse blood ]]> https://biorxiv.org/cgi/content/short/2023.01.30.526343v1?rss=1" Bonder, M. J. Clark, S. Krueger, F. Luo, S. Agostinho de Sousa, J. Hashtroud, A. M. Stubbs, T. M. Stark, A.-K. Rulands, S. Stegle, O. Reik, W. von Meyenn, F. 2023-02-01 doi:10.1101/2023.01.30.526343 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ The LCLAT1/LYCAT acyltransferase supports EGF-mediated phosphatidylinositol-3,4,5-trisphosphate and Akt signalling ]]> https://biorxiv.org/cgi/content/short/2023.01.26.524308v1?rss=1" Chan, V. Bone, L. Anderson, K. E. Zhang, K. Orofiamma, L. Awadeh, Y. Lee, D. K. C. Fu, N. J. Chow, J. T. S. Salmena, L. Stephens, L. R. Hawkins, P. T. Antonescu, C. N. Botelho, R. J. 2023-01-27 doi:10.1101/2023.01.26.524308 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification ]]> https://biorxiv.org/cgi/content/short/2023.01.11.523441v1?rss=1" Parry, A. J. Krueger, C. Lohoff, T. Wingett, S. Schoenfelder, S. Reik, W. 2023-01-11 doi:10.1101/2023.01.11.523441 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Dynamic protein deacetylation is a limited carbon source for acetyl-CoA-dependent metabolism ]]> https://biorxiv.org/cgi/content/short/2022.12.28.522149v1?rss=1" Soaita, I. Megill, E. Kantner, D. Chatoff, A. Arany, Z. Snyder, N. W. Wellen, K. E. Trefely, S. W. 2022-12-29 doi:10.1101/2022.12.28.522149 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Time-dependent regulation of cytokine production by RNA binding proteins defines T cell effector function ]]> https://biorxiv.org/cgi/content/short/2021.11.03.467112v1?rss=1" 130 RBPs interacting with the IFNG, TNF and IL2 3UTRs in human T cells. T cell activation altered RBP-RNA interactions, revealing that RBP-target mRNA interactions rapidly respond to stimulation. Furthermore, we uncovered the intricate and time-dependent regulation of cytokine production by RBPs: whereas HuR supports early cytokine production, ZFP36L1, ATXN2L and ZC3HAV1 dampen and shorten the production duration, each at different time points. Strikingly, even though ZFP36L1 deletion did not phenotypically rescue T cell dysfunction in tumors, the increased production of cytokines and cytotoxic molecules resulted in superior anti-tumoral T cell responses in vivo. Our findings thus show that identifying RBP-RNA interactions reveals key modulators of T cell responses in health and disease. ]]> Popovic, B. Guislain, A. Engels, S. Nicolet, B. Jurgens, A. P. Paravinja, N. Freen-van Heeren, J. J. van Alphen, F. P. van den Biggelaar, M. Salerno, F. Wolkers, M. 2021-11-03 doi:10.1101/2021.11.03.467112 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Decoding gene regulation in the mouse embryo using single-cell multi-omics ]]> https://biorxiv.org/cgi/content/short/2022.06.15.496239v1?rss=1" Argelaguet, R. Lohoff, T. Li, J. G. Nakhuda, A. Drage, D. Krueger, F. Velten, L. Clark, S. J. Reik, W. 2022-06-15 doi:10.1101/2022.06.15.496239 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ High-resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn's Disease aetiology ]]> https://biorxiv.org/cgi/content/short/2022.10.19.512842v1?rss=1" Malysheva, V. Ray-Jones, H. Cazares, T. A. Clay, O. Ohayon, D. Artemov, P. Wayman, J. A. Della Rosa, M. Petitjean, C. Ellaway, J. I. J. Orchard, W. Chen, X. Parameswaran, S. Nagano, T. Fraser, P. Schoenfelder, S. Weirauch, M. Kottyan, L. C. Smith, D. F. Powell, N. Weimer, J. Wallace, C. Miraldi, E. R. Waggoner, S. Spivakov, M. 2022-10-21 doi:10.1101/2022.10.19.512842 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ FOXA2 controls the antioxidant response in FH-deficient cells independent of NRF2 ]]> https://biorxiv.org/cgi/content/short/2022.07.04.498412v1?rss=1" Rogerson, C. Sciacovelli, M. Maddalena, L. A. Valcarcel-Jimenez, L. Schmidt, C. Yang, M. Ivanova, E. Kent, J. Cheeseman, D. Carroll, J. S. Kelsey, G. Frezza, C. 2022-07-04 doi:10.1101/2022.07.04.498412 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies ]]> https://biorxiv.org/cgi/content/short/2022.09.27.509783v1?rss=1" Rosen, L. U. Stapel, L. C. Argelaguet, R. Barker, C. G. Yang, A. Reik, W. Marioni, J. C. 2022-09-28 doi:10.1101/2022.09.27.509783 