The DOI matches its Crossref record; 49 of the 51 references it cites were found in a registry or an index.
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.
Overview
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
Verification
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?
In the citing paper
“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.
Citations
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
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
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
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
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
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
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
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
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
McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195
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
- Sambrook, J & Russell, D. W. Molecular Cloning: A Laboratory Manual Vol. 3, A9.25–A9.34 (Cold Spring Harbor Laboratory Press, 2001)
Cited by
Sorted by citations
Items 201–300 of 475
Imaging the dynamics of transcription loops in living chromosomes
Morgan, G. T. (2018) · Chromosoma · doi:10.1007/s00412-018-0667-8 · Cited by 25
“complexes shunting other molecular machines such as cohesin along a loop during divergent, bidirectional transcription (Busslinger et al. 2017).”
BackgroundEctopic expression of meiotic cohesin generates chromosome instability in cancer cell line
Boukaba, A., Liu, J., Ward, C., Wu, Q., Arnaoutov, A., Liang, J., Pugacheva, E. M., Dasso, M., Lobanenkov, V. V., Esteban, M. A., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2204071119 · Cited by 24
“G. Wutz et al., Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.”
BackgroundInfluentialŁaźniewski, M., Dawson, W., Rusek, A. M., & Plewczyński, D. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.08.003 · Cited by 24
“sister chromatids (for review, see [13]).”
BackgroundInfluentialPower-law behavior of transcriptional bursting regulated by enhancer–promoter communicationPreprint
Wang, Z., Zhang, Z., Luo, S., Zhou, T., & Zhang, J. (2024) · Genome Research · doi:10.1101/gr.278631.123 · Cited by 27
“For example, some experimental studies reported that transcription can affect chromatin structure (Busslinger et al. 2017; Heinz et al. 2018), and we can incorporate this feedback to our model by modifying the gene-state-dependent drift function V ( r , s ; t ) in Equation 1.”
MethodSAFB restricts contact domain boundaries associated with L1 chimeric transcription
Hong, Y., Bie, L., Zhang, T., Yan, X., Jin, G., Chen, Z., Wang, Y., Li, X., Pei, G., Zhang, Y., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.03.021 · Cited by 27
Brca2, Pds5 and Wapl differentially control cohesin chromosome association and function
Misulovin, Z., Pherson, M., Gause, M., & Dorsett, D. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007225 · Cited by 23
“Recent studies show that transcription, the CTCF architectural protein, and Wapl position cohesin in mammalian cells [49, 50].”
BackgroundResultInfluentialRelating SMCHD1 structure to its function in epigenetic silencing
Gurzau, A. D., Blewitt, M. E., Czabotar, P. E., Murphy, J. M., & Birkinshaw, R. W. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200242 · Cited by 24
Senescence: An Identity Crisis Originating from Deep Within the Nucleus
Olan, I., & Narita, M. (2022) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-013537 · Cited by 25
Morao, A. K., Kim, J., Obaji, D., Sun, S., & Ercan, S. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.10.002 · Cited by 24
Osmotic mechanism of the loop extrusion process.
Yamamoto, T., & Schiessel, H. (2017) · Physical Review E · doi:10.1103/physreve.96.030402 · Cited by 20
The transcriptional regulator CCCTC-binding factor limits oxidative stress in endothelial cells
Roy, A. R., Ahmed, A., DiStefano, P. V., Chi, L., Khyzha, N., Galjart, N., Wilson, M. D., Fish, J. E., & Delgado-Olguı́n, P. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.814699 · Cited by 24
Self-citationA tour of 3D genome with a focus on CTCF
Wang, D. C., Wang, W. Y., Zhang, L., & Wang, X. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.020 · Cited by 25
Cohesin supercoils DNA during loop extrusion
Davidson, I. F., Barth, R., Nagasaka, K., Tang, W., Wutz, G., Horn, S., Janissen, R., Stocsits, R. R., Chlosta, E., Bauer, B. W., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115856 · Cited by 24
Self-citationRNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes
Rivosecchi, J., Jost, D., Vachez, L., Gautier, F. D., Bernard, P., & Vanoosthuyse, V. (2021) · Life Science Alliance · doi:10.26508/lsa.202101046 · Cited by 20
“In eukaryotes, transcription is also a positioning device for the SMC complex cohesin in interphase (Lengronne et al, 2004; Bausch et al, 2007; Busslinger et al, 2017; Heinz et al, 2018), suggesting that transcription is a conserved regulator of SMC occupancy.”
