Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl
Open accessAbstract
Mammalian genomes are spatially organized by CCCTC-binding factor (CTCF) and cohesin into chromatin loops and topologically associated domains, which have important roles in gene regulation and recombination. By binding to specific sequences, CTCF defines contact points for cohesin-mediated long-range chromosomal cis-interactions. Cohesin is also present at these sites, but has been proposed to be loaded onto DNA elsewhere and to extrude chromatin loops until it encounters CTCF bound to DNA. How cohesin is recruited to CTCF sites, according to this or other models, is unknown. Here we show that the distribution of cohesin in the mouse genome depends on transcription, CTCF and the cohesin release factor Wings apart-like (Wapl). In CTCF-depleted fibroblasts, cohesin cannot be properly recruited to CTCF sites but instead accumulates at transcription start sites of active genes, where the cohesin-loading complex is located. In the absence of both CTCF and Wapl, cohesin accumulates in up to 70 kilobase-long regions at 3'-ends of active genes, in particular if these converge on each other. Changing gene expression modulates the position of these 'cohesin islands'. These findings indicate that transcription can relocate mammalian cohesin over long distances on DNA, as previously reported for yeast cohesin, that this translocation contributes to positioning cohesin at CTCF sites, and that active genes can be freed from cohesin either by transcription-mediated translocation or by Wapl-mediated release.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Cohesin can remain topologically engaged and slide on both naked DNA and chromatin.
“Since cohesin can remain topologically engaged and slide on both naked DNA42–44 and chromatin,45,46”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [46]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works
McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195 · see citing works
Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003 · see citing works
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works
Mediator and cohesin connect gene expression and chromatin architecture
Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939 · see citing works
MEME-ChIP: motif analysis of large DNA datasets
Machanick, P., & Bailey, T. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr189 · Cited by 1,815 · see citing works
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730 · see citing works
Cohesin mediates transcriptional insulation by CCCTC-binding factor
Wendt, K. S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., et al. (2008) · Nature · doi:10.1038/nature06634 · Cited by 1,193 · see citing works
Self-citationArchitectural protein subclasses shape 3D organization of genomes during lineage commitment
Phillips-Cremins, J. E., Sauria, M. E. G., Sanyal, A., Gerasimova, T. I., Lajoie, B. R., Bell, J. S. K., Ong, C.-T., Hookway, T. A., Guo, C., Sun, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.053 · Cited by 1,187 · see citing works
High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP
Rodríguez, C. I., Buchholz, F., Galloway, J. L., Sequerra, R., Kasper, J. S., Ayala, R., Stewart, A. F., & Dymecki, S. M. (2000) · Nature Genetics · doi:10.1038/75973 · Cited by 1,162 · see citing works
Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · see citing works
Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms
Parelho, V., Hadjur, S., Spivakov, M., Leleu, M., Sauer, S., Gregson, H. C., Jarmuz, A., Canzonetta, C., Webster, Z., Nesterova, T., et al. (2008) · Cell · doi:10.1016/j.cell.2008.01.011 · Cited by 900 · see citing works
Nasmyth, K. (2001) · Annual Review of Genetics · doi:10.1146/annurev.genet.35.102401.091334 · Cited by 805 · see citing works
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
Zuin, J., Dixon, J. R., van der Reijden, M. I. J. A., Ye, Z., Kolovos, P., Brouwer, R. W. W., van de Corput, M. P. C., van de Werken, H. J. G., Knoch, T. A., van IJcken, W. F. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317788111 · Cited by 779 · see citing works
Wapl controls the dynamic association of cohesin with chromatin
Kueng, S., Hegemann, B., Peters, B. H., Lipp, J. J., Schleiffer, A., Mechtler, K., & Peters, J.-M. (2006) · Cell · doi:10.1016/j.cell.2006.09.040 · Cited by 624 · see citing works
Self-citationCohesin relocation from sites of chromosomal loading to places of convergent transcription
Lengronne, A., Katou, Y., Mori, S., Yokobayashi, S., Kelly, G. P., Itoh, T., Watanabe, Y., Shirahige, K., & Uhlmann, F. (2004) · Nature · doi:10.1038/nature02742 · Cited by 588 · see citing works
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus
Hadjur, S., Williams, L. M., Ryan, N. K., Cobb, B. S., Sexton, T., Fraser, P., Fisher, A. G., & Merkenschlager, M. (2009) · Nature · doi:10.1038/nature08079 · Cited by 525 · see citing works
CEAS: <i>cis</i>-regulatory element annotation system
Shin, H., Liu, T., Manrai, A. K., & Liu, X. S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp479 · Cited by 461 · see citing works
Cohesion between sister chromatids must be established during DNA replication
Uhlmann, F., & Nasmyth, K. (1998) · Current Biology · doi:10.1016/s0960-9822(98)70463-4 · Cited by 454 · see citing works
Genome-Wide Mapping of the Cohesin Complex in the Yeast Saccharomyces cerevisiae
Glynn, E. F., Megee, P. C., Yu, H.-G., Mistrot, C., Ünal, E., Koshland, D. E., DeRisi, J. L., & Gerton, J. L. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020259 · Cited by 431 · see citing works