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ GLP is critical for oogenesis exhibiting a G9A-independent role in transcriptional repression ]]> https://biorxiv.org/cgi/content/short/2021.12.20.473460v1?rss=1" Demond, H. Hanna, C. W. Castillo-Fernandez, J. Santos, F. Papachristou, E. K. Segonds-Pichon, A. Kishore, K. D'Santos, C. S. Kelsey, G. 2021-12-21 doi:10.1101/2021.12.20.473460 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Structural determinants of homophilic adhesion by receptor tyrosine phosphatases ]]> https://biorxiv.org/cgi/content/short/2022.06.23.497309v1?rss=1" Hay, I. M. Shamin, M. Caroe, E. R. Mohammed, A. S. A. Svergun, D. I. Jeffries, C. M. Graham, S. C. Sharpe, H. J. Deane, J. E. 2022-06-23 doi:10.1101/2022.06.23.497309 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naive pluripotent stem cells ]]> https://biorxiv.org/cgi/content/short/2022.08.18.504441v1?rss=1" Maskalenka, K. Alagoz, G. Krueger, F. Wright, J. Rostovskaya, M. Nakhuda, A. Bendall, A. Krueger, C. Walker, S. Scally, A. Rugg-Gunn, P. 2022-08-19 doi:10.1101/2022.08.18.504441 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Native size exclusion chromatography-based mass spectrometry (SEC-MS) identifies novel components of the Heat Shock Protein 90-dependent proteome ]]> https://biorxiv.org/cgi/content/short/2022.05.23.492985v1?rss=1" Samant, R. S. Batista, S. Larance, M. Ozer, B. Milton, C. I. Bludau, I. Biggins, L. Andrews, S. Hervieu, A. Johnston, H. E. Al-Lazikhani, B. Lamond, A. I. Clarke, P. A. Workman, P. 2022-05-23 doi:10.1101/2022.05.23.492985 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters. ]]> https://biorxiv.org/cgi/content/short/2022.04.26.489502v1?rss=1" Richer, S. Yuan, T. Schoenfelder, S. Hurst, L. Murrell, A. Pisignano, G. 2022-04-27 doi:10.1101/2022.04.26.489502 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells ]]> https://biorxiv.org/cgi/content/short/2022.04.07.487453v1?rss=1" Zorzan, I. Betto, R. M. Rossignoli, G. Arboit, M. Drusin, A. Martini, P. Martello, G. 2022-04-08 doi:10.1101/2022.04.07.487453 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ The AppNL-G-F mouse model of Alzheimer's disease is refractory to regulatory T cell treatment ]]> https://biorxiv.org/cgi/content/short/2022.03.11.483903v1?rss=1" Yshii, L. Mascali, L. Kouser, L. Lemaitre, P. Marino, M. Dooley, J. Burton, O. Haughton, J. Callaerts-Vegh, Z. de Strooper, B. Holt, M. Pasciuto, E. Liston, A. 2022-03-14 doi:10.1101/2022.03.11.483903 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Polypyrimidine Tract Binding Protein 1 regulates the activation of mouse CD8 T cells ]]> https://biorxiv.org/cgi/content/short/2022.03.03.482829v1?rss=1" D'Angeli, V. Monzon-Casanova, E. Matheson, L. S. Gizlenci, O. Petkau, G. Gooding, C. Berrens, R. V. Smith, C. W. J. Turner, M. 2022-03-04 doi:10.1101/2022.03.03.482829 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain ]]> https://biorxiv.org/cgi/content/short/2022.03.01.482519v1?rss=1" Lemaitre, P. Tareen, S. Pasciuto, E. Mascali, L. Martirosyan, A. Callaerts-Vegh, Z. Dooley, J. Holt, M. Yshii, L. Liston, A. 2022-03-04 doi:10.1101/2022.03.01.482519 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Astrocyte-targeted gene delivery of interleukin 2 specifically increases brain-resident regulatory T cell numbers and protects against pathological neuroinflammation ]]> https://biorxiv.org/cgi/content/short/2022.02.28.482297v1?rss=1" Yshii, L. Pasciuto, E. Bielefeld, P. Mascali, L. Lemaitre, P. Marino, M. Dooley, J. Kouser, L. Verschoren, S. Lagou, V. Kemps, H. Gervois, P. de Boer, A. Burton, O. Wahis, J. Tareen, S. Roca, C. Singh, K. Whyte, C. Kerstens, A. Callaerts-Vegh, Z. Poovathingal, S. Prezzemolo, T. Wierda, K. Dashwood, A. Xie, J. Van Wonterghem, E. Creemers, E. Aloulou, M. Gsell, W. Abiega, O. Munck, S. Vandenbroucke, R. Lemmens, R. De Strooper, B. Van Den Bosch, L. Himmelreich, U. Fitzsimons, C. P. Holt, M. Liston, A. 2022-03-02 doi:10.1101/2022.02.28.482297 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming ]]> https://biorxiv.org/cgi/content/short/2022.01.20.477063v1?rss=1" Chondronasiou, D. Gill, D. Mosteiro, L. Urdinguio, R. G. Berenguer, A. Aguilera, M. Durand, S. Aprahamian, F. Nirmalathasan, N. Abad, M. Martin-Herranz, D. E. Stephan-Otto Attolini, C. Prats, N. Kroemer, G. Fraga, M. F. Reik, W. Serrano, M. 2022-01-21 doi:10.1101/2022.01.20.477063 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Plasma cell maintenance and antibody secretion are under the control of Sec22b-mediated regulation of organelle dynamics ]]> https://biorxiv.org/cgi/content/short/2022.01.14.476154v1?rss=1" Bonaud, A. Gargowitsch, L. Gilbert, S. Rajan, E. Canales-Herrerias, P. Stockholm, D. Rahman, N. Collins, M. Hill, D. L. Alloatti, A. Alouche, N. Balor, S. Soldan, V. Gillet, D. Barbier, J. Bachelerie, F. Smith, K. G. C. Bruhns, P. Amigorena, S. Balabanian, K. Linterman, M. A. Peden, A. Espeli, M. 2022-01-15 doi:10.1101/2022.01.14.476154 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function ]]> https://biorxiv.org/cgi/content/short/2021.12.29.474486v1?rss=1" Ravichandran, M. Rafalski, D. Ortega-Recalde, O. Davies, C. I. Glanfield, C. R. Kotter, A. Misztal, K. Wang, A. H. Wojciechowski, M. Razew, M. Mayyas, I. M. Kardailsky, O. Schwarz, U. Zembrzycki, K. Morison, I. M. Helm, M. Weichenhan, D. Jurkowska, R. Z. Krueger, F. Plass, C. Zacharias, M. Hore, T. A. Bochtler, M. Jurkowski, T. P. 2021-12-30 doi:10.1101/2021.12.29.474486 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses ]]> https://biorxiv.org/cgi/content/short/2021.12.20.473453v1?rss=1" Rodriguez-Ubreva, J. Arutyunyan, A. Bonder, M. J. Del Pino-Molina, L. Clark, S. de la Calle-Fabregat, C. Garcia-Alonso, L. Handfield, L.-F. Ciudad, L. Andres-Leon, E. Krueger, F. Catala-Moll, F. Rodriguez-Cortez, V. C. Polanski, K. Mamanova, L. van Dongen, S. Kiselev, V. Y. Martinez-Saavedra, M. T. Heyn, H. Martin, J. Warnatz, K. Lopez-Granados, E. Rodriguez-Gallego, C. Stegle, O. Kelsey, G. D. Vento-Tormo, R. Ballestar, E. 2021-12-21 doi:10.1101/2021.12.20.473453 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Genome wide efficiency profiling reveals modulation of maintenance and de novo methylation by Tets ]]> https://biorxiv.org/cgi/content/short/2020.08.06.236307v1?rss=1" Giehr, P. Kyriakopoulos, C. Karl Nordström, K. Salhab, A. Müller, F. von Meyenn, F. Ficz, G. Reik, W. Wolf, V. Walter, J. 2020-08-07 doi:10.1101/2020.08.06.236307 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Modelling human zygotic genome activation in 8C-like cells in vitro ]]> https://biorxiv.org/cgi/content/short/2021.10.28.466259v1?rss=1" Taubenschmid-Stowers, J. Rostovskaya, M. Santos, F. Ljung, S. Argelaguet, R. Krueger, F. Nichols, J. Reik, W. 2021-10-29 doi:10.1101/2021.10.28.466259 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival ]]> https://biorxiv.org/cgi/content/short/2021.09.13.460183v1?rss=1" Kubinyecz, O. Santos, F. Drage, D. Reik, W. Eckersley-Maslin, M. A. 2021-09-14 doi:10.1101/2021.09.13.460183 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Single-cell bisulfite sequencing of spermatozoa from lean and obese humans reveals potential for the transmission of epimutations ]]> https://biorxiv.org/cgi/content/short/2021.07.09.451752v1?rss=1" Barres, R. Andersen, E. Reik, W. Clark, S. Ingerslev, L. Lundell, L. 2021-07-10 doi:10.1101/2021.07.09.451752 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ GABARAP membrane conjugation sequesters the FLCN-FNIP tumor suppressor complex to activate TFEB and lysosomal biogenesis ]]> https://biorxiv.org/cgi/content/short/2021.02.22.432209v1?rss=1" Goodwin, J. Walkup, W. G. Hooper, K. Li, T. Kishi-Itakura, C. Ng, A. Lehmberg, T. Jha, A. Kommineni, S. Fletcher, K. Garcia-Fortanet, J. Fan, Y. Tang, Q. Wei, M. Agrawal, A. Budhe, S. R. Rouduri, S. R. Baird, D. Saunders, J. Kiselar, J. Chance, M. R. Ballabio, A. Appleton, B. A. Brumell, J. H. Florey, O. Murphy, L. O. 2021-02-22 doi:10.1101/2021.02.22.432209 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Three-dimensional interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis ]]> https://biorxiv.org/cgi/content/short/2021.02.03.429496v1?rss=1" 500 kbp), appear to drive host gene dysregulation through the disruption of local