Peripolli, S., Meneguello, L., Perrod, C., Singh, T., Patel, H., Rahman, S. T., Kiso, K., Thorpe, P. H., Calvanese, V., Bertoli, C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45955-z · Cited by 26
“Recent evidencecon fi rmed thatin mammalian cells, as previously reported in budding yeast 21 , cohesin rings are able to move along the DNA in a transcription-dependent manner 22 .”
BackgroundThe interplay between asymmetric and symmetric DNA loop extrusion
Banigan, E., & Mirny, L. (2020) · bioRxiv · doi:10.7554/elife.63528 · Cited by 19
“In particular, we previously showed that the physical principles underlying mitotic chromosome formation by loop extrusion are relevant for topologically associated domain (TAD) formation in interphase (Banigan et al., 2020), where extrusion by the SMC complex cohesin can be paused by barriers such as CTCF (Sanborn et…”
BackgroundInfluentialUniform dynamics of cohesin-mediated loop extrusion in living human cells
Sabaté, T., Lelandais, B., Robert, M.-C., Szalay, M., Tinevez, J.-Y., Bertrand, E., & Zimmer, C. (2025) · Nature Genetics · doi:10.1038/s41588-025-02406-9 · Cited by 32
“Likewise, other factors (for example, WAPL or STAG subunits) can potentially tune the loading and release rates of cohesin in vivo 33–36 .”
González-Almela, E., Castells-García, Á., Dily, F. L., Fernández, M., Carnevali, D., Cuscó, P., Croce, L. D., & Cosma, M. P. (2025) · Nature Communications · doi:10.1038/s41467-025-60534-6 · Cited by 24
Nakato, R., Sakata, T., Wang, J., Nagai, L. A. E., Nagaoka, Y., Oba, G. M., Bando, M., & Shirahige, K. (2023) · Nature Communications · doi:10.1038/s41467-023-41316-4 · Cited by 22
Active regulatory elements recruit cohesin to establish cell specific chromatin domains
Georgiades, E., Harrold, C., Roberts, N., Kassouf, M. T., Riva, S. G., Sanders, E., Downes, D., Francis, H. S., Blayney, J., Oudelaar, A. M., et al. (2023) · bioRxiv · doi:10.1038/s41598-025-96248-4 · Cited by 18
TAD-free analysis of architectural proteins and insulators
Mourad, R., & Cuvier, O. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1246 · Cited by 21
“Supporting this idea, recent results showed that cohesin is recruited at transcription start sites and positioned to CTCF sites by transcription-mediated translocation (56).”
ResultLarge-scale chromatin organisation in interphase, mitosis and meiosis
MacGregor, I. A., Adams, I. R., & Gilbert, N. (2019) · Biochemical Journal · doi:10.1042/bcj20180512 · Cited by 23
The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development
Li, F., An, Z., & Zhang, Z. (2019) · Cells · doi:10.3390/cells8080788 · Cited by 21
“In both yeast and mouse, transcription can relocate cohesin over long distances on DNA [53,54].”
BackgroundInfluentialCuadrado, A., Giménez-Llorente, D., Koninck, M. D., Ruiz‐Torres, M., Kojic, A., Rodríguez-Corsino, M., & Losada, A. (2022) · Epigenetics & Chromatin · doi:10.1186/s13072-022-00469-0 · Cited by 21
In silico discovery of repetitive elements as key sequence determinants of 3D genome folding
Gunsalus, L. M., Keiser, M. J., & Pollard, K. S. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100410 · Cited by 21
“31,32 To test this hypothesis, we evaluated all single-nucleotide mutations in the 300 bp on either side of the transcription start site (TSS) of the 1,789 highest expressed protein-coding genes in HFFc6 29 and compared disruption scores with expression level in regions where CTCF motifs are…”
MethodLoss of cohesin regulator PDS5A reveals repressive role of Polycomb loops
Bsteh, D., Moussa, H. F., Michlits, G., Yelagandula, R., Wang, J.-K., Elling, U., & Bell, O. (2021) · bioRxiv · doi:10.1038/s41467-023-43869-w · Cited by 19
4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction
Wang, Z., Luo, S., Zhang, Z., Zhou, T., & Zhang, J. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011722 · Cited by 23
Han, F., Miyagawa, Y., Verlengia, G., Ingusci, S., Soukupovà, M., Simonato, M., Glorioso, J. C., & Cohen, J. B. (2018) · Journal of Virology · doi:10.1128/jvi.00536-18 · Cited by 21
“Moreover, in concert with cohesin, CTCF mediates DNA looping to distal CTCF-binding sites (44, 45), suggesting the potential for various types of regulatory interactions among the CTCF-binding regions of HSV (46, 47).”
BackgroundChromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture
Sawyer, I. A., & Dundr, M. (2017) · Chromosoma · doi:10.1007/s00412-017-0632-y · Cited by 20
Matityahu, A., & Onn, I. (2021) · Journal of Cell Science · doi:10.1242/jcs.247577 · Cited by 22
The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks
van Schie, J. J. M., & de Lange, J. (2021) · Cells · doi:10.3390/cells10123455 · Cited by 22
CTCF and cellular heterogeneity
Ren, G., & Zhao, K. (2019) · Cell & Bioscience · doi:10.1186/s13578-019-0347-2 · Cited by 20
Genome organization via loop extrusion, insights from polymer physics models
Ghosh, S. K., & Jost, D. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz023 · Cited by 24
“Along this line, recent experiments showed that transcription may influence cohesin localization [108,109] or translocation [77, 103] but may also act as moving barriers against condensin progression [104].”
BackgroundComplementary chromosome folding by transcription factors and cohesinPreprint
Pereira, M. C. F., Brackley, C. A., Michieletto, D., Annunziatella, C., Bianco, S., Chiariello, A. M., Nicodemi, M., & Marenduzzo, D. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/305359 · Cited by 19
A functional overlap between actively transcribed genes and chromatin boundary elementsPreprint
Harrold, C. L., Gosden, M. E., Hanssen, L. L. P., Stolper, R. J., Downes, D. J., Telenius, J. M., Biggs, D., Preece, C., Alghadban, S., Sharpe, J. A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.01.182089 · Cited by 18
“can affect 3D genome structure independently of CTCF (36-38).”
BackgroundNoncoding RNA transcription at enhancers and genome folding in cancer
Isoda, T., Morio, T., & Takagi, M. (2019) · Cancer Science · doi:10.1111/cas.14107 · Cited by 19
TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene
Kabirova, E., Ryzhkova, A., Lukyanchikova, V., Khabarova, A. A., Korablev, A. N., Шнайдер, Т. А., Nuriddinov, M., Belokopytova, P. S., Smirnov, A. V., Хоцкин, Н. В., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48523-7 · Cited by 17
“Ef fi ciency of DNA digestion and ligation was assessed with gel electrophoresis.”
BackgroundInfluentialTranscriptional machinery as an architect of genome structure
Fursova, N. A., & Larson, D. R. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102920 · Cited by 18
DNA's secret weapon against knots and tangles
Dolgin, E. (2017) · Nature · doi:10.1038/544284a · Cited by 18
Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome
Papantonis, A., & Oudelaar, A. M. (2025) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120423-012301 · Cited by 19
The dynamic role of cohesin in maintaining human genome architecture
Agarwal, A., Korsak, S., Choudhury, A., & Plewczynski, D. M. (2023) · Bioessays · doi:10.1002/bies.202200240 · Cited by 13
Transcription induces context-dependent remodeling of chromatin architecture during differentiation
Chahar, S., Zouari, Y. B., Salari, H., Molitor, A. M., Kobi, D., Maroquenne, M., Erb, C., Mossler, A., Karasu, N., Jost, D., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002424 · Cited by 21
Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome
Magnitov, M. D., & de Wit, E. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102194 · Cited by 16
Cordero, J., Swaminathan, G., Rogel-Ayala, D. G., Rubio, K., Elsherbiny, A., Mahmood, S., Szymański, W., Graumann, J., Braun, T., Günther, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54740-x · Cited by 13
“Furthermore, a Venn diagram using the same data sets together with the data from a GRO-seq experiment 41 showed 3583 common loci (Fig.”
