The DOI matches its Crossref record; 96 of the 97 references it cites were found in a registry or an index.
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins
Open accessPublished version of a preprint
Abstract
Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Contacts between convergent CTCF binding sites are established by the extrusion of chromatin loops with cohesin [42,46,48,93].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [48]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Convergent binding sites for the versatile transcription factor CTCF (CCCTC-binding factor) located at TAD borders [46] block the movement of loop extruders [47,48,49].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [48]
In the citing paper
“The CTCF Y226A F228A mutation, like CTCF depletion, only slightly affects the contact probability profile.”
From The structural basis for cohesin–CTCF-anchored loops (2020) · cites this paper as [12]
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
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
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
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
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
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
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2016.07.002 · Cited by 3,860
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895
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
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
Cited by
Sorted by citations
Items 501–600 of 880
Regulation of cholesterol biosynthesis by CTCF and H3K27 methylation is critical for cell migration
Kaczmarczyk, L. S., Babele, D., Levi, N., Gunasekaran, G., Salmon‐Divon, M., & Gerlitz, G. (2024) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2024.151454 · Cited by 7
Replisomes restrict SMC translocation in vivo
Liao, Q., Brandão, H. B., Ren, Z., & Wang, X.-D. (2025) · Nature Communications · doi:10.1038/s41467-025-62596-y · Cited by 6
“10e, f, 11), further lowering the chance of SMCs bypassing the replisome in real life.”
Gene Clusters Reveal Fundamental Principles of Genome Folding and Transcriptional Regulation
Buckley, A. R., Vetralla, C., & Canzio, D. (2025) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-111822-122324 · Cited by 8
Chromatin organization and DNA damage
Minami, K., Iida, S., & Maeshima, K. (2022) · The Enzymes · doi:10.1016/bs.enz.2022.08.003 · Cited by 8
3C methods in cancer research: recent advances and future prospects
Yoon, I., Kim, U., Jung, K. O., Song, Y., Park, T., & Lee, D.-S. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01236-9 · Cited by 7
“It also contributes to maintaining the 3D architecture of interphase chromosomes 8,33,89 .”
Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology
Golov, A. K., & Gavrilov, A. A. (2024) · Biochemistry (Moscow) · doi:10.1134/s0006297924040023 · Cited by 9
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data
Patel, R. V., Pham, K., Chandrashekar, H., & Phillips‐Cremins, J. E. (2025) · Nature Methods · doi:10.1038/s41592-025-02688-1 · Cited by 8
The Cohesin Complex and Its Interplay with Non-Coding RNAs
Kuru-Schors, M., Hämmerle, M., & Gutschner, T. (2021) · Non-Coding RNA · doi:10.3390/ncrna7040067 · Cited by 7
Genetically induced redox stress occurs in a yeast model for Roberts syndrome
Mfarej, M. G., & Skibbens, R. V. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab426 · Cited by 7
“…registration various DNA elements (promoters, enhancers, and insulators) through which gene transcription is regulated (Kim et al. 2008; Rao et al. 2014; Banerji et al. 2016, 2017; Gassler et al. 2017; Wutz et al. 2017; Guo et al. 2018; Davidson et al. 2019; Kim et al. 2019; Golfier et al. 2020).”
BackgroundThe N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
Kamalyan, S., Kyrchanova, O., Klimenko, N. S., Babosha, V., Vasileva, Y., Belova, E., Фурсенко, Д. В., Maksimenko, O. G., & Georgiev, P. G. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00534-w · Cited by 7
“It is assumed that in mammals, chromatin loops are formed by cohesin complexes whose movement along the chromatin fiber is blocked at the most stable CTCF binding sites [11–17].”
BackgroundGenome Topology Control of Antigen Receptor Gene Assembly
Allyn, B. M., Lee, K. D., & Bassing, C. H. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1901356 · Cited by 6
“It has been proposed that CDs might stimulate gene expression by concentrating TFs, promoters, and enhancers within transcription factories (86).”
BackgroundInfluentialRovirosa, L., Ramos-Morales, A., & Javierre, B. M. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.592087 · Cited by 5
“Architectural proteins, including CTCF and cohesins, play an important role in establishing and maintaining chromatin loops (27,28), facilitating communication of gene promoters with some regulatory elements while reducing contacts with others (29-31).”