Cohesin-mediated interactions organize chromosomal domain architecture
Sofueva, S., Yaffe, E., Chan, W., Georgopoulou, D., Vietri Rudan, M., Mira‐Bontenbal, H., Pollard, S. M., Schroth, G. P., Tanay, A., & Hadjur, S. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.237 · Cited by 394 · see citing works
Sororin Mediates Sister Chromatid Cohesion by Antagonizing Wapl
Nishiyama, T., Ladurner, R., Schmitz, J., Kreidl, E., Schleiffer, A., Bhaskara, V., Bando, M., Shirahige, K., Hyman, A. A., Mechtler, K., et al. (2010) · Cell · doi:10.1016/j.cell.2010.10.031 · Cited by 392 · see citing works
Self-citationWapl is an essential regulator of chromatin structure and chromosome segregation
Tedeschi, A., Wutz, G., Huet, S., Jaritz, M., Wuensche, A., Schirghuber, E., Davidson, I. F., Tang, W., Cisneros, D. A., Bhaskara, V., et al. (2013) · Nature · doi:10.1038/nature12471 · Cited by 359 · see citing works
Self-citationCohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus
Nativio, R., Wendt, K. S., Ito, Y., Huddleston, J. E., Uribe‐Lewis, S., Woodfine, K., Krueger, C., Reik, W., Peters, J., & Murrell, A. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000739 · Cited by 325 · see citing works
Self-citationRapid generation of inducible mouse mutants
Seibler, J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng012 · Cited by 305 · see citing works
CTCF-binding elements mediate control of V(D)J recombination
Guo, C., Yoon, H. S., Franklin, A., Jain, S., Ebert, A., Cheng, H.-L., Hansen, E., Despo, O., Bossen, C., Vettermann, C., et al. (2011) · Nature · doi:10.1038/nature10495 · Cited by 277 · see citing works
Tachibana-Konwalski, K., Godwin, J., van der Weyden, L., Champion, L., Kudo, N. R., Adams, D. J., & Nasmyth, K. (2010) · Genes & Development · doi:10.1101/gad.605910 · Cited by 265 · see citing works
Rapid movement and transcriptional re-localization of human cohesin on DNA
Davidson, I. F., Goetz, D., Zaczek, M. P., Molodtsov, M. I., Huis in 't Veld, P. J., Weissmann, F., Litos, G., Cisneros, D. A., Ocampo‐Hafalla, M., Ladurner, R., et al. (2016) · The EMBO Journal · doi:10.15252/embj.201695402 · Cited by 246 · see citing works
A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation
Seitan, V. C., Hao, B., Tachibana-Konwalski, K., Lavagnolli, T., Mira-Bontenbal, H., Brown, K. E., Teng, G., Carroll, T., Terry, A. V., Horan, K., et al. (2011) · Nature · doi:10.1038/nature10312 · Cited by 234 · see citing works
Revilla‐i‐Domingo, R., Bilić, I., Vilagos, B., Tagoh, H., Ebert, A., Tamir, I., Smeenk, L., Trupke, J., Sommer, A., Jaritz, M., et al. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.155 · Cited by 232 · see citing works
Single-molecule imaging reveals a collapsed conformational state for DNA-bound cohesin
Stigler, J., Çamdere, G. Ö., Koshland, D. E., & Greene, E. C. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.003 · Cited by 229 · see citing works
Cohesin Complex Promotes Transcriptional Termination between Convergent Genes in S. pombe
Gullerová, M., & Proudfoot, N. J. (2008) · Cell · doi:10.1016/j.cell.2008.02.040 · Cited by 208 · see citing works
A CTCF Code for 3D Genome Architecture
Nichols, M. H., & Corces, V. G. (2015) · Cell · doi:10.1016/j.cell.2015.07.053 · Cited by 186 · see citing works
CTCF regulates cell cycle progression of αβ T cells in the thymus
Heath, H., de Almeida, C. R., Sleutels, F., Dingjan, G. M., van de Nobelen, S., Jonkers, I. H., Ling, K., Gribnau, J. H., Renkawitz, R., Grosveld, F. G., et al. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.214 · Cited by 182 · see citing works
Self-citationHu, B., Petela, N. J., Kurze, A., Chan, K.-L., Chapard, C., & Nasmyth, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv670 · Cited by 155 · see citing works
Izumi, K., Nakato, R., Zhang, Z., Edmondson, A. C., Noon, S. E., Dulik, M. C., Rajagopalan, R., Venditti, C. P., Gripp, K. W., Samanich, J. M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3229 · Cited by 143 · see citing works
A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS
Zuin, J., Franke, V., van IJcken, W. F. J., van der Sloot, A., Krantz, I. D., van der Reijden, M. I. J. A., Nakato, R., Lenhard, B., & Wendt, K. S. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004153 · Cited by 141 · see citing works
Medvedovic, J., Ebert, A., Tagoh, H., Tamir, I., Schwickert, T. A., Novatchkova, M., Sun, Q., Veld, P. J. H. I. ’., Guo, C., Yoon, H. S., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.08.011 · Cited by 136 · see citing works
Genome-Wide Control of RNA Polymerase II Activity by Cohesin
Schaaf, C. A., Kwak, H., Koenig, A. N., Misulovin, Z., Gohara, D. W., Watson, A. R., Zhou, Y., Lis, J. T., & Dorsett, D. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003382 · Cited by 107 · see citing works
MULTOVL: fast multiple overlaps of genomic regions
Aszódi, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts607 · Cited by 37 · see citing works
Swain, A., Misulovin, Z., Pherson, M., Gause, M., Mihindukulasuriya, K. A., Rickels, R. A., Shilatifard, A., & Dorsett, D. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006331 · Cited by 33 · see citing works
Flagged first, then by citations
2 of the 51 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- [36]Sambrook J Russell DW Molecular Cloning: A Laboratory Manual Cold Spring Harbor Laboratory Press 2001
Cited by
Sorted by citations
HiGlass: web-based visual exploration and analysis of genome interaction maps