Arruda, N. L., Bryan, A. F., & Dowen, J. M. (2022) · Epigenetics & Chromatin · doi:10.1186/s13072-022-00463-6 · Cited by 17
“Depletion of CTCF strongly reduces SMC3ac, supporting the model that the CTCF–PDS5 interaction is important for SMC3 acetylation and stable cohesin residency [32, 43].”
BackgroundDefining a core configuration for human centromeres during mitosis
Gupta, A. S., Seidel, C. W., Tsuchiya, D., McKinney, S., Yu, Z., Smith, S. E., Unruh, J. R., & Gerton, J. L. (2023) · Nature Communications · doi:10.1038/s41467-023-42980-2 · Cited by 16
“The established workflow has potential to be used for further studies.”
A CTCF-dependent mechanism underlies the Hox timer: relation to a segmented body plan
Rekaik, H., & Duboule, D. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102160 · Cited by 16
“Concomitantly with the early activation, an enrichment of cohesin loading is observed over this CTCT-free segment, likely due to its transcriptional activity [12].”
Are SMC Complexes Loop Extruding Factors? Linking Theory With Fact
Baxter, J., Oliver, A. W., & Schalbetter, S. A. (2018) · BioEssays · doi:10.1002/bies.201800182 · Cited by 18
Understanding transcription across scales: From base pairs to chromosomes
Vos, S. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.002 · Cited by 18
Engineering three-dimensional genome folding
Zhang, D., Lam, J. C., & Blobel, G. A. (2021) · Nature Genetics · doi:10.1038/s41588-021-00860-9 · Cited by 17
Liu, Y., & Dekker, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.24.457555 · Cited by 16
Between form and function: the complexity of genome folding
Oudelaar, A. M., Hanssen, L. L. P., Hardison, R. C., Kassouf, M. T., Hughes, J. R., & Higgs, D. R. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx306 · Cited by 16
Schooley, A., Venev, S. V., Aksenova, V., Lehman, J. W., Navarrete, E., Pai, A. A., Dasso, M., & Dekker, J. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01828-1 · Cited by 20
“Furthermore, loop extrusion is blocked in a directional manner at CTCF-bound sites 9,19–21 and cohesin complexes are unloaded near the 3′ ends of active genes 16,22 .”
Dynamics of transcriptional enhancers and chromosome topology in gene regulation
Yokoshi, M., & Fukaya, T. (2019) · Development Growth & Differentiation · doi:10.1111/dgd.12597 · Cited by 14
“Also, in mammalian cells, formation of “cohesin islands” at 3′ ends of active genes was seen in CTCF/ Wapl double- knockout cells (Busslinger et al., 2017).”
BackgroundStructure-function relationships of SMC protein complexes for DNA loop extrusion
Lee, H., Noh, H., & Ryu, J. (2021) · Korean Society for Structural Biology · doi:10.34184/kssb.2021.9.1.1 · Cited by 15
“…of CCCTCbinding factor (CTCF)-binding sites (Dixon et al., 2012; Sofueva et al., 2013; de Wit et al., 2015; Guo et al., 2015; Holzmann et al., 2019; Busslinger et al., 2017; Wutz et al., 2017), and stable corner peaks at some TADs are observed at convergent CTCF sites, suggesting the cohesin…”
BackgroundLi, D., Mosbruger, T., Verma, D., & Swaminathan, S. (2019) · Journal of Virology · doi:10.1128/jvi.01279-19 · Cited by 15
Vanhaeren, T., Divina, F., García-Torres, M., Gómez-Vela, F., Vanhoof, W., & Martínez‐García, P. M. (2020) · Genes · doi:10.3390/genes11090985 · Cited by 15
Establishment of chromatin architecture interplays with embryo hypertranscription
Yu, G., Xu, K., Xia, W., Zhang, K., Xu, Q., Li, L., Lin, Z., Liu, L., Liu, B., Du, Z., et al. (2025) · Nature · doi:10.1038/s41586-025-09400-5 · Cited by 16
“RNA polymerase is thought to push cohesin or hinder it from sliding along chromatin 13,14,18,32 .”