host:host 3D interactions known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a cancer-causing gene is not essential to influence such genes within an entire TAD and that these modifications to 3D interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression. ]]> Groves, I. J. Drane, E. L. Michalski, M. Monahan, J. M. Scarpini, C. G. Smith, S. P. Bussotti, G. Varnai, C. Schoenfelder, S. Fraser, P. Enright, A. J. Coleman, N. 2021-02-03 doi:10.1101/2021.02.03.429496 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Inhibiting glycogen synthase kinase 3 suppresses TDP-43-mediated neurotoxicity in a caspase-dependant manner ]]> https://biorxiv.org/cgi/content/short/2021.02.03.429569v1?rss=1" White, M. A. Massenzio, F. Li, X. Coleman, M. P. Barmada, S. J. Sreedharan, J. 2021-02-03 doi:10.1101/2021.02.03.429569 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Enhancer priming by H3K4 methylation safeguards germline competence ]]> https://biorxiv.org/cgi/content/short/2020.07.07.192427v1?rss=1" Bleckwehl, T. Schaaf, K. Crispatzu, G. Respuela, P. Bartusel, M. Benson, L. Clark, S. J. Dorighi, K. M. Barral, A. Laugsch, M. Manzanares, M. Wysocka, J. Reik, W. Rada-Iglesias, A. 2020-07-07 doi:10.1101/2020.07.07.192427 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw ]]> https://biorxiv.org/cgi/content/short/2021.01.12.426343v1?rss=1" Hirschberger, C. Sleight, V. A. Criswell, K. E. Clark, S. Gillis, J. A. 2021-01-12 doi:10.1101/2021.01.12.426343 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates ]]> https://biorxiv.org/cgi/content/short/2020.12.30.424823v1?rss=1" Olmeda, F. Lohoff, T. Clark, S. Benson, L. Krueger, F. Reik, W. Rulands, S. 2021-01-01 doi:10.1101/2020.12.30.424823 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Sex of donor cell and reprogramming conditions predict the extent and nature of imprinting defects in mouse iPSCs ]]> https://biorxiv.org/cgi/content/short/2020.11.20.370973v1?rss=1" Arez, M. Eckersley-Maslin, M. Klobucar, T. von Gilsa Lopes, J. Krueger, F. A. Raposo, A. Gendrel, A.-V. Bernardes de Jesus, B. Teixeira da Rocha, S. 2020-11-20 doi:10.1101/2020.11.20.370973 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Subtractive CRISPR screen identifies factors involved in non-canonical LC3 lipidation. ]]> https://biorxiv.org/cgi/content/short/2020.11.18.388306v1?rss=1" Ulferts, R. Marcassa, E. Timimi, L. Lee, L. C. Daley, A. Montaner, B. Turner, S. D. Florey, O. Baillie, J. K. Beale, R. 2020-11-18 doi:10.1101/2020.11.18.388306 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Histone modifications form a cell-type-specific chromosomal bar code that modulates and maintains patterns of gene expression through the cell cycle ]]> https://biorxiv.org/cgi/content/short/2020.10.16.341446v1?rss=1" Halsall, J. A. Andrews, S. Krueger, F. Rutledge, C. Ficz, G. Reik, W. Turner, B. M. 2020-10-16 doi:10.1101/2020.10.16.341446 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ MSK phosphorylation of H3S28 is required for immediate early gene induction and cardiac hypertrophy ]]> https://biorxiv.org/cgi/content/short/2020.07.28.224832v1?rss=1" Robinson, E. L. Drawnel, F. M. Mehdi, S. Archer, C. R. Liu, W. Okkenhaug, H. Alkass, K. Aronsen, J. M. Nagaraju, C. K. Sjaastad, I. Sipido, K. R. Bergmann, O. Arthur, J. S. C. Wang, X. Roderick, H. L. 2020-07-29 doi:10.1101/2020.07.28.224832 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Epigenetic change induced by in utero dietary challenge provokes phenotypic variability across multiple generations of mice ]]> https://biorxiv.org/cgi/content/short/2020.08.07.241034v1?rss=1" Van de Pette, M. Galvao, A. Millership, S. J. To, W. Dimond, A. Prodani, C. McNamara, G. Bruno, L. Sardini, A. Webster, Z. McGinty, J. French, P. M. Uren, A. Castillo-Fernandez, J. John, R. M. Ferguson-Smith, A. Merkenschlager, M. Kelsey, G. D. Fisher, A. G. 2020-08-07 doi:10.1101/2020.08.07.241034 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Regulation of IFNgamma production by ZFP36L2 in T cells is context-dependent ]]> https://biorxiv.org/cgi/content/short/2024.02.09.579641v1?rss=1" Zandhuis, N. D. Guislain, A. Popalzij, A. Engels, S. Popovic, B. Turner, M. Wolkers, M. C. 