Kerpedjiev, P., Abdennur, N. A., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S., Azhir, A., Kumar, N., et al. (2017) · Genome Biology · doi:10.1186/s13059-018-1486-1 · Cited by 2,057 · see citing works
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883 · see citing works
Organizational principles of 3D genome architecture
Rowley, M. J., & Corces, V. G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0060-8 · Cited by 1,171 · see citing works
Long-range enhancer–promoter contacts in gene expression control
Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102 · see citing works
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Bintu, B., Mateo, L. J., Su, J.-H., Sinnott-Armstrong, N. A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A. N., & Zhuang, X. (2018) · Science · doi:10.1126/science.aau1783 · Cited by 976 · see citing works
Wutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., et al. (2017) · The EMBO Journal · doi:10.15252/embj.201798004 · Cited by 864 · see citing works
“…36 | No 24 | 2017 that cohesin’s function in gene regulation is related to CTCF, as this DNA binding protein recruits cohesin to specific sites in mammalian genomes and depends on cohesin for its ability to mediate gene regulation (Parelho et al, 2008; Wendt et al, 2008; Busslinger et al, 2017).”
InfluentialSelf-citationDNA loop extrusion by human cohesin
Davidson, I. F., Bauer, B., Goetz, D., Tang, W., Wutz, G., & Peters, J.-M. (2019) · Science · doi:10.1126/science.aaz3418 · Cited by 863 · see citing works
Self-citationThe role of 3D genome organization in development and cell differentiation
Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Rando, O. J., Tjian, R., & Darzacq, X. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.002 · Cited by 661 · see citing works
Chromatin organization by an interplay of loop extrusion and compartmental segregation
Nuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N. A., & Mirny, L. A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717730115 · Cited by 617 · see citing works
“Furthermore, experiments are at odds with a simple picture where the sole function of the Nipbl complex (also termed SCC2/SCC4) is to facilitate cohesin loading while WAPL determines its residence time on chromatin, and rather suggest that SCC4 also regulates the processivity and/or the residence time of cohesin on DN…”
BackgroundPrinciples of genome folding into topologically associating domains
Szabo, Q., Bantignies, F., & Cavalli, G. (2019) · Science Advances · doi:10.1126/sciadv.aaw1668 · Cited by 594 · see citing works
The Energetics and Physiological Impact of Cohesin Extrusion
Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.072 · Cited by 581 · see citing works
Genome folding through loop extrusion by SMC complexes
Davidson, I. F., & Peters, J. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00349-7 · Cited by 507 · see citing works
Self-citationTranscription Elongation Can Affect Genome 3D Structure
Heinz, S., Texari, L., Hayes, M. G. B., Urbanowski, M., Chang, M. W., Givarkes, N., Rialdi, A., White, K. M., Albrecht, R. A., Pache, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.047 · Cited by 453 · see citing works
Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Darzacq, X., & Tjian, R. (2022) · Nature Genetics · doi:10.1038/s41588-022-01223-8 · Cited by 406 · see citing works
A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture
Gassler, J., Brandão, H. B., Imakaev, M., Flyamer, I. M., Ladstätter, S., Bickmore, W. A., Peters, J., Mirny, L. A., & Tachibana, K.-E. K. (2017) · The EMBO Journal · doi:10.15252/embj.201798083 · Cited by 363 · see citing works
“Transcription, however, can affect loading and positioning of cohesin (Kagey et al., 2010; Busslinger et al., 2017).”
BackgroundSelf-citationZhang, Y., Li, T., Preißl, S., Amaral, M. L., Grinstein, J. D., Farah, E. N., Destici, E., Qiu, Y., Hu, R., Lee, A. Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0479-7 · Cited by 367 · see citing works
Organization of Chromosomal DNA by SMC Complexes
Yatskevich, S., Rhodes, J., & Nasmyth, K. (2019) · Annual Review of Genetics · doi:10.1146/annurev-genet-112618-043633 · Cited by 337 · see citing works
Isoda, T., Moore, A. J., He, Z., Chandra, V. K., Aida, M., Denholtz, M., van Hamburg, J. P., Fisch, K. M., Chang, A. N., Fahl, S. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.001 · Cited by 311 · see citing works
The epigenetic basis of cellular heterogeneity
Carter, B. C., & Zhao, K. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00300-0 · Cited by 314 · see citing works
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
Phanstiel, D. H., Van Bortle, K., Spacek, D., Hess, G. T., Shamim, M. S., Machol, I., Love, M. I., Aiden, E. L., Bassik, M. C., & Snyder, M. P. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.08.006 · Cited by 299 · see citing works
Despang, A., Schöpflin, R., Franke, M., Ali, S., Jerković, I., Paliou, C., Chan, W.-L., Timmermann, B., Wittler, L., Vingron, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0466-z · Cited by 306 · see citing works
Emerging Evidence of Chromosome Folding by Loop ExtrusionPreprint
Fudenberg, G., Abdennur, N. A., Imakaev, M., Goloborodko, A. A., & Mirny, L. A. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.034710 · Cited by 287 · see citing works
“Future simulations and experiments will be valuable for probing the consequences of multiple simultaneous perturbations (Busslinger et al. 2017; Wutz et al. 2017).”
