Nishiyama T. Cohesion and cohesin-dependent chromatin organization. Curr Opin Cell Biol. 2019;58:8–14.
Article
CAS
Google Scholar
Losada A, Yokochi T, Kobayashi R, Hirano T. Identification and characterization of SA/Scc3p subunits in the Xenopus and human cohesin complexes. J Cell Biol. 2000;150:405–16.
Article
CAS
Google Scholar
Watrin E, Schleiffer A, Tanaka K, Eisenhaber F, Nasmyth K, Peters JM. Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression. Curr Biol. 2006;16:863–74.
Article
CAS
Google Scholar
Carretero M, Ruiz-Torres M, Rodriguez-Corsino M, Barthelemy I, Losada A. Pds5B is required for cohesion establishment and Aurora B accumulation at centromeres. EMBO J. 2013;32:2938–49.
Article
CAS
Google Scholar
Morales C, Ruiz-Torres M, Rodriguez-Acebes S, Lafarga V, Rodríguez-Corsino M, Megias D, Cisneros DA, Peters J-M, Méndez J, Losada A. PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection. J Biol Chem. 2020;2895:146–57.
Article
Google Scholar
Nishiyama T, Ladurner R, Schmitz J, Kreidl E, Schleiffer A, Bhaskara V, Bando M, Shirahige K, Hyman AA, Mechtler K, et al. Sororin mediates sister chromatid cohesion by antagonizing Wapl. Cell. 2010;143:737–49.
Article
CAS
Google Scholar
Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 2017;36:3573–99.
Article
CAS
Google Scholar
Losada A, Yokochi T, Hirano T. Functional contribution of Pds5 to cohesin-mediated cohesion in human cells and Xenopus egg extracts. J Cell Sci. 2005;118:2133–41.
Article
CAS
Google Scholar
Minamino M, Ishibashi M, Nakato R, Akiyama K, Tanaka H, Kato Y, Negishi L, Hirota T, Sutani T, Bando M, et al. Esco1 Acetylates Cohesin via a Mechanism Different from that of Esco2. Curr Biol. 2015;25:1694–706.
Article
CAS
Google Scholar
Casa V, Gines MM, Gusmao EG, Slotman JA, Zirkel A, Josipovic N, Oole E, Van Ijcken WFJ, Houtsmuller AB, Papantonis A, et al. Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control. Genome Res. 2020;30:515–27.
Article
CAS
Google Scholar
Cuadrado A, Losada A. Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture. Curr Opin Genet Dev. 2020;61:9–16.
Article
CAS
Google Scholar
Viny AD, Bowman RL, Liu Y, Lavallée V-P, Eisman SE, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, et al. Cohesin members Stag1 and Stag2 display distinct roles in chromatin accessibility and topological control of HSC self-renewal and differentiation. Cell Stem Cell. 2019;25:682-696.e8.
Article
CAS
Google Scholar
Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, et al. ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL. Elife. 2020;9:e52091.
Article
CAS
Google Scholar
De Koninck M, Lapi E, Badía-Careaga C, Cossío I, Giménez-Llorente D, Rodríguez-Corsino M, Andrada E, Hidalgo A, Manzanares M, Real FX, et al. Essential roles of cohesin STAG2 in mouse embryonic development and adult tissue homeostasis. Cell Rep. 2020. https://doi.org/10.1016/j.celrep.2020.108014.
Article
Google Scholar
Remeseiro S, Cuadrado A, Carretero M, Martínez P, Drosopoulos WC, Cañamero M, Schildkraut CL, Blasco MA, Losada A. Cohesin-SA1 deficiency drives aneuploidy and tumourigenesis in mice due to impaired replication of telomeres. EMBO J. 2012;31:2076–89.
Article
CAS
Google Scholar
De Koninck M, Losada A. Cohesin mutations in cancer. Cold Spring Harb Perspect Med. 2016;6:a026476.
Article
Google Scholar
Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, et al. Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med. 2019;21:663–75.
Article
CAS
Google Scholar
Rao SS, Huang SC, St Hilaire BG, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X. Cohesin loss eliminates all loop domains. Cell. 2017;171(2):305–20.
Article
CAS
Google Scholar
Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017;551:51–6.
Article
Google Scholar
Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of chromosomal domains by loop extrusion. Cell Rep. 2016;15:2038–49.
Article
CAS
Google Scholar
Haarhuis JHI, van der Weide RH, Blomen VA, Yáñez-Cuna JO, Amendola M, van Ruiten MS, Krijger PHL, Teunissen H, Medema RH, van Steensel B, et al. The cohesin release factor WAPL restricts chromatin loop extension. Cell. 2017;169:693-707.e14.