2024-02-12 doi:10.1101/2024.02.09.579641 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ The consequences of mismatched buffers in spectral cell sorting ]]> https://biorxiv.org/cgi/content/short/2024.08.19.608560v1?rss=1" Dapaah, R. A. S. Ferrer Font, L. Shi, X. Hall, C. Thompson, S. Catharina Costa, L. Mage, P. L. Tyznik, A. J. Lundsten, K. Walker, R. V. 2024-08-19 doi:10.1101/2024.08.19.608560 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Protein degradation shapes developmental tempo in mouse and human neural progenitors ]]> https://biorxiv.org/cgi/content/short/2024.08.01.604391v1?rss=1" Nakanoh, S. Stamataki, D. Garcia-Perez, L. Azzi, C. Carr, H. L. Pokhilko, A. Howell, S. Yu, L. Skehel, M. Oxley, D. Andrews, S. Briscoe, J. Rayon, T. 2024-08-01 doi:10.1101/2024.08.01.604391 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ RAF inhibitors activate the integrated stress response by direct activation of GCN2 ]]> https://biorxiv.org/cgi/content/short/2024.08.15.607884v1?rss=1" Gilley, R. Kidger, A. M. Neill, G. Severson, P. Byrne, D. P. Kenneth, N. S. Bollag, G. Zhang, C. de Oliveira, T. M. Eyers, P. Bayliss, R. Masson, G. R. Cook, S. J. 2024-08-16 doi:10.1101/2024.08.15.607884 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Eomes directs the formation of spatially and functionally diverse extra-embryonic hematovascular tissues ]]> https://biorxiv.org/cgi/content/short/2024.08.13.607790v1?rss=1" Theeuwes, B. Harland, L. T. Bisia, A. Costello, I. Ton, M.-L. Lohoff, T. Clark, S. J. Argelaguet, R. Wilson, N. K. Reik, W. Bikoff, E. Robertson, E. J. Gottgens, B. 2024-08-16 doi:10.1101/2024.08.13.607790 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ The tissue-resident regulatory T cell pool is shaped by transient multi-tissue migration and a conserved residency program ]]> https://biorxiv.org/cgi/content/short/2023.08.14.553196v1?rss=1" Burton, O. Bricard, O. Tareen, S. Gergelits, V. Andrews, S. Roca, C. P. Whyte, C. Junius, S. Brajic, A. Pasciuto, E. Ali, M. Lemaitre, P. Schlenner, S. M. Ishigame, H. Brown, B. Dooley, J. Liston, A. 2023-08-14 doi:10.1101/2023.08.14.553196 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunisation in the pig lung ]]> https://biorxiv.org/cgi/content/short/2023.12.19.572318v1?rss=1" Muir, A. Paudyal, B. Schmidt, S. Sedaghat-Rostani, E. Chakravarti, S. Villanueva Hernandez, S. Moffat, K. Polo, N. Angelopoulos, N. Schmidt, A. Tenbusch, M. Freimanis, G. Gerner, W. Richard, A. C. Tchilian, E. 2023-12-19 doi:10.1101/2023.12.19.572318 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Paradoxical Activation of GCN2 by ATP-competitive inhibitors via allosteric activation and autophosphorylation ]]> https://biorxiv.org/cgi/content/short/2024.08.14.606984v1?rss=1" Masson, G. R. Neill, G. Vinciauskaite, V. Paul, M. Gilley, R. Cook, S. J. 2024-08-14 doi:10.1101/2024.08.14.606984 Cold Spring Harbor Laboratory Press 2024-08-14 <![CDATA[ Investigating the effects of radiation, T cell depletion, and bone marrow transplantation on murine gut microbiota ]]> https://biorxiv.org/cgi/content/short/2023.07.10.547212v1?rss=1" Kreisinger, J. Dooley, J. Singh, K. Cizkova, D. Schmiedova, L. Bendova, B. Liston, A. Moudra, A. 2023-07-10 doi:10.1101/2023.07.10.547212 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Phospholipase Cgamma regulates lacrimal gland branching by competing with PI3K in phosphoinositide metabolism ]]> https://biorxiv.org/cgi/content/short/2024.06.28.601066v1?rss=1" Wang, Q. Tao, C. Wu, Y. Anderson, K. E. Hannan, A. Lin, C.-s. Hawkins, P. T. Stephens, L. Zhang, X. 2024-07-02 doi:10.1101/2024.06.28.601066 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aging Brain ]]> https://biorxiv.org/cgi/content/short/2023.09.29.560184v1?rss=1" Mancino, S. Seneviratne, J. Mupo, A. Krueger, F. Oxley, D. Eckersley-Maslin, M. da Rocha, S. T. 2023-09-30 doi:10.1101/2023.09.29.560184 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Whole Genome Methylation Sequencing via Enzymatic Conversion (EM-seq): Protocol, Data Processing and Analysis ]]> https://biorxiv.org/cgi/content/short/2023.10.07.561361v1?rss=1" Olova, N. N. Andrews, S. 2023-10-10 doi:10.1101/2023.10.07.561361 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ A distinctive PI(4,5)P2 compartment forms during entosis and related engulfment processes ]]> https://biorxiv.org/cgi/content/short/2024.10.22.619613v1?rss=1" Durgan, J. Sloan, K. Domart, M.