BackgroundRecent evidence that TADs and chromatin loops are dynamic structures
Hansen, A. S., Cattoglio, C., Darzacq, X., & Tjian, R. (2018) · Nucleus · doi:10.1080/19491034.2017.1389365 · Cited by 266 · see citing works
Kruse, K., Hug, C., & Vaquerizas, J. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02215-9 · Cited by 216 · see citing works
The role of transcription in shaping the spatial organization of the genome
van Steensel, B., & Furlong, E. E. M. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0114-6 · Cited by 247 · see citing works
Transcription shapes 3D chromatin organization by interacting with loop extrusion
Banigan, E. J., Tang, W., van den Berg, A. A., Stocsits, R. R., Wutz, G., Brandão, H. B., Busslinger, G. A., Peters, J., & Mirny, L. A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2210480120 · Cited by 216 · see citing works
“Cohesin accumulation is greater for higher levels of transcription (6), and both dots and insulation at cohesin islands are partially suppressed in DKO by treatment with the transcription elongation inhibitor DRB (SI Appendix, Fig.”
BackgroundResultInfluentialSelf-citationTwo major mechanisms of chromosome organization
Mirny, L. A., Imakaev, M., & Abdennur, N. A. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.05.001 · Cited by 222 · see citing works
“The process of transcription can also play a role in pausing loop extrusion and/or relocalizing cohesin [54,85], thereby influencing chromosome organization.”
BackgroundCTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention
Pugacheva, E. M., Kubo, N., Loukinov, D. I., Tajmul, M., Kang, S., Kovalchuk, A. L., Strunnikov, A. V., Zentner, G. E., Ren, B., & Lobanenkov, V. V. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1911708117 · Cited by 215 · see citing works
“These data are wholly consistent with the results from the previous studies using CTCF auxininducible degron system and with CTCF knockout mouse fibroblasts where, in the absence of CTCF, cohesin is no longer able to occupy CTCF binding sites (30, 31).”
ResultMolecular basis of CTCF binding polarity in genome folding
Nora, E. P., Caccianini, L., Fudenberg, G., So, K., Kameswaran, V., Nagle, A., Uebersohn, A., Hajj, B., Saux, A. L., Coulon, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19283-x · Cited by 206 · see citing works
Canela, A., Maman, Y., Huang, S.-Y. N., Wutz, G., Tang, W., Zagnoli-Vieira, G., Callén, E., Wong, N., Day, A., Peters, J., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.04.030 · Cited by 202 · see citing works
“To determine how cohesin affects the distribution of TOP2 lesions, we examined mouse embryonic fibroblasts (MEFs) in which SMC3, a cohesin subunit, was depleted by CRE-mediated recombination, resulting in the disruption of nuclear architecture (Busslinger et al., 2017) (Smc3+CRE; Figures 1A–1D).”
InfluentialSelf-citationCTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion
Davidson, I. F., Barth, R., Zaczek, M., van der Torre, J., Tang, W., Nagasaka, K., Janissen, R., Kerssemakers, J. W. J., Wutz, G., Dekker, C., et al. (2023) · Nature · doi:10.1038/s41586-023-05961-5 · Cited by 190 · see citing works
Self-citationScc2 Is a Potent Activator of Cohesin’s ATPase that Promotes Loading by Binding Scc1 without Pds5
Petela, N. J., Gligoris, T. G., Metson, J., Lee, B., Voulgaris, M., Hu, B., Kikuchi, S., Chapard, C., Chen, W., Rajendra, E., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.022 · Cited by 187 · see citing works
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
Harris, H. L., Gu, H., Olshansky, M., Wang, A., Farabella, I., Eliaz, Y., Kalluchi, A., Krishna, A., Jacobs, M., Cauer, G., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38429-1 · Cited by 184 · see citing works
“In vitro studies have found that large chromatin complexes can impede looping factors 61,62 , and cohesin was shown to build up near transcriptionally active regions 63 .”
BackgroundA Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans
Tsai, P.-F., Dell’Orso, S., Rodriguez, J., Vivanco, K. O., Ko, K.-D., Jiang, K., Juan, A. H., Sarshad, A. A., Vian, L., Tran, M. D., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.008 · Cited by 178 · see citing works
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL
Wutz, G., Ladurner, R., Hilaire, B. G. S., Stocsits, R. R., Nagasaka, K., Pignard, B., Sanborn, A. L., Tang, W., Várnai, C., Ivanov, M. P., et al. (2020) · eLife · doi:10.7554/elife.52091 · Cited by 167 · see citing works
“as we had previously observed in primary Ctcf “knockout” MEFs arrested in G0 (Busslinger et al., 2017).”