A Cohesin Traffic Pattern Genetically Linked to Gene Regulation
Valton, A.-L., Dekker, J., Venev, S. V., Mair, B., Khokhar, E. S., Pai, A. A., & Moffat, J. (2021) · HAL · Cited by 18
Wang, J., Bando, M., Shirahige, K., & Nakato, R. (2022) · Nature Communications · doi:10.1038/s41467-022-30792-9 · Cited by 15
Unraveling quiescence-specific repressive chromatin domains
Swygert, S. G., & Tsukiyama, T. (2019) · Current Genetics · doi:10.1007/s00294-019-00985-9 · Cited by 15
Multi-Dimensional Gene Regulation in Innate and Adaptive Lymphocytes: A View From Regulomes
Fernando, N., Sciumè, G., O’Shea, J. J., & Shih, H. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.655590 · Cited by 14
Principles of Meiotic Chromosome AssemblyPreprint
Schalbetter, S., Fudenberg, G., Baxter, J., Pollard, K., & Neale, M. (2018) · bioRxiv · doi:10.1101/442038 · Cited by 16
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosisPreprint
Zhang, S., Übelmesser, N., Josipovic, N., Forte, G., Slotman, J., Chiang, M., Gothe, H., Gusmao, E., Becker, C., Altmuller, J., et al. (2020) · bioRxiv · doi:10.1101/2020.10.27.356915 · Cited by 105
“The latter effect is more perplexing, but agrees with NIPBL binding active gene promoters before cohesin does following mitotic exit (Zuin et al, 2014; Busslinger et al, 2017) – and, thus, raises three key questions.”
BackgroundA cohesin traffic pattern genetically linked to gene regulationPreprint
Valton, A.-L., Venev, S. V., Mair, B., Khokhar, E. S., Tong, A. H. Y., Ušaj, M., Chan, K. S. K., Pai, A. A., Moffat, J., & Dekker, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.29.454218 · Cited by 15
“Previous studies had shown that in cells depleted for CTCF and the cohesin unloading factor WAPL, cohesin accumulates at 3’ ends of active genes and especially at sites of convergent transcription (Busslinger et al., 2017).”
BackgroundInfluentialXu, Y., & Yang, L. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2023.1194865 · Cited by 16
“Generally, the nucleotide translocation might disrupt the transcription of itself or nearby genes by affecting the cis/trans-acting regulatory factors from the transcription units and consequently deleterious changes in the expression and protein level (89, 104).”
BackgroundThe α-globin super-enhancer acts in an orientation-dependent manner
Kassouf, M. T., Francis, H. S., Gosden, M. E., Suciu, M., Downes, D. J., Harrold, C. L., Larke, M., Oudelaar, A. M., Cornell, L., Blayney, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56380-1 · Cited by 13
High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion
Sept, C., Tak, Y. E., Goel, V. Y., Bhakta, M. S., Cerda-Smith, C. G., Hutchinson, H. M., Blanchette, M., Eyler, C. E., Johnstone, S. E., Joung, J. K., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57775-w · Cited by 17
Kim, M., Wang, P., Clow, P. A., Chien, E., Wang, X., Peng, J., Chai, H., Liu, X., Lee, B., Ngan, C. Y., et al. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01708-0 · Cited by 13
“Several studies hinted that cohesin may facilitate transcriptional activity by genome-wide correlation or by testing at a selected few loci 7,15,23,24,49,50 , but lack systematic evidence.”
Analysis of high-resolution 3D intrachromosomal interactions aided by Bayesian network modeling
Zhang, X., Branciamore, S., Gogoshin, G., Rodin, A. S., & Riggs, A. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620425114 · Cited by 12
“Very recently, while our manuscript was under review, Busslinger et al. (51) and Haarhuis et al. (52) reported that the distribution and directionality of movement of cohesin in the mouse genome is influenced by transcription.”