-C. Collinson, L. Florey, O. 2024-10-22 doi:10.1101/2024.10.22.619613 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment. ]]> https://biorxiv.org/cgi/content/short/2023.10.29.564595v1?rss=1" Wapenaar, H. Clifford, G. Rolls, W. Burdett, H. Zhang, Y. Deak, G. Zou, J. Taylor, M. R. Mills, J. Watson, J. A. Kumar, D. Das, A. Valsakumar, D. Bramham, J. Voigt, P. Wilson, M. D. 2023-10-29 doi:10.1101/2023.10.29.564595 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation ]]> https://biorxiv.org/cgi/content/short/2023.07.11.548598v1?rss=1" Lee, S. C. Adams, D. W. Ipsaro, J. J. Cahn, J. Lynn, J. Kim, H.-S. Berube, B. Major, V. Calarco, J. P. LeBlanc, C. Bhattacharjee, S. Ramu, U. Grimanelli, D. Jacob, Y. Voigt, P. Joshua-Tor, L. Martienssen, R. A. 2023-07-11 doi:10.1101/2023.07.11.548598 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Histone marks are drivers of the splicing changes necessary for an epithelial-to-mesenchymal transition ]]> https://biorxiv.org/cgi/content/short/2021.05.04.442453v1?rss=1" Segelle, A. Nunez-Alvarez, Y. Oldfield, A. J. Webb, K. M. Voigt, P. Luco, R. F. 2021-05-04 doi:10.1101/2021.05.04.442453 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ H3K36 methylation and DNA-binding are critical for Ioc4 recruitment and Isw1b remodeller function ]]> https://biorxiv.org/cgi/content/short/2021.02.26.432832v1?rss=1" Li, J. Bergmann, L. Webb, K. M. Gogol, M. M. Voigt, P. Liu, Y. Liang, H. Smolle, M. M. 2021-02-26 doi:10.1101/2021.02.26.432832 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ The memory B cell response to influenza vaccination is impaired in older persons ]]> https://biorxiv.org/cgi/content/short/2021.03.04.433942v1?rss=1" Carr, E. J. Wheatley, A. K. Hill, D. L. Linterman, M. A. 2021-03-04 doi:10.1101/2021.03.04.433942 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ The Fork Protection Complex protects long replicons from DNA damage at the cost of genome instability induced by DNA topological stress. ]]> https://biorxiv.org/cgi/content/short/2023.08.04.551986v1?rss=1" Keszthelyi, A. Whale, A. Houseley, J. Baxter, J. 2023-08-04 doi:10.1101/2023.08.04.551986 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ p110α-dependent hepatocyte signaling is critical for liver gene expression and its rewiring in MASLD ]]> https://biorxiv.org/cgi/content/short/2024.01.09.574858v1?rss=1" Regnier, M. Polizzi, A. Fougeray, T. Fougerat, A. Perrier, P. Anderson, K. Lippi, Y. Smati, S. Lukowicz, C. Lasserre, F. Fouche, E. Huillet, M. Rives, C. Tramunt, B. Naylies, C. Garcia, G. Rousseau-Bacquie, E. Bertrand-Michel, J. Canlet, C. Chevolleau-Mege, S. Debrauwer, L. Heymes, C. Burcelin, R. Levade, T. Gourdy, P. Wahli, W. Blum, Y. Gamet-Payrastre, L. Ellero-Simatos, S. Guillermet-Guibert, J. Hawkins, P. Stephens, L. Montagner, A. Loiseau, N. Guillou, H. 2024-01-10 doi:10.1101/2024.01.09.574858 Cold Spring Harbor Laboratory Press 2024-01-10 <![CDATA[ A targetable PREX2/RAC1/PI3Kβ signalling axis confers resistance to clinically relevant therapeutic approaches in melanoma ]]> https://biorxiv.org/cgi/content/short/2024.02.26.580534v1?rss=1" Ford, C. A. Koludrovic, D. Centeno, P. P. Foth, M. Tsonou, E. Vlahov, N. Sphyris, N. Gilroy, K. Bull, C. Nixon, C. Serrels, B. Munro, A. F. Dawson, J. C. Carragher, N. O. Pavet, V. Hornigold, D. C. Dunne, P. D. Downward, J. Welch, H. C. E. Barry, S. T. Sansom, O. J. Campbell, A. D. 2024-02-28 doi:10.1101/2024.02.26.580534 Cold Spring Harbor Laboratory Press 2024-02-28 <![CDATA[ Dbx2, an aging-related homeobox gene, inhibits the proliferation of adult neural progenitors ]]> https://biorxiv.org/cgi/content/short/2023.01.16.524218v1?rss=1" Giuliani, A. Licursi, V. Nisi, P. S. Fiore, M. Biagioni, S. Negri, R. Rugg-Gunn, P. Cacci, E. Lupo, G. 2023-01-19 