BackgroundSelf-citationThiecke, M. J., Wutz, G., Muhar, M., Tang, W., Bevan, S., Malysheva, V., Stocsits, R., Neumann, T., Zuber, J., Fraser, P., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107929 · Cited by 177 · see citing works
Self-citationEnhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion
Zhang, S., Übelmesser, N., Barbieri, M., & Papantonis, A. (2023) · Nature Genetics · doi:10.1038/s41588-023-01364-4 · Cited by 165 · see citing works
“In addition, based on the documented co-association of cohesin subunits and RNAPII (Busslinger et al, 2017; Zhang et al., 2021), we introduced a weak interaction potential between cohesins and polymerases.”
BackgroundInfluentialWang, Q., Sun, Q., Czajkowsky, D. M., & Shao, Z. (2018) · Nature Communications · doi:10.1038/s41467-017-02526-9 · Cited by 166 · see citing works
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation
Liu, N. Q., Maresca, M., van den Brand, T., Braccioli, L., Schijns, M. M. G. A., Teunissen, H., Bruneau, B. G., Nora, E. P., & de Wit, E. (2021) · Nature Genetics · doi:10.1038/s41588-020-00744-4 · Cited by 162 · see citing works
Uyehara, C. M., & Apostolou, E. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112068 · Cited by 143 · see citing works
Kaaij, L. J. T., Mohn, F., van der Weide, R. H., de Wit, E., & Bühler, M. (2019) · Cell · doi:10.1016/j.cell.2019.08.007 · Cited by 133 · see citing works
Towards a unified Model of SMC Complex Function
Hassler, M., Shaltiel, I. A., & Haering, C. (2018) · Current Biology · doi:10.1016/j.cub.2018.08.034 · Cited by 162 · see citing works
Loop extrusion: theory meets single-molecule experiments
Banigan, E. J., & Mirny, L. A. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.04.011 · Cited by 160 · see citing works
MCM complexes are barriers that restrict cohesin-mediated loop extrusion
Dequeker, B. J. H., Scherr, M. J., Brandão, H. B., Gassler, J., Powell, S. T., Gáspár, I., Flyamer, I. M., Lalic, A., Tang, W., Stocsits, R. R., et al. (2022) · Nature · doi:10.1038/s41586-022-04730-0 · Cited by 149 · see citing works
Self-citationHuman T Cell Leukemia Virus Type 1: Persistence and Pathogenesis
Bangham, C. R. M. (2017) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042617-053222 · Cited by 147 · see citing works
Chromosome organization by one-sided and two-sided loop extrusion
Banigan, E. J., van den Berg, A. A., Brandão, H. B., Marko, J. F., & Mirny, L. A. (2020) · eLife · doi:10.7554/elife.53558 · Cited by 146 · see citing works
“Although current experimental evidence does not support preferential loading of cohesin at CTCF sites in mammals (Busslinger et al., 2017; Fudenberg et al., 2017; Nora et al., 2019, 2017; Parelho et al., 2008; Wendt et al., 2008) , such a mechanism of TAD, stripe, and dot formation is feasible and may be operational i…”
BackgroundInfluentialGuided nuclear exploration increases CTCF target search efficiency
Hansen, A. S., Amitai, A., Cattoglio, C., Tjian, R., & Darzacq, X. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0422-3 · Cited by 145 · see citing works
“The similar diffusion mechanisms are especially interesting in light of the fact that how and where cohesin is loaded onto the genome remains poorly understood (Busslinger et al., 2017).”
BackgroundRNA polymerases as moving barriers to condensin loop extrusion
Brandão, H. B., Paul, P., van den Berg, A. A., Rudner, D. Z., Wang, X., & Mirny, L. A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907009116 · Cited by 143 · see citing works
“This idea emerged from the observation that cohesin SMCs are enriched at sites of convergent transcription in yeast (50, 51) and in mammalian cells (35); this is further supported by other experiments demonstrating localization of cohesin mediated by transcription in cells (32) and in vitro (52).”
Developing in 3D: the role of CTCF in cell differentiation
Arzate‐Mejía, R. G., Targa, F. R., & Corces, V. G. (2018) · Development · doi:10.1242/dev.137729 · Cited by 139 · see citing works
“For example, inactivation of the Ctcf gene in primary mouse embryonic fibroblasts results in the mis-regulation of 698 genes (Busslinger et al., 2017), whereas similar experiments in post-mitotic embryonic and postnatal neurons results in changes in the expression of about 400 and 800 genes, respectively (Hirayama et…”
BackgroundThree-dimensional chromatin packing and positioning of plant genomes
Doğan, E. S., & Liu, C. (2018) · Nature Plants · doi:10.1038/s41477-018-0199-5 · Cited by 138 · see citing works
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III
Jiang, Y.-P., Huang, J., Lun, K., Li, B., Zheng, H., Li, Y.-J., Zhou, R., Duan, W.-J., Wang, C., Feng, Y.-Q., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-02067-3 · Cited by 31 · see citing works
“On the other hand, many studies have shown that transcription inhibition affects 3D genome structures and Cohesin [15, 16], which seems to conflict with our conclusion.”