BackgroundWagner, T., Pérez‐Martínez, L., Schellhaas, R., Barrientos‐Moreno, M., Öztürk, M., Prado, F., Butter, F., & Luke, B. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008603 · Cited by 7
Petela, N. J., Gligoris, T. G., Metson, J., Lee, B., Voulgaris, M., Hu, B., Kikuchi, S., Chapard, C., Chen, W., Rajendra, E., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/205914 · Cited by 7
L1 and B1 repeats blueprint the spatial organization of chromatinPreprint
Lu, J. Y., Chang, L., Li, T., Wang, T., Yin, Y., Zhan, G., Zhang, K., Percharde, M., Wang, L., Peng, Q., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/802173 · Cited by 7
Systematic identification of cis-interacting lncRNAs and their targetsPreprint
Agrawal, S., Kulakovskiy, I. V., Severin, J., Koido, M., Alam, T., Abugessaisa, I., Buyan, A., Chang, H. Y., Dostie, J., Itoh, M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.13.426305 · Cited by 7
Rekaik, H., Lopez‐Delisle, L., Hintermann, A., Mascrez, B., Bochaton, C., & Duboule, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.29.505673 · Cited by 7
“Alternatively, the progression could be actively regulated by some CTCF cofactors such as MAZ, which was shown to contribute to CTCF insulation in the HoxA cluster (Ortabozkoyun et al., 2022) or by the WAPL binding partner PDS5 that also contributes to boundary function (Wutz et al., 2017).”
BackgroundTranscription-Driven Translocation of Cohesive and Non-Cohesive Cohesin In Vivo
Borrie, M. S., Kraycer, P. M., & Gartenberg, M. R. (2023) · Molecular and Cellular Biology · doi:10.1080/10985549.2023.2199660 · Cited by 6
“Both Eco1 and Wpl1 influence the size and distribution of chromosome loops in yeast, as do their homologs in higher eukaryotes.(7,8,29,30,31,58,59) Whereas Wpl1 restricts loop size by limiting the residence time and location of loop extruding complexes on DNA, Eco1 acts by limiting loop extruding activity via recruitm…”
BackgroundCohesin mutations and chromatin changes in cancer
Swett, A. D., & Tóthová, Z. (2025) · International Journal of Cancer · doi:10.1002/ijc.35378 · Cited by 7
“78,79 It is possible that cohesin may not directly regulate compartmentalization itself and may instead regulate proteins in the transcription complex 80 and histone modifications 81 that more directly influence this process.”
Xiang, J.-W., Lai, Y., & He, Z. (2025) · Research · doi:10.34133/research.0757 · Cited by 6
Dynamical properties of chromatin provide insights into key folding principles
Kadam, S., Sahoo, S., Kumar, P., & Padinhateeri, R. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2025.08.018 · Cited by 5
The mitotic STAG3–cohesin complex shapes male germline nucleome
Nagano, M., Hu, B., Ogata, K., Umemura, F., Ishikura, Y., Suzuki, S., Katsifis, C. C., Yoshinaga, M., Litos, G., Nagasaka, K., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01647-w · Cited by 6
Self-citationFine-scale 3D chromatin architectures and their regulatory mechanisms in plants
Xiao, S., Luo, L., Yang, M., He, H., & Zhou, Y. (2025) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2025.102786 · Cited by 8
Many faces of mammalian NSD methyltransferases
Tiukacheva, E. A., Vassetzky, Y. S., Razin, S. V., Fang, D., & Ulianov, S. V. (2026) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-025-00848-x · Cited by 7
“Compartments consist of TADs, self-interacting chromatin domains characterized by distinct transcriptional and epigenetic features [110].”
Condensin accelerates long-range intra-chromosomal interactions
Zou, F., Li, Y., Földes, T., Pinholt, H. D., Smith, C. B., Mirny, L. A., & Bai, L. (2026) · Nature Communications · doi:10.1038/s41467-026-70538-5 · Cited by 7
“By extruding DNA until stalling at CTCF binding sites, cohesin is thought to promote chromosomal contacts within the topologically associating domains (TADs) while reducing contacts across TAD boundaries in higher eukaryotes 9 .”