doi:10.1101/2023.01.16.524218 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Delay of human early development via in vitro diapause ]]> https://biorxiv.org/cgi/content/short/2023.05.29.541316v1?rss=1" Bulut-Karslioglu, A. Iyer, D. van der Weijden, V. Heidari Khoei, H. McCarthy, A. Rayon, T. Simon, C. Dunkel, I. Wamaitha, S. Schulz, E. Niakan, K. Rivron, N. C. 2023-05-29 doi:10.1101/2023.05.29.541316 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ KRAS G12 mutant alleles differentially control glutamine metabolism via FOXO1 ]]> https://biorxiv.org/cgi/content/short/2024.10.19.618135v1?rss=1" View larger version (101K): org.highwire.dtl.DTLVardef@1459558org.highwire.dtl.DTLVardef@14fcd43org.highwire.dtl.DTLVardef@2d22ccorg.highwire.dtl.DTLVardef@147b068_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDifferent KRAS mutations trigger distinct metabolic phenotypes in colorectal cell lines C_LIO_LIGlutamine metabolism and nitrogen recycling are upregulated in KRAS mutant cells C_LIO_LIFOXO1 is a key regulator of KRAS-induced rewiring of glutamine and nitrogen metabolism C_LIO_LIInhibition of glutamine synthetase and glutaminase selectively kills mutant KRAS lines C_LI ]]> Ber, S. Yang, M. Sciacovelli, M. Samarajiwa, S. Patel, K. Nikitopoulou, E. Howitt, A. Cook, S. J. Venkitaraman, A. R. Frezza, C. Esposito, A. 2024-10-22 doi:10.1101/2024.10.19.618135 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ A maternal-effect Padi6 variant results in abnormal nuclear localization of DNMT1 and failure of epigenetic reprogramming and zygotic genome activation in mouse embryos ]]> https://biorxiv.org/cgi/content/short/2023.10.09.561545v1?rss=1" Giaccari, C. Cecere, F. Argenziano, L. Galvao, A. Acampora, D. Rossi, G. Hay Mele, B. Cubellis, M. V. Cerrato, F. Andrews, S. Cecconi, S. Kelsey, G. Riccio, A. 2023-10-10 doi:10.1101/2023.10.09.561545 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ MiR-155 epigenetically counteracts hypoxia for mitochondrial fitness during germinal center positive selection ]]> https://biorxiv.org/cgi/content/short/2023.07.31.551250v1?rss=1" Nakagawa, R. Llorian-Sopena, M. Varsani-brown, S. Chakravarty, P. Camarillo, J. M. Barry, D. George, R. Blackledge, N. P. Duddy, G. Klose, R. Turner, M. Calado, D. P. 2023-08-02 doi:10.1101/2023.07.31.551250 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ A quantitative and site-specific atlas of the in vivo citrullinome reveals widespread existence of citrullination ]]> https://biorxiv.org/cgi/content/short/2022.12.22.521572v1?rss=1" Rebak, A. Hendriks, I. A. Buch-Larsen, S. C. Elsborg, J. D. Kirsch, R. Doncheva, N. T. Jensen, L. J. Christophorou, M. A. Nielsen, M. L. 2022-12-22 doi:10.1101/2022.12.22.521572 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Intracellular calcium elevations drive the nucleation of FIP200- and ATG13-containing pre-autophagosomal structures that become omegasomes ]]> https://biorxiv.org/cgi/content/short/2022.11.02.514842v1?rss=1" Smith, M. Schoenfelder, P. Manifava, M. Polson, H. Tooze, S. Roderick, L. Ktistakis, N. 2022-11-02 doi:10.1101/2022.11.02.514842 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Tissue-resident regulatory T cells exert dualistic anti-tumour and pro-repair function in the exocrine pancreas ]]> https://biorxiv.org/cgi/content/short/2024.02.15.580302v1?rss=1" Stockis, J. Yip, T. Raghunathan, S. Garcia, C. Lee, S. Simpson, C. Silvain, S. Schuijs, M. J. Araos, J. Png, S. Raddi, G. Bricard, O. So, T. Y. Mack, S. Papadopoulos, P. Sawle, A. Jodrell, D. I. McKenzie, A. N. J. Thaventhiran, J. Clatworthy, M. Biffi, G. Saeb-Parsy, K. Liston, A. Halim, T. Y. F. 2024-02-19 doi:10.1101/2024.02.15.580302 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Ageing impairs the regenerative capacity of regulatory T cells in central nervous system remyelination ]]> https://biorxiv.org/cgi/content/short/2023.01.25.525562v1?rss=1" de la Fuente, A. G. Dittmer, M. Heesbeen, E. de la Vega-Gallardo, N. White, J. A. Young, A. Mayne, K. Falconer, J. McMurran, C. E. Innayatulah, M. Tiwari, V. Penalva, R. Ingram, R. J. Dombrowski, Y. Fitzgerald, D. C. 2023-01-25 doi:10.1101/2023.01.25.525562 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Protein tyrosine phosphatase receptor kappa regulates glycolysis and de novo lipogenesis to promote hepatocyte metabolic reprogramming in obesity ]]> https://biorxiv.org/cgi/content/short/2023.12.01.569004v1?rss=1" Gilglioni, E. H. Li, A. Saint-Pierre Wijckmans, W. Shen, T.