BackgroundPeltier, D., & Reddy, P. R. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01110 · Cited by 13
One ring to bind them – Cohesin’s interaction with chromatin fibers
Gines, M. M., van Staveren, T., & Wendt, K. S. (2019) · Essays in Biochemistry · doi:10.1042/ebc20180064 · Cited by 14
Cohesin as an essential disruptor of chromosome organization
Bird, A. P. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.010 · Cited by 13
Sun, T., Xu, Y., Angel, N., Chen, L., Zhang, K., Hoffman, B. D., Ou, J., Meng, Z., Varghese, S., & Diao, Y. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01770-2 · Cited by 12
Two CTCF motifs impede cohesin-mediated DNA loop extrusion
Barth, R., Janissen, R., Muras, L., van der Torre, J., Litos, G., van der Sluis, E. O., van den Berg, A., Davidson, I. F., Peters, J., & Dekker, C. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.11.001 · Cited by 14
Self-citationCohesin-Mediated Chromatin Interactions and Autoimmunity
Chandrasekaran, V., Oparina, N. Y., García-Bonete, M.-J., Wasén, C., Erlandsson, M. C., Malmhäll-Bah, E., Andersson, K., Jensen, M., Silfverswärd, S. T., Katona, G., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.840002 · Cited by 13
“CTCF is essential for the insulation activity of cohesin on chromatin (13).”
BackgroundInfluentialCostea, J., Schoeberl, U. E., Malzl, D., von der Linde, M., Fitz, J., Gupta, A., Makharova, M., Goloborodko, A. A., & Pavri, R. (2022) · Molecular Cell · doi:10.1016/j.molcel.2023.01.014 · Cited by 12
Alpsoy, A., Sood, S., & Dykhuizen, E. C. (2021) · Biology · doi:10.3390/biology10040272 · Cited by 13
“The motor for this movement might simply result from transcription-induced supercoiling [78,88], passive diffusion coupled with transcription [89], or other processive enzymes moving along the DNA during transcription [90].”
BackgroundCTCF supports preferentially short lamina-associated domains
Kaczmarczyk, L. S., Levi, N., Segal, T., Salmon‐Divon, M., & Gerlitz, G. (2022) · Chromosome Research · doi:10.1007/s10577-022-09686-5 · Cited by 12
“Since cohesin position is also determined by CTCF (Davidson et al. 2016; Busslinger et al. 2017; Racko et al. 2018), we decided to evaluate if CTCF importance for the LADs landscape is increased upon inhibition of RNA polymerase II.”
BackgroundJones, B. G., Sealy, R. E., Penkert, R. R., Surman, S. L., Birshtein, B. K., Xu, B., Neale, G. A. M., Maul, R. W., Gearhart, P. J., & Hurwitz, J. L. (2020) · Viral Immunology · doi:10.1089/vim.2019.0144 · Cited by 12
“In contrast, CCCTC-binding factor (CTCF) and the subunits of cohesin (SMC1, SMC3) (93) are preferentially bound farther downstream in the insulator region (6).”
RNA interactions with CTCF are essential for its proper functionPreprint
Saldaña-Meyer, R., Rodriguez-Hernaez, J., Nishana, M., Jácome-López, K., Nora, E. P., Bruneau, B. G., Furlan-Magaril, M., Skok, J. A., & Reinberg, D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/530014 · Cited by 12
“…a positive-feedback loop that contributes to the stability of gene expression programs” (Sigova et al., 2015) and 5) highly expressed genes can sometimes displace CTCF and push cohesin to intergenic CTCF sites where they can form chromatin loops (Busslinger et al., 2017; Heinz et al., 2018).”
BackgroundPDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes
Wutz, G., Davidson, I. F., Banigan, E. J., Stocsits, R. R., Kawasumi, R., Tang, W., Nagasaka, K., Costantino, L., Jansen, R., Hirota, K., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.025 · Cited by 12
Self-citationLocus folding mechanisms determine modes of antigen receptor gene assembly
Allyn, B. M., Hayer, K. E., Oyeniran, C., Nganga, V. K., Lee, K. D., Mishra, B., Saçan, A., Oltz, E. M., & Bassing, C. H. (2023) · The Journal of Experimental Medicine · doi:10.1084/jem.20230985 · Cited by 10
“Additional impediments to cohesin can anchor loops, including active transcription and chromatin-bound proteins other than CTCF (Busslinger et al., 2017; Jeppsson et al., 2022; Wutz et al., 2017; Zhang et al., 2019).”
BackgroundFrom compartments to loops: understanding the unique chromatin organization in neuronal cells
Zagirova, D., Kononkova, A. D., Vaulin, N., & Khrameeva, E. E. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00538-6 · Cited by 12
“These modifications are known to be associated with transcription start sites (TSSs), which are important sites for cohesin recruitment [32].”