InfluentialShah, R., Tortora, M. M. C., Louafi, N., Rahmaninejad, H., Hansen, K. L., Anderson, E. C., Bonitto, K., Wen, D., Giorgetti, L., Fudenberg, G., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.037 · Cited by 27
Coßmann, J., Kos, P. I., Varamogianni‐Mamatsi, V., Assenheimer, D. S., Bischof, T. A., Kuhn, T., Vomhof, T., Papantonis, A., Giorgetti, L., & Gebhardt, J. C. M. (2025) · Nature Communications · doi:10.1038/s41467-025-56889-5 · Cited by 6
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00533-x · Cited by 6
Strasser, A. S., Gonzalez-Reiche, A. S., Zhou, X., Valdebenito‐Maturana, B., Ye, X., Zhang, B., Wu, M., van Bakel, H., & Jabs, E. W. (2024) · Nature Communications · doi:10.1038/s41467-024-51328-3 · Cited by 6
“…chromatids together until their separation during anaphase 30,31 ; for the extrusion of DNA loops that modulate genome organization and gene transcription 32 – 36 , and for facilitating the repair of double-strand DNA breaks by inducing genome-wide cohesion duringhomologousrecombination 37 – 41 .”
Phase Separation Mediated Sub-Nuclear Compartmentalization of Androgen Receptors
Yavuz, S., Abraham, T. E., Houtsmuller, A. B., & van Royen, M. E. (2024) · Cells · doi:10.3390/cells13201693 · Cited by 6
“High-resolution contact maps have shown that these highly conserved intrachromosomal interactions are separated by sharp genomic boundaries, referred to as topologically associated domains (TADs), that are held together by chromosome structuring complexes such as cohesin [75–77].”
BackgroundTransient promoter interactions modulate developmental gene activation
Mahara, S., Prüssing, S., Smialkovska, V., Krall, S., Holliman, S., Blum, B., Dachtler, V., Borgers, H., Sollier, E., Plass, C., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.10.005 · Cited by 9
Chromosomal localization of cohesin is differentially regulated by WIZ, WAPL, and G9a
Justice, M., Bryan, A. F., Limas, J. C., Cook, J. G., & Dowen, J. M. (2022) · BMC Genomics · doi:10.1186/s12864-022-08574-w · Cited by 6
“from the cohesin unloading factor WAPL WAPL was termed a cohesin unloader after the loss of WAPL was shown to increase the total levels of cohesin on chromatin [10, 12, 19].”
BackgroundRosa, C., Singh, P., Chen, P. B., Sinha, A., Claës, A., Preiser, P. R., Dedon, P. C., Baumgarten, S., Scherf, A., & Bryant, J. M. (2023) · EMBO Reports · doi:10.15252/embr.202357090 · Cited by 5
Li, G., Pu, P., Pan, M., Weng, X., Qiu, S., Li, Y., Abbas, S. J., Zou, L., Liu, K., Wang, Z., et al. (2023) · Frontiers of Medicine · doi:10.1007/s11684-023-1008-8 · Cited by 6
Nuclear position modulates long-range chromatin interactions
Finn, E. H., & Misteli, T. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010451 · Cited by 6
“Sequence-specific chromatin loops are generated by loop extrusion, in which the cohesin motor protein complex spools the chromatin fiber through its ring until it meets the boundary protein CTCF, and the cohesin complex stalls and stabilizes associations between two distal CTCF sites in the form of a loop (7-10).”
BackgroundMod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers
Takeuchi, C., Yokoshi, M., Kondo, S., Shibuya, A., Saito, K., Fukaya, T., Siomi, H., & Iwasaki, Y. W. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1034 · Cited by 6
“CTCF is necessary for enhancer-blocking and chromatin domain formation (Merkenschlager and Duncan, 2013; Rao et al., 2014), and most chromatin domain boundaries depend on CTCF and cohesin in vertebrates (Nora et al., 2017; Rao et al., 2017; Wutz et al., 2017).”