SMC Complexes Can Traverse Physical Roadblocks Bigger Than Their Ring Size
Pradhan, B., Barth, R., Kim, E., Davidson, I. F., Bauer, B. W., van Laar, T., Yang, W., Ryu, J., van der Torre, J., Peters, J., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111491 · Cited by 131 · see citing works
Self-citationPrinciples of meiotic chromosome assembly revealed in S. cerevisiae
Schalbetter, S., Fudenberg, G., Baxter, J., Pollard, K., & Neale, M. (2019) · Nature Communications · doi:10.1038/s41467-019-12629-0 · Cited by 113 · see citing works
Nonequilibrium Chromosome Looping via Molecular Slip Links
Brackley, C. A., Johnson, J., Michieletto, D., Morozov, A. N., Nicodemi, M., Cook, P. R., & Marenduzzo, D. (2017) · Physical Review Letters · doi:10.1103/physrevlett.119.138101 · Cited by 128 · see citing works
“Experiments show that cohesin topologically links to DNA (with binding mediated by “loader proteins” [11, 16]), can slide along DNA or chromatin diffusively, and remains bound for τ ∼ 20 minutes before dissociating (a process mediated by “unloader proteins”) [16–21].”
BackgroundInfluentialAttenuated chromatin compartmentalization in meiosis and its maturation in sperm development
Alavattam, K. G., Maezawa, S., Sakashita, A., Khoury, H., Barski, A., Kaplan, N., & Namekawa, S. H. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0189-y · Cited by 136 · see citing works
The three-dimensional genome: regulating gene expression during pluripotency and development
Andrey, G., & Mundlos, S. (2017) · Development · doi:10.1242/dev.148304 · Cited by 129 · see citing works
“Moreover, two studies have shown that transcription can relocate cohesin over long distances and that its chromatin loading/ unloading rate controls the extension of chromatin loops (Busslinger et al., 2017; Haarhuis et al., 2017).”
BackgroundCTCF shapes chromatin structure and gene expression in health and disease
Dehingia, B., Milewska, M., Janowski, M., & Pękowska, A. (2022) · EMBO Reports · doi:10.15252/embr.202255146 · Cited by 128 · see citing works
“In the absence of CTCF, cohesins accumulate at sites of convergent transcription which might in principle lead to enhanced contact insulation and boundary formation (Busslinger et al , 2017).”
Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes
Fang, Z., Weng, C., Li, H., Tao, R., Mai, W., Liu, X., Lu, L., Lai, S., Duan, Q., Álvarez‐González, C. A., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.043 · Cited by 124 · see citing works
“In the mammalian genome, Nipbl mainly binds to promoters and enhancers, while the strongest peaks of cohesin are at intergenic CTCF sites (Busslinger et al., 2017; Kagey et al., 2010; Zuin et al., 2014).”
The chromosome folding problem and how cells solve it
Dekker, J., & Mirny, L. A. (2024) · Cell · doi:10.1016/j.cell.2024.10.026 · Cited by 112 · see citing works
The Mediator complex regulates enhancer-promoter interactions
Ramasamy, S., Aljahani, A., Karpińska, M. A., Cao, T. B. N., Velychko, T., Cruz, J., Lidschreiber, M., & Oudelaar, A. M. (2022) · bioRxiv · doi:10.1038/s41594-023-01027-2 · Cited by 104 · see citing works
MyoD is a 3D genome structure organizer for muscle cell identity
Wang, R.-C., Chen, F., Chen, Q., Wan, X., Shi, M.-L., Chen, A. K., Ma, Z., Li, G.-H., Wang, M., Ying, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27865-6 · Cited by 106 · see citing works
Pelham-Webb, B., Polyzos, A., Wojenski, L., Kloetgen, A., Li, J.-X., Giammartino, D. C. D., Sakellaropoulos, T., Tsirigos, A., Core, L., & Apostolou, E. (2021) · Molecules and Cells · doi:10.1016/j.molcel.2021.02.032 · Cited by 92 · see citing works
“However, since our experimental perturbations did not fully eliminate transcription, it is plausible that the remaining transcriptional activity promotes proper chromatin organization, in agreement with its previously instructive role in genome folding (Busslinger et al., 2017; Heinz et al., 2018; Hsieh et al., 2020;…”
BackgroundRowley, M. J., Lyu, X., Rana, V., Ando‐Kuri, M., Karns, R., Bosco, G., & Corces, V. G. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.116 · Cited by 114 · see citing works
CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning
Ba, Z., Lou, J., Ye, A. Y., Dai, H., Dring, E. W., Lin, S. G., Jain, S., Kyritsis, N., Kieffer-Kwon, K.-R., Casellas, R. C., et al. (2020) · Nature · doi:10.1038/s41586-020-2578-0 · Cited by 115 · see citing works
Organization of DNA in Mammalian Mitochondria
Farge, G., & Falkenberg, M. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20112770 · Cited by 118 · see citing works
“This structure folds into a chromatin fiber, which is further organized into chromatin loops by proteins such as cohesin and the CCCTC-binding factor (CTCF) [27].”
BackgroundLooping the Genome with SMC Complexes
Kim, E., Barth, R., & Dekker, C. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-032620-110506 · Cited by 96 · see citing works
“In particular, the notion that cohesin is found in islands be-tween two convergently oriented genes led to the idea that active transcription can push intragenic cohesin toward transcription termination sites ( Figure 6 d ) (126, 166).”
Absolute quantification of cohesin, CTCF and their regulators in human cells
Holzmann, J., Politi, A. Z., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., Dürnberger, G., Tang, W., Ladurner, R., et al. (2019) · eLife · doi:10.7554/elife.46269 · Cited by 109 · see citing works
“, 2016) and ChIP-seq studies in bacteria, yeast and mammalian cells have all revealed that cohesin/SMC enrichment sites can vary in their positions (Lengronne et al., 2004; Hu et al., 2015; Ocampo-Hafalla et al., 2016; Busslinger et al., 2017; Wang et al., 2017; Petela et al., 2018; Wang et al., 2018).”