-K. Perez-Chavez, I. Hovhannisyan, G. Lisjak, M. Negueruela, J. Vandenbempt, V. Bauza-Martinez, J. Herranz, J. M. Ezerina, D. Demine, S. Feng, Z. Vignane, T. Otero-Sanchez, L. Lambertucci, F. Prasnicka, A. Deviere, J. Hay, D. C. Encinar, J. A. N. Singh, S. P. Messens, J. Filipovic, M. R. Sharpe, H. J. Trepo, E. Wu, W. Gurzov, E. N. 2023-12-01 doi:10.1101/2023.12.01.569004 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ RNA-binding proteins control the G2-M checkpoint of the germinal centre B cell ]]> https://biorxiv.org/cgi/content/short/2024.12.01.626220v1?rss=1" Salerno, F. Whale, A. Matheson, L. S. Foster, W. Stammers, M. Bell, S. E. Hidson, D. J. Linterman, M. A. Houseley, J. A. Turner, M. 2024-12-05 doi:10.1101/2024.12.01.626220 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ RNA helicase DDX1 regulates germinal centre selection and affinity maturation by promoting tRNA ligase activity ]]> https://biorxiv.org/cgi/content/short/2025.01.10.632317v1?rss=1" Kimber, R. Ingelsfield, S. Screen, M. Salerno, F. Matheson, L. S. Okkenhaug, H. Whale, A. Assalaarachchi, J. Stammers, M. Akdeniz, D. Andrews, S. Ribeiro de Almeida, C. 2025-01-14 doi:10.1101/2025.01.10.632317 Cold Spring Harbor Laboratory Press 2025-01-14 <![CDATA[ Re-engineering of acetyl coenzyme A metabolism prevents senescence in budding yeast ]]> https://biorxiv.org/cgi/content/short/2025.03.27.645766v1?rss=1" View larger version (74K): org.highwire.dtl.DTLVardef@173a897org.highwire.dtl.DTLVardef@4166c3org.highwire.dtl.DTLVardef@1c1c1aeorg.highwire.dtl.DTLVardef@19295c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hadj-Moussa, H. Ulusan, M. Horkai, D. Mirza, M. K. A. Houseley, J. 2025-03-27 doi:10.1101/2025.03.27.645766 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ Pervanadate-induced oxidation relieves autoinhibition of SRC protein tyrosine kinase ]]> https://biorxiv.org/cgi/content/short/2025.04.27.650842v1?rss=1" Mulholland, K. E. Bourguet, M. Cheng, N. Rahman, O. Ezerina, D. Daly, L. A. Lai, T. Casanova, S. A. Creixell, P. Eyers, C. Eyers, P. Messens, J. Byrne, D. Sharpe, H. 2025-04-27 doi:10.1101/2025.04.27.650842 Cold Spring Harbor Laboratory Press 2025-04-27 <![CDATA[ TrAEL-seq captures DNA replication dynamics in mammalian cells ]]> https://biorxiv.org/cgi/content/short/2025.06.09.658559v1?rss=1" 1Mb). Short and long replication regions are not intrinsically different, and instead replication forks accelerate across the first [~]1 Mb of travel such that forks progress faster in the middle of regions lying between widely spaced Initiation Zones. We propose that this is a natural consequence of fewer replication forks being active later in S phase when these distal regions are replicated and there being less competition for replication factors. ]]> Kara, N. Biggins, L. Grinkevich, V. Whale, A. Garran Garcia, P. Srinivasan, J. Rugg-Gunn, P. Andrews, S. Parry, A. Robinson, H. M. R. Houseley, J. 2025-06-11 doi:10.1101/2025.06.09.658559 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ A post-transcriptional regulatory checkpoint controls the response of tumor-infiltrating cytotoxic CD4+ T cells to immunotherapy ]]> https://biorxiv.org/cgi/content/short/2025.09.09.675154v1?rss=1" Vila de Mucha, M. Hlond, J. Costoya, C. Lau, C.-I. Sledzinska, A. Uddin, I. Navarrete, M. Shah, M. Mastrokalos, G. Karagianni, D. Bell, S. E. Nattress, C. Beattie, G. Tape, C. J. Turner, M. Quezada, S. A. Jenner, R. G. 2025-09-12 doi:10.1101/2025.09.09.675154 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability ]]> https://biorxiv.org/cgi/content/short/2024.12.09.627617v1?rss=1" Yuan, W. Huang, Y.-C. LeBlanc, C. Poulet, A. Valsakumar, D. van Wolfswinkel, J. C. Voigt, P. Jacob, Y. 2024-12-11 doi:10.1101/2024.12.09.627617 Cold Spring Harbor Laboratory Press 2024-12-11