BackgroundQi, S., Shi, Z., & Yu, H. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102310 · Cited by 13
Datta, S., Sherva, R., Cruz, M. D., Long, M. T., Roy, P., Backman, V., Chowdhury, S., & Roy, H. K. (2018) · Neoplasia · doi:10.1016/j.neo.2018.01.003 · Cited by 11
Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription controlPreprint
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. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/642959 · Cited by 11
Transcription Pause and Escape in Neurodevelopmental Disorders
Eigenhuis, K. N., Somsen, H. B., & van den Berg, D. L. C. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.846272 · Cited by 8
“Widespread NIPBL binding in the absence of cohesin was detected at active promoters and enhancers in mouse embryonic fibroblasts, neural progenitor cells, and lymphoblastoid cells (Zuin et al., 2014; Busslinger et al., 2017; van den Berg et al., 2017).”
BackgroundGenome folding dynamics during the M-to-G1-phase transition
Zhang, H., & Blobel, G. A. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102036 · Cited by 13
Genome Organization: Cohesin on the Move
Richterova, J., Huraiová, B., & Gregáň, J. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.05.002 · Cited by 10
“Busslinger et al. (2017) reveal that transcription moves cohesin along DNA to CTCF-binding sites, providing insights into how cohesin and CTCF mediate chromosomal interactions by formation of chromatin loops.”
BackgroundInfluentialUSP13 interacts with cohesin and regulates its ubiquitination in human cells
He, X., Kim, J.-S., Díaz-Martínez, L. A., Han, C., Lane, W. S., Budnik, B., & Waldman, T. A. (2021) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.015762 · Cited by 10
“Chromatin-associated proteins and total soluble proteins were prepared as described (30).”
BackgroundDysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host–virus interactions
Perez, S., Gevor, M., Davidovich, A., Kaspi, A., Yamin, K., Domovich, T., Meirson, T., Matityahu, A., Brody, Y., Stemmer, S. M., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz052 · Cited by 10
“In WAPL depleted MEF cells, cohesin relocalizes and accumulates at sites of convergent transcription (23,24).”
BackgroundCohesin positions the epigenetic reader Phf2 within the genome
Tang, W., Costantino, L., Stocsits, R. R., Wutz, G., Ladurner, R., Hudecz, O., Mechtler, K., & Peters, J. (2025) · The EMBO Journal · doi:10.1038/s44318-024-00348-2 · Cited by 9
“To test this hypothesis further, we performed Phf2 ChIP-seq experiments using MEFs depleted of either Wapl or of Wapl and CTCF, in which cohesin accumulates in different regions than in wild type cells (Busslinger et al, 2017; Tedeschi et al, 2013).”
InfluentialSelf-citationMetelova, M., Vigh, M. L., & Krietenstein, N. (2025) · Nature Communications · doi:10.1038/s41467-025-64350-w · Cited by 11
“Despite extensive evidence supporting the role of chromatin architectural proteins in E-P/P-P interactions 14,16,54,55 , recent high-resolution studies report minimal alterations in the E-P/P-P connectome following their depletion 2,22,48 .”
Under the magnifying glass: The ups and downs of rDNA copy number
Kindelay, S. M., & Maggert, K. A. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.05.006 · Cited by 11
RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin
Lebreton, J., Colin, L., Chatre, E., & Bernard, P. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113901 · Cited by 10
Cohesin — bridging the gap among gene transcription, genome stability, and human diseases
Nardo, M. D., & Musio, A. (2024) · FEBS Letters · doi:10.1002/1873-3468.14949 · Cited by 10
Zhou, Y., Jay, A., Burget, N. G., Friedrich, T., Yoon, S., Alsing, J., Nir, G., Grosschedl, R., Vahedi, G., & Faryabi, R. B. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01827-2 · Cited by 8
Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains
Yeo, S. J., Chen, Y., Fullwood, M. J., & Tergaonkar, V. (2023) · Trends in Genetics · doi:10.1016/j.tig.2022.12.003 · Cited by 7
Loop extrusion drives very different dynamics for Rouse chains in bulk solutions and at interfaces
Yamamoto, T., Sakaue, T., & Schießel, H. (2019) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/127/38002 · Cited by 8
Metadata
- 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