BackgroundEnhancers as regulators of antigen receptor loci three-dimensional chromatin structure
Barajas-Mora, E. M., & Feeney, A. J. (2019) · Transcription · doi:10.1080/21541264.2019.1699383 · Cited by 7
“However, complete removal of CTCF only mildly affected transcription genome-wide suggesting that CTCF only restricts or controls a subset of enhancer-promoter LRCIs [118,119].”
BackgroundA major role for Eco1 in regulating cohesin-mediated mitotic chromosome foldingPreprint
Dauban, L., Montagne, R., Thierry, A., Lazar‐Stefanita, L., Gadal, O., Cournac, A., Koszul, R., & Beckouët, F. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/589101 · Cited by 6
Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundariesPreprint
Islam, Z., Saravanan, B., Walavalkar, K., Thakur, J., Farooq, U., Singh, A. K., Sabarinathan, R., Pandit, A., Henikoff, S., & Notani, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.13.452118 · Cited by 7
Condensin I folds the C. elegans genomePreprint
Das, M., Semple, J. I., Haemmerli, A., Volodkina, V., Scotton, J., Gitchev, T., Annan, A., Campos, J., Statzer, C., Dakhovnik, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.14.495661 · Cited by 6
“In mammalian cells, cohesin is involved in interphase chromosome folding besides its role in mitosis (Wutz et al. 2017; Schwarzer et al. 2017; Rao et al. 2017).”
BackgroundInfluentialHan, R., Huang, Y., Robers, M., Magnitov, M. D., Vaandrager, I., Allahyar, A., Verstegen, M. J. A. M., Zhang, K., de Wit, E., de Laat, W. L., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.04.522689 · Cited by 6
Cohesin and CTCF do not assemble TADs inXenopussperm and male pronucleiPreprint
Jessberger, G., Várnai, C., Stocsits, R. R., Tang, W., Stary, G., & Peters, J. (2023) · Genome Research · doi:10.1101/gr.277865.123 · Cited by 6
“Chromatin compartmentalization does not depend on cohesin-mediated loop extrusion and, to the contrary, is partially suppressed by this process (Gassler et al. 2017; Rao et al. 2017; Schwarzer et al. 2017; Wutz et al. 2017).”
InfluentialSelf-citationTonelli, A., Cousin, P., Jankowski, A., Wang, B., Dorier, J., Barraud, J. F., Zunjarrao, S. S., & Gambetta, M. C. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.10.017 · Cited by 6
“13,14 19 In flies, IBPs such as CTCF, suppressor of Hairy wing [Su(Hw)], and boundary element-associated factor of 32 kDa (BEAF-32) bind specific DNA sequences and interact with Centrosomal protein 190 kDa (Cp190), an insulator cofactor.”
In vitro dynamics of DNA loop extrusion by structural maintenance of chromosomes complexes
Rutkauskas, M., & Kim, E. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102284 · Cited by 6
Regulation of somatic hypermutation by higher-order chromatin structure
Schoeberl, U. E., Fitz, J., von der Linde, M., Valieris, R., Bauer, B., Malzl, D., Froussios, K., Costea, J., Schmidt, F., Pflaum, J., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.06.003 · Cited by 5
RNA Pol II-based regulations of chromosome folding
Chapard, C., Bastié, N., Cournac, A., Chaptal, L., Mboumba, H., Queillé, S., Thierry, A., Gadal, O., Lengronne, A., Koszul, R., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100970 · Cited by 6
Cohesin regulation of genome organization in mature granule neurons in the mouse cerebellum
Parra, O. A. P., Zhao, Z., Yamada, T., & Yang, Y. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00625-2 · Cited by 6
“Notably, cohesin appears to suppress inter-TAD compartment interactions in proliferating cells [13, 21].”
Jia, L., Hou, Y., Cui, Z., Luo, X., Duan, J., Guo, J., You, B., Fang, Q., Wang, X., Shi, M., et al. (2025) · Neuron · doi:10.1016/j.neuron.2025.09.008 · Cited by 5
Unique territorial and compartmental organization of chromosomes in the holocentric silkworm
Gil, J., Navarrete, E., Hockens, C. B., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Banigan, E. J., Rosin, L. F., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00694-3 · Cited by 7
“Suppressing cohesin activity removes chromatin loops and thereby weakens TADs, while also strengthening compartments (Rao et al, 2017; Schwarzer et al, 2017; Gassler et al, 2017; Wutz et al, 2017).”