Article
CAS
Google Scholar
de Wit E, Vos ESM, Holwerda SJB, Valdes-Quezada C, Verstegen MJAM, Teunissen H, Splinter E, Wijchers PJ, Krijger PHL, de Laat W. CTCF binding polarity determines chromatin looping. Mol Cell. 2015;60:676–84.
Article
Google Scholar
Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell. 2008;132:422–33.
Article
CAS
Google Scholar
Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, Schirghuber E, Tsutsumi S, Nagae G, Ishihara K, Mishiro T, et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature. 2008;451:796–801.
Article
CAS
Google Scholar
Hara K, Zheng G, Qu Q, Liu H, Ouyang Z, Chen Z, Tomchick DR, Yu H. Structure of cohesin subcomplex pinpoints direct shugoshin-Wapl antagonism in centromeric cohesion. Nat Struct Mol Biol. 2014;21:864–70.
Article
CAS
Google Scholar
Li Y, Haarhuis JHI, Cacciatore ÁS, Oldenkamp R, van Ruiten MS, Willems L, Teunissen H, Muir KW, de Wit E, Rowland BD, et al. The structural basis for cohesin–CTCF-anchored loops. Nature. 2020. https://doi.org/10.1038/s41586-019-1910-z.
Article
Google Scholar
van Ruiten MS, van Gent D, Sedeño Cacciatore Á, Fauster A, Willems L, Hekkelman ML, Hoekman L, Altelaar M, Haarhuis JHI, Brummelkamp TR, et al. The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism. Nat Struct Mol Biol. 2022;29:586–91.
Article
Google Scholar
Davidson IF, Bauer B, Goetz D, Tang W, Wutz G, Peters J-M. DNA loop extrusion by human cohesin. Science. 2019;366:1338–45.
Article
CAS
Google Scholar
Kim Y, Shi Z, Zhang H, Finkelstein IJ, Yu H. Human cohesin compacts DNA by loop extrusion. Science. 2019. https://doi.org/10.1126/science.aaz4475.
Article
Google Scholar
Kikuchi S, Borek DM, Otwinowski Z, Tomchick DR, Yu H. Crystal structure of the cohesin loader Scc2 and insight into cohesinopathy. Proc Natl Acad Sci U S A. 2016;113:12444–9.
Article
CAS
Google Scholar
Petela NJ, Gligoris TG, Metson J, Lee BG, Voulgaris M, Hu B, Kikuchi S, Chapard C, Chen W, Rajendra E, et al. Scc2 is a potent activator of cohesin’s ATPase that promotes loading by binding Scc1 without Pds5. Mol Cell. 2018;70:1134–48.
Article
CAS
Google Scholar
Busslinger GA, Stocsits RR, Van Der Lelij P, Axelsson E, Tedeschi A, Galjart N, Peters JM. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl. Nature. 2017;44:503–7.
Article
Google Scholar
Ivanov MP, Ladurner R, Poser I, Beveridge R, Rampler E, Hudecz O, Novatchkova M, Hériché J, Wutz G, van der Lelij P, et al. The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion. EMBO J. 2018;37:e97150.
Article
Google Scholar
Rahman S, Jones MJ, Jallepalli PV. Cohesin recruits the Esco1 acetyltransferase genome wide to repress transcription and promote cohesion in somatic cells. Proc Natl Acad Sci U S A. 2015;112:11270–5.
Article
CAS
Google Scholar
Arruda NL, Carico ZM, Justice M, Liu YF, Zhou J, Stefan HC, Dowen JM. Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells. Epigenetics Chromatin. 2020. https://doi.org/10.1186/s13072-020-00353-9.
Article
Google Scholar
Cuadrado A, Giménez-Llorente D, Kojic A, Rodríguez-Corsino M, Cuartero Y, Martín-Serrano G, Gómez-López G, Marti-Renom MA, Losada A. Specific contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb domains in Embryonic stem cells. Cell Rep. 2019;27:3500-3510.e4.
Article
CAS
Google Scholar
Kojic A, Cuadrado A, De Koninck M, Giménez-Llorente D, Rodríguez-Corsino M, Gómez-López G, Le Dily F, Marti-Renom MA, Losada A. Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization. Nat Struct Mol Biol. 2018;25:496–504.
Article
CAS
Google Scholar
Richart L, Lapi E, Pancaldi V, Cuenca-Ardura M, Pau ECDS, Madrid-Mencía M, Neyret-Kahn H, Radvanyi F, Rodríguez JA, Cuartero Y, et al. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Nucleic Acids Res. 2021;49:11005–21.
Article
CAS
Google Scholar
Remeseiro S, Cuadrado A, Gómez-López G, Pisano DG, Losada A. A unique role of cohesin-SA1 in gene regulation and development. EMBO J. 2012;31:2090–102.