BackgroundSelf-citationCTCF and R-loops are boundaries of cohesin-mediated DNA looping
Zhang, H., Shi, Z., Banigan, E. J., Kim, Y., Yu, H., Bai, X., & Finkelstein, I. J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.07.006 · Cited by 116 · see citing works
Emerging themes in cohesin cancer biology
Waldman, T. A. (2020) · Nature reviews. Cancer · doi:10.1038/s41568-020-0270-1 · Cited by 117 · see citing works
Barrington, C., Georgopoulou, D., Pezic, D., Varsally, W., Herrero, J., & Hadjur, S. (2019) · Nature Communications · doi:10.1038/s41467-019-10725-9 · Cited by 102 · see citing works
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis
Zhang, S., Übelmesser, N., Josipović, N., Forte, G., Slotman, J. A., Chiang, M., Gothe, H. J., Gusmao, E. G., Becker, C., Altmüller, J., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg8205 · Cited by 114 · see citing works
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open QuestionsPreprint
Mirny, L. A., & Dekker, J. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040147 · Cited by 102 · see citing works
Transcription-mediated supercoiling regulates genome folding and loop formation
Neguembor, M. V., Martin, L., Castells-García, Á., Gómez-García, P. A., Vicario, C., Carnevali, D., Abed, J. A., Granados, A., Sebastián-Pérez, R., Sottile, F., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.06.009 · Cited by 102 · see citing works
Transcription-factor-mediated supervision of global genome architecture maintains B cell identity
Johanson, T. M., Lun, A. T. L., Coughlan, H. D., Tan, T., Smyth, G. K., Nutt, S. L., & Allan, R. S. (2018) · Nature Immunology · doi:10.1038/s41590-018-0234-8 · Cited by 104 · see citing works
CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism
Hansen, A. S. (2020) · Nucleus · doi:10.1080/19491034.2020.1782024 · Cited by 101 · see citing works
“Consistent with this model, RNAi-mediated depletion of ESCO1 and CTCF both decreased cohesin’s residence time [38] and SMC3 acetylation [38,76].”
BackgroundRibosomal DNA and the nucleolus in the context of genome organization
Potapova, T., & Gerton, J. L. (2019) · Chromosome Research · doi:10.1007/s10577-018-9600-5 · Cited by 96 · see citing works
Mondal, G., Stevers, M., Goode, B., Ashworth, A., & Solomon, D. A. (2019) · Nature Communications · doi:10.1038/s41467-019-09659-z · Cited by 105 · see citing works
Scc2/Nipbl hops between chromosomal cohesin rings after loading
Rhodes, J., Mazza, D., Nasmyth, K., & Uphoff, S. (2017) · eLife · doi:10.7554/elife.30000 · Cited by 99 · see citing works
Loop extrusion mediates physiological Igh locus contraction for RAG scanning
Dai, H., Hu, H., Lou, J., Ye, A. Y., Ba, Z., Zhang, X., Zhang, Y., Zhao, L., Yoon, H. S., Chapdelaine-Williams, A. M., et al. (2021) · Nature · doi:10.1038/s41586-020-03121-7 · Cited by 96 · see citing works
Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners
Dauban, L., Montagne, R., Thierry, A., Lazar‐Stefanita, L., Bastié, N., Gadal, O., Cournac, A., Koszul, R., & Beckouët, F. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.019 · Cited by 104 · see citing works
CTCF: a Swiss-army knife for genome organization and transcription regulation
Braccioli, L., & de Wit, E. (2019) · Essays in Biochemistry · doi:10.1042/ebc20180069 · Cited by 101 · see citing works
A Brownian ratchet model for DNA loop extrusion by the cohesin complex
Higashi, T. L., Tang, M., Pobegalov, G. E., Uhlmann, F., & Molodtsov, M. I. (2021) · eLife · doi:10.7554/elife.67530 · Cited by 95 · see citing works
“plexes as they move along chromosomes during gene transcription (Lengronne et al., 2004; Davidson et al., 2016; Ocampo-Hafalla et al., 2016; Busslinger et al., 2017).”
BackgroundWang, X., Cui, W., & Peng, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx735 · Cited by 93 · see citing works
“However, recent research showed that transcription could contribute to the formation of chromatin domains by helping position another key architectural protein complex, cohesion (47).”
BackgroundKhoury, A., Achinger-Kawecka, J., Bert, S. A., Smith, G. C., French, H. J., Luu, P., Peters, T. J., Du, Q., Parry, A., Valdés‐Mora, F., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13753-7 · Cited by 90 · see citing works
New insights into genome folding by loop extrusion from inducible degron technologies
de Wit, E., & Nora, E. P. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00530-4 · Cited by 86 · see citing works
Casà, V., Gines, M. M., Gusmao, E. G., Slotman, J. A., Zirkel, A., Josipović, N., Oole, E., van IJcken, W. F. J., Houtsmuller, A. B., Papantonis, A., et al. (2020) · Genome Research · doi:10.1101/gr.253211.119 · Cited by 91 · see citing works
SMC Complexes: Universal DNA Looping Machines with Distinct Regulators
van Ruiten, M. S., & Rowland, B. D. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.03.003 · Cited by 85 · see citing works
The Birth of the 3D Genome during Early Embryonic Development
Hug, C. B., & Vaquerizas, J. M. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.09.002 · Cited by 86 · see citing works
LINE-1 transcription activates long-range gene expression
Li, X., Bie, L., Wang, Y., Hong, Y., Zhou, Z., Fan, Y., Yan, X., Tao, Y., Huang, C., Zhang, Y., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01789-5 · Cited by 91 · see citing works
The expanding phenotypes of cohesinopathies: one ring to rule them all!