InfluentialCorticosteroid‐induced chromatin loop dynamics at the FKBP5 gene
Wang, C., Manders, F., Groh, L., Oldenkamp, R., & Logie, C. (2023) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15064 · Cited by 3
Zhu, T., Li, C., & Chu, X. (2024) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.4c02453 · Cited by 5
Wu, Y., Jia, Z., Ge, X., & Wu, Q. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1598-4 · Cited by 5
The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome
Li, G. (2020) · Science China Life Sciences · doi:10.1007/s11427-020-1723-y · Cited by 5
MEIOSIN directs initiation of meiosis and subsequent meiotic prophase program during spermatogenesis
Ishiguro, K., & Shimada, R. (2021) · Genes & Genetic Systems · doi:10.1266/ggs.21-00054 · Cited by 7
“It is known that mitotic cohesin establishes chromatin loops by cooperating with CTCF, and forms topologically associated domains (TADs) in mitotic interphase nuclei (Zuin et al., 2014; Ghirlando and Felsenfeld, 2016; Gassler et al., 2017; Haarhuis et al., 2017; Wutz et al., 2017).”
BackgroundChromosome organization through the cell cycle at a glance
Srinivasan, D., Shisode, T., Shrinet, J., & Fraser, P. (2022) · Journal of Cell Science · doi:10.1242/jcs.244004 · Cited by 6
Self-citationThe magic of unraveling genome architecture and function
Cosma, M. P., & Neguembor, M. V. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112361 · Cited by 7
The Mechanism, Regulation and Evolution of V(D)J Recombination
Schatz, D. G., Zhang, Y., Xiao, J., Zha, S., Zhang, Y., & Alt, F. W. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95895-0.00004-0 · Cited by 5
Godschalk, R., Faulk, C. D., LaRocca, J. L., van Benthem, J., & Marchetti, F. (2024) · Environmental and Molecular Mutagenesis · doi:10.1002/em.22626 · Cited by 8
“…2022; Marina et al., 2016; Shukla et al., 2011), nuclear architecture (Soujanya et al., 2023), and chromosomal three-dimension organization (Hsieh et al., 2020; Wutz et al., 2017), formation of heterochromatin or euchromatin with poised or active transcriptional activities (Macrae et al., 2023).”
Promotion of Hyperthermic-Induced rDNA Hypercondensation in Saccharomyces cerevisiae
Shen, D., & Skibbens, R. V. (2020) · Genetics · doi:10.1534/genetics.119.302994 · Cited by 5
Zanandrea, R., Wiprich, M. T., Altenhofen, S., Rübensam, G., dos Santos, T. M., Wyse, Â. T. D. S., & Bonan, C. D. (2021) · Amino Acids · doi:10.1007/s00726-021-03019-2 · Cited by 5
Loop Extrusion Mediates Physiological Locus Contraction for V(D)J RecombinationPreprint
Dai, H., Hu, H., Lou, J., Ye, A. Y., Chapdelaine-Williams, A. M., Kyritsis, N., Zhang, Y., Manfredonia, N., Judson, R., Chen, H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.30.181222 · Cited by 5
NIPBL and WAPL balance cohesin activity to regulate chromatin folding and gene expressionPreprint
Luppino, J. M., Field, A. R., Nguyen, S. C., Park, D. S., Shah, P. P., Lan, Y., Yunker, R., Jain, R., Adelman, K., & Joyce, E. F. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.19.488785 · Cited by 5
“Given that NIPBL and WAPL are opposing regulators of cohesin (18, 21, 29, 38), one prediction might be that each of their knockdowns would alter the same set of genes but in opposite directions.”