Article
CAS
Google Scholar
Surdez D, Zaidi S, Grossetête S, Laud-Duval K, Ferre AS, Mous L, Vourc’h, T., Tirode, F., Pierron, G., Raynal, V., et al. STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma. Cancer Cell. 2021;39:810-826.e9.
Article
CAS
Google Scholar
Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, et al. The energetics and physiological impact of cohesin extrusion. Cell. 2018;173:1165-1178.e20.
Article
CAS
Google Scholar
Zuin J, Franke V, van Ijcken WF, van der Sloot A, Krantz ID, van der Reijden MI, Nakato R, Lenhard B, Wendt KS. A cohesin-independent role for NIPBL at promoters provides insights in CdLS. PLoS Genet. 2014;10:e1004153.
Article
Google Scholar
Muñoz S, Minamino M, Casas-Delucchi CS, Patel H, Uhlmann F. A role for chromatin remodeling in cohesin loading onto chromosomes. Mol Cell. 2019;74:664-673.e5.
Article
Google Scholar
Tedeschi A, Wutz G, Huet S, Jaritz M, Wuensche A, Schirghuber E, Davidson IF, Tang W, Cisneros DA, Bhaskara V, et al. Wapl is an essential regulator of chromatin structure and chromosome segregation. Nature. 2013;501:564–8.
Article
CAS
Google Scholar
Pugacheva EM, Kubo N, Loukinov D, Tajmul M, Kang S, Kovalchuk AL, Strunnikov AV, Zentner GE, Ren B, Lobanenkov VV. CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention. Proc Natl Acad Sci U S A. 2020;117:2020–31.
Article
CAS
Google Scholar
Liu Y, Dekker J. Biochemically distinct cohesin complexes mediate positioned loops between CTCF sites and dynamic loops within chromatin domains. BioRxiv. 2021. https://doi.org/10.1101/2021.08.24.457555.
Article
Google Scholar
Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters J-M, Mirny LA. Transcription shapes 3D chromatin organization by interacting with loop extrusion. BioRxiv. 2022. https://doi.org/10.1101/2022.01.07.475367.
Article
Google Scholar
Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, et al. BRD4 orchestrates genome folding to promote neural crest differentiation. Nat Genet. 2021;53:1480–92.
Article
CAS
Google Scholar
Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe HJ, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv. 2021. https://doi.org/10.1126/sciadv.abg8205.
Article
Google Scholar
Zhu Y, Denholtz M, Lu H, Murre C. Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization. Genes Dev. 2021;35:65–81.
Article
CAS
Google Scholar
Bastié N, Chapard C, Dauban L, Gadal O, Beckouët F, Koszul R. Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops. Nat Struct Mol Biol. 2022;29:575–85.
Article
Google Scholar
Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, et al. Molecular basis of CTCF binding polarity in genome folding. Nat Commun. 2020. https://doi.org/10.1038/s41467-020-19283-x.
Article
Google Scholar
Ouyang Z, Zheng G, Tomchick DR, Luo X, Yu H. Structural basis and IP requirement for Pds5-dependent cohesin dynamics. Mol Cell. 2016;62:248–59.
Article
CAS
Google Scholar
Heath H, De Almeida CR, Sleutels F, Dingjan G, Van De Nobelen S, Jonkers I, Ling KW, Gribnau J, Renkawitz R, Grosveld F, et al. CTCF regulates cell cycle progression of αβ T cells in the thymus. EMBO J. 2008;27:2839–50.
Article
CAS
Google Scholar
Serrano A, Rodriguez-Corsino M, Losada A. Heterochromatin protein 1 (HP1) proteins do not drive pericentromeric cohesin enrichment in human cells. PLoS ONE. 2009;4: e5118.
Article
Google Scholar
Mendez J, Stillman B. Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis. Mol Cell Biol. 2000;20:8602–12.
Article
CAS
Google Scholar
Ladurner R, Kreidl E, Ivanov MP, Ekker H, Idarraga-Amado MH, Busslinger GA, Wutz G, Cisneros DA, Peters J. Sororin actively maintains sister chromatid cohesion. EMBO J. 2016;35:635–53.
Article
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
Article
Google Scholar
Machanick P, Bailey TL. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics. 2011;27:1696–7.
Article
CAS
Google Scholar
Hu B, Petela N, Kurze A, Chan KL, Chapard C, Nasmyth K. Biological chromodynamics: A general method for measuring protein occupancy across the genome by calibrating ChIP-seq. Nucleic Acids Res. 2015;43:e132.
Google Scholar
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–5.
Article
Google Scholar
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215–6.
Article
CAS
Google Scholar
Graña O, Rubio-Camarillo M, Fdez-Riverola F, Pisano DG, Glez-Peña D. Nextpresso: next generation sequencing expression analysis pipeline. Curr Bioinform. 2018;13:583–91.
Article
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
Google Scholar