Piché, J., Vliet, P. P. V., Pucéat, M., & Andelfinger, G. (2019) · Cell Cycle · doi:10.1080/15384101.2019.1658476 · Cited by 89 · see citing works
Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis
Lambing, C., Tock, A. J., Choi, K., Topp, S. D., Kuo, P. C., Blackwell, A. R., Zhao, X., Osman, K., Higgins, J. D., Franklin, F. C. H., et al. (2020) · The Plant Cell · doi:10.1105/tpc.19.00866 · Cited by 81 · see citing works
A Role for Chromatin Remodeling in Cohesin Loading onto Chromosomes
Muñoz, S., Minamino, M., Casas-Delucchi, C. S., Patel, H., & Uhlmann, F. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.027 · Cited by 88 · see citing works
“Along human chromosomes, the CCCTC-binding factor (CTCF) forms alternative cohesin retention sites (Busslinger et al., 2017; Davidson et al., 2016; Ocampo-Hafalla et al., 2016).”
BackgroundSpatial patterns of CTCF sites define the anatomy of TADs and their boundaries
Nanni, L., Ceri, S., & Logie, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02108-x · Cited by 88 · see citing works
“In human cells, Cohesin complexes only accumulate at RNA polymerase II polyadenylation sites when CTCF is absent [48].”
BackgroundKadota, S.-I., Ou, J.-H., Shi, Y., Lee, J. T., Sun, J., & Yildirim, E. (2020) · Nature Communications · doi:10.1038/s41467-020-16394-3 · Cited by 15 · see citing works
Establishing and dissolving cohesion during the vertebrate cell cycle
Morales, C., & Losada, A. (2018) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2018.01.010 · Cited by 80 · see citing works
Wu, Q., Guo, Y., Lu, Y., Li, J., Guo, Y., & Jia, Z. (2020) · Genome biology · doi:10.1186/s13059-020-01984-7 · Cited by 81 · see citing works
“CTCF mediates specific directional loop formation through asymmetric anchoring of the ring-shaped cohesin complex, which slides along chromatin fibers to actively extrude loops [3, 12, 18, 19, 33, 51] .”
BackgroundStructural basis for Scc3-dependent cohesin recruitment to chromatin
Li, Y., Muir, K., Bowler, M. W., Metz, J., Haering, C. H., & Panne, D. (2018) · eLife · doi:10.7554/elife.38356 · Cited by 84 · see citing works
“Whereas the essential role of cohesin in modulating genome architecture, gene expression and DNA damage repair is increasingly well established, comparatively little information is available concerning the molecular determinants of its association with chromatin (Busslinger et al., 2017; Haarhuis et al., 2017; Schwarz…”
BackgroundXiao, T., Li, X., & Felsenfeld, G. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023127118 · Cited by 83 · see citing works
Forces driving the three‐dimensional folding of eukaryotic genomes
Rada-Iglesias, Á., Grosveld, F. G., & Papantonis, A. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188214 · Cited by 81 · see citing works
“This possibility would also be in agreement with cohesin positioning being regulated by the very act of transcription (Busslinger et al , 2017) and its ensuing supercoiling (Racko et al , 2018), as well as by the increased mobility of genes and enhancers once they transition from an inactive to an…”
- Authors
- Busslinger, G. A., Stocsits, R. R., van der Lelij, P., Axelsson, E., Tedeschi, A., Galjart, N., & Peters, J.-M.
- Affiliations
- Research Institute of Molecular Pathology (AT)
- Erasmus MC (NL)
- Corresponding author
- Peters, Jan-Michael
- ORCID
- Venue
- Nature
- Published
- 2017-04
- Volume
- 544
- Issue
- 7651
- Pages
- 503-507
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6080695
- OpenAlex
- W2607008467
- Cited by
- 468
- References
- 51
- Citations by year
- 2026: 30 · 2025: 36 · 2024: 36 · 2023: 45 · 2022: 58 · 2021: 52 · 2020: 59 · 2019: 67 · 2018: 50 · 2017: 35
- FWCI
- 23.91
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- cohesin, CTCF, WAPL, transcription, cohesin loading, chromatin looping, topologically associating domains, 3D genome organization, transcription start sites, mouse genome, cis-interactions, gene expression regulation, recombination, mouse fibroblasts
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Animals, Binding Sites, Cells, Cultured, Chromatin, Chromosomal Proteins, Non-Histone, DNA, Female, Fibroblasts, Male, Proteins, Chondroitin Sulfate Proteoglycans, Repressor Proteins, Transcription, Genetic, Genome, Cell Cycle Proteins, Protein Transport, Transcription Initiation Site, Chromosomes, Mammalian, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