BackgroundCTCF blocks anti-sense transcription initiation at divergent gene promotersPreprint
Luan, J. Y., Syrett, C. M., Vermunt, M. W., Coté, A., Tome, J. M., Zhang, H., Huang, A., Luppino, J. M., Keller, C. A., Giardine, B. M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.30.465508 · Cited by 5
Chapard, C., Bastié, N., Cournac, A., Gadal, O., Koszul, R., & Beckouët, F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.29.573667 · Cited by 6
HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisationPreprint
Karagyozova, T., Gatto, A., Forest, A., Quivy, J., Marti-Renom, M., Mirny, L., & Almouzni, G. (2024) · bioRxiv · doi:10.1101/2024.08.27.609896 · Cited by 3
“Indeed, they are enriched at the borders of self-interacting domains (Dixon et al., 2012) and involved in their insulation (Nora et al., 2017; Wutz et al., 2017).”
BackgroundDo, C., Jiang, G., Cova, G., Zappile, P., Heguy, A., & Skok, J. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.02.620823 · Cited by 5
Cohesin guides homology search during DNA repair via loops and sister chromatid linkagesPreprint
Teloni, F., Takács, Z., Mitter, M., Langer, C. C. H., Prlesi, I., Steinacker, T. L., Reuter, V. P., Mylarshchikov, D. E., & Gerlich, D. W. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.10.637359 · Cited by 5
Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction
Nguyen, S. A., Sakata, T., Shirahige, K., & Sutani, T. (2025) · iScience · doi:10.1016/j.isci.2025.112322 · Cited by 6
Cohesin: an emerging master regulator at the heart of cardiac development
Mfarej, M. G., Hyland, C., Sanchez, A. C., Falk, M. M., Iovine, M. K., & Skibbens, R. V. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-12-0557 · Cited by 4
“…induced or repressed by chromatin-modifying complexes, producing spatially defined and unique transcriptional domains (Figure 2; Hansen, 2020; Rao et al., 2014; Merkenschlager and Nora, 2016; Wutz et al., 2017; Gassler et al., 2017; Rowley and Corces, 2018; Davidson et al., 2019; Kim et al., 2019).”
Yuan, T., Yan, H., Li, K., Surovtsev, I. V., King, M. C., & Mochrie, S. G. J. (2024) · Genome biology · doi:10.1186/s13059-024-03432-2 · Cited by 7
The synergy between compartmentalization and motorization in chromatin architecture
de Oliveira, R. J., Junior, A. B. D. O., Contessoto, V. G., & Onuchic, J. N. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0239634 · Cited by 4
Barrier effects on the kinetics of cohesin-mediated loop extrusion
Chen, L., Zhang, Z., Wang, Z., Hong, L., Wang, H., & Zhang, J. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2025.03.026 · Cited by 4
Yin, L., Zhang, Y., Zhang, B.-Q., Zhang, J., Xiong, M., Jiang, N., Xiao, J., Gao, H., Xiong, W., Wang, X., et al. (2025) · Advanced Science · doi:10.1002/advs.202506600 · Cited by 4
Tei, S., Bando, M., Sakata, T., Yoshimura, A., Natsume, T., Kanemaki, M. T., Sutani, T., & Shirahige, K. (2026) · Nature Communications · doi:10.1038/s41467-026-76738-3 · Cited by 4
Telomeric function and regulation during male meiosis in mice and humans
Yin, L., Jiang, N., Li, T., Zhang, Y., & Yuan, S. (2024) · Andrology · doi:10.1111/andr.13631 · Cited by 4
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription
Ding, T., Fu, S., Zhang, X., Yang, F., Zhang, J., Xu, H., Yang, J., Chen, C., Shi, Y., Bai, Y., et al. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae034 · Cited by 4
Singh, G., & Skibbens, R. V. (2024) · Genetics · doi:10.1093/genetics/iyae128 · Cited by 4
“2017; Wutz et al .”
Gomes, M. V., Landwerlin, P., Diebold, M.-L., Shaik, T. B., Durand, A., Troesch, E., Weber, C., Brillet, K., Lemée, M. V., Decroos, C., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114656 · Cited by 4
CTCF-RNA interactions orchestrate cell-specific chromatin loop organization
Lucero, K., Han, S., Huang, P., Qiu, X., Mazzoni, E. O., & Reinberg, D. (2025) · Science Advances · doi:10.1126/sciadv.ady5507 · Cited by 6
Yang, T., Huang, Z. J., Li, H., Wang, L., & Chen, Y. (2020) · Developmental Biology · doi:10.1016/j.ydbio.2020.07.003 · Cited by 4
Tang, R., Li, Y., Han, F., Li, Z., Lin, X., Sun, H., Zhang, X., Jiang, Q., Nie, H., & Li, Y. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2021.821495 · Cited by 4
“Cohesin was considered to appear on CTCF-binding sites and contribute to establishment of chromatin loops (21, 39, 46).”
BackgroundMamberti, S., Pabba, M. K., Rapp, A. W., Cardoso, M. C., & Scholz, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23073896 · Cited by 4
Irvin, E. M., & Wang, H. (2023) · DNA repair · doi:10.1016/j.dnarep.2023.103528 · Cited by 4
Viushkov, V. S., Lomov, N. A., & Rubtsov, M. A. (2024) · Cells · doi:10.3390/cells13171440 · Cited by 3
“This hypothesis has been confirmed using Hi-C on cells in which cohesin [33–35], CTCF [35,36], and the cohesin unloader factor WAPL were depleted [33,35,37].”
ResultRazin, S. V., Ulianov, S. V., & Gavrilov, A. A. (2019) · Molecular Biology · doi:10.1134/s0026893319060153 · Cited by 4
“The mean size of experimentally detectable loop contact domains increases upon depletion of the WAPL cohesion unloading factor [73].”
BackgroundChang, L., Li, M., Shao, S., Xue, B., Hou, Y., Zhang, Y., Li, R., Li, C., & Sun, Y. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/601849 · Cited by 4
Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecturePreprint
Cremer, M., Brandstetter, K., Maiser, A., Rao, S. S. P., Schmid, V. J., Mitra, N., Mamberti, S., Klein, K. N., Gilbert, D. M., Leonhardt, H., et al. (2019) · Open access LMU (Ludwid Maxmilian's Universitat Munchen) · doi:10.1101/816611 · Cited by 5
RNA surveillance controls 3D genome structure via stable cohesin-chromosome interactionPreprint
Chun, Y., Han, S., Kim, T., Choi, Y., & Lee, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.31.446489 · Cited by 4
Kohwi, Y., Wong, X., Grange, M., Sexton, T., Richards, H. W., Kitagawa, Y., Sakaguchi, S., Liang, Y., Chuong, C., Botchkarev, V. A., et al. (2025) · eLife · doi:10.7554/elife.105915 · Cited by 4
“Acute depletion of CTCF ( Nora et al., 2017 ), cohesin ( Rao et al., 2017 ; Wutz et al., 2017 ) or induced removal of cohesin loading factor NIPBL ( Schwarzer et al., 2017 ) results in a major loss of TADs.”
Loop Extrusion Accelerates Long-Range Enhancer-Promoter Searches in Living EmbryosPreprint
Choppakatla, P., Patel, A. L., Borjigin, T., Udomlumleart, T., Hu, J. H., Gregor, T., Boettiger, A. N., & Levine, M. S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.17.706355 · Cited by 6
“Prior studies in mammalian cells have shown that depletion of WAPL results in less cohesin unloading and longer loops 6,59 .”
RobusTAD: reference panel based annotation of nested topologically associating domains
Zhang, Y., Dali, R., & Blanchette, M. (2025) · Genome biology · doi:10.1186/s13059-025-03568-9 · Cited by 3
Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions
Smith, R. G., Fu, Y., Schiela, K. L., Dautle, M., Williams, R. A., Wilson, H. M., Azadegan, C., Whetstine, J. R., Dekker, J., & Liu, Y. (2026) · Nature Communications · doi:10.1038/s41467-026-75818-8 · Cited by 3
“Thederivative plotsrepresent signalsfromboth typesof cohesin-mediated loops 1,2,18,31,33 .”
Chromatin factor YY1 controls fetal hematopoietic stem cell migration and engraftment in mice
Saka, S., Lu, Z., Wang, Y., Liu, P., Singh, D. K., Lee, J. P., Palii, C. G., Alvarez, T. R., Assumpção, A. L. F. V., You, X., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci188140 · Cited by 3
“It colocalizes with chromatin structural regulators such as CCCTC-binding factor (CTCF) and cohesin to regulate long-range chromatin interactions, bringing enhancers and promoters into spatial proximity (22–26).”
Dimond, A., Gim, D. H., Ing‐Simmons, E., Whilding, C., Kramer, H., Djeghloul, D., Montoya, A., Patel, B., Cheriyamkunnel, S. J., Brown, K. E., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63740-4 · Cited by 5
Gene Doping Detection From the Perspective of 3D Genome
Ren, X., Shi, Y., Xiao, B., Su, X., Shi, H., He, G., Chen, P., Wu, D., & Shi, Y. Y. (2025) · Drug Testing and Analysis · doi:10.1002/dta.3850 · Cited by 3
Conformational asymmetry of replicated human chromosomes
Corsi, F., Kolesnikova, S., Steinacker, T. L., Takács, Z., Batty, P., Mitter, M., Gerlich, D. W., & Goloborodko, A. A. (2026) · Science · doi:10.1126/science.aea4611 · Cited by 3
Disorder of three‐dimensional chromosome structure plays a role in carcinogenesis
Zhang, L., Liu, F., Wu, L., Fu, S., Xing, L., Zhang, L., Wang, X., & Wang, Y.-X. (2021) · Clinical and Translational Discovery · doi:10.1002/ctd2.17 · Cited by 3
Osadská, M., Selicky, T., Kretová, M., Jurcik, J., Sivakova, B., Cipakova, I., & Cipak, L. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23073939 · Cited by 2
“Recently, it has been shown that WAPL and PDS5 also play roles in DNA replication, chromosome organization, gene expression, and DNA damage repair [75,76].”
BackgroundBuskirk, S. W., & Skibbens, R. V. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac157 · Cited by 3
“…roles played by Rad61/WAPL include dissociating cohesin from DNA during S phase and altering DNA extrusion loop lengths during G1 (Guacci and Koshland, 2012; Tedeschi et al., 2013; Lopez-Serra et al., 2013; Wutz et al., 2017; Haarhuis et al., 2017; Gassler et al., 2017; Bloom et al., 2018).”
BackgroundAcute Protein Depletion Strategies to Functionally Dissect the 3D Genome
Maresca, M., Liu, N. Q., & de Wit, E. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2497-5_15 · Cited by 3
Metadata
- Authors
- Wutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., Walther, N., Koch, B., Kueblbeck, M., Ellenberg, J., Zuber, J., Fraser, P., & Peters, J.
- Affiliations
- Research Institute of Molecular Pathology (AT)
- Babraham Institute (GB)
- European Molecular Biology Laboratory (DE)
- Florida State University (US)
- Corresponding author
- Peters, Jan‐Michael
- ORCID
- Venue
- The EMBO Journal
- Published
- 2017-12-07
- Volume
- 36
- Issue
- 24
- Pages
- 3573-3599
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC5730888
- OpenAlex
- W2775505403
- Cited by
- 864
- References
- 97
- Citations by year
- 2026: 83 · 2025: 77 · 2024: 102 · 2023: 97 · 2022: 119 · 2021: 127 · 2020: 112 · 2019: 87 · 2018: 49 · 2017: 11
- FWCI
- 29.61
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Funders
- Boehringer Ingelheim
- Austrian Research Promotion Agency (FFG‐834223)
- UK Biotechnology and Biological Sciences Research Council (BB/J004480/1)
- European Research Council Advanced Grant (DEVOCHROMO)
- EMBO Long Term Fellowship (ALTF 1335‐2016)
- Austrian Science Fund (SFB F34, Z196‐B20)
- Human Frontier Science Program (LT001527/2017)
- 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
- topologically associating domains, chromatin looping, cohesin, CTCF, WAPL, Pds5, loop extrusion, chromatin compartments, long-range chromatin interactions, chromosome condensation, vermicelli, 3D genome organization
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Carrier Proteins, Chromatin, Chromosomal Proteins, Non-Histone, Chromosomes, DNA-Binding Proteins, HeLa Cells, Humans, Nuclear Proteins, Proto-Oncogene Proteins, Transcription Factors, Genome, Human, Cell Cycle Proteins
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
