{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T12:05:04Z","timestamp":1793189104430,"version":"4.5.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32570639"],"award-info":[{"award-number":["32570639"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82173052"],"award-info":[{"award-number":["82173052"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32402860"],"award-info":[{"award-number":["32402860"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81901421"],"award-info":[{"award-number":["81901421"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012620","name":"Taishan Scholar Foundation of Shandong Province","doi-asserted-by":"publisher","award":["NO.tstp20250753"],"award-info":[{"award-number":["NO.tstp20250753"]}],"id":[{"id":"10.13039\/100012620","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012620","name":"Taishan Scholar Foundation of Shandong Province","doi-asserted-by":"publisher","award":["NO.tstp20250755"],"award-info":[{"award-number":["NO.tstp20250755"]}],"id":[{"id":"10.13039\/100012620","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Gouvernement du Canada | Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["142246"],"award-info":[{"award-number":["142246"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Genet"],"published-print":{"date-parts":[[2026,8]]},"DOI":"10.1038\/s41588-026-02688-7","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T09:01:45Z","timestamp":1784192505000},"page":"1988-1999","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pioneer transcription factors direct tissue-specific cohesin chromatin entry and three-dimensional genome organization"],"prefix":"10.1038","volume":"58","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0326-686X","authenticated-orcid":false,"given":"Song","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianglin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianwei","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenzheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoran","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-6982-8484","authenticated-orcid":false,"given":"Dongqing","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianli","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7973-3930","authenticated-orcid":false,"given":"Jing","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunshan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2751-6413","authenticated-orcid":false,"given":"Haojie","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2825-2667","authenticated-orcid":false,"given":"Zhao","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2898-3363","authenticated-orcid":false,"given":"Housheng Hansen","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5503-6922","authenticated-orcid":false,"given":"Haiyang","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"key":"2688_CR1","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1016\/j.tcb.2021.03.005","volume":"31","author":"C Perea-Resa","year":"2021","unstructured":"Perea-Resa, C., Wattendorf, L., Marzouk, S. & Blower, M. D. Cohesin: behind dynamic genome topology and gene expression reprogramming. Trends Cell Biol. 31, 760\u2013773 (2021).","journal-title":"Trends Cell Biol."},{"key":"2688_CR2","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/S1097-2765(00)80420-7","volume":"5","author":"R Ciosk","year":"2000","unstructured":"Ciosk, R. et al. Cohesin\u2019s binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins. Mol. Cell 5, 243\u2013254 (2000).","journal-title":"Mol. Cell"},{"key":"2688_CR3","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1016\/j.cell.2006.09.040","volume":"127","author":"S Kueng","year":"2006","unstructured":"Kueng, S. et al. Wapl controls the dynamic association of cohesin with chromatin. Cell 127, 955\u2013967 (2006).","journal-title":"Cell"},{"key":"2688_CR4","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.15252\/embj.201798004","volume":"36","author":"G Wutz","year":"2017","unstructured":"Wutz, G. et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 36, 3573\u20133599 (2017).","journal-title":"EMBO J."},{"key":"2688_CR5","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/s41586-020-2151-x","volume":"583","author":"F Grubert","year":"2020","unstructured":"Grubert, F. et al. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 583, 737\u2013743 (2020).","journal-title":"Nature"},{"key":"2688_CR6","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/nature12867","volume":"505","author":"Y Murayama","year":"2014","unstructured":"Murayama, Y. & Uhlmann, F. Biochemical reconstitution of topological DNA binding by the cohesin ring. Nature 505, 367\u2013371 (2014).","journal-title":"Nature"},{"key":"2688_CR7","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1016\/j.molcel.2019.02.027","volume":"74","author":"S Munoz","year":"2019","unstructured":"Munoz, S., Minamino, M., Casas-Delucchi, C. S., Patel, H. & Uhlmann, F. A role for chromatin remodeling in cohesin loading onto chromosomes. Mol. Cell 74, 664\u2013673 (2019).","journal-title":"Mol. Cell"},{"key":"2688_CR8","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/nsmb.3228","volume":"23","author":"BN Devaiah","year":"2016","unstructured":"Devaiah, B. N. et al. BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat. Struct. Mol. Biol. 23, 540\u2013548 (2016).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2688_CR9","doi-asserted-by":"publisher","first-page":"1480","DOI":"10.1038\/s41588-021-00934-8","volume":"53","author":"R Linares-Saldana","year":"2021","unstructured":"Linares-Saldana, R. et al. BRD4 orchestrates genome folding to promote neural crest differentiation. Nat. Genet. 53, 1480\u20131492 (2021).","journal-title":"Nat. Genet."},{"key":"2688_CR10","doi-asserted-by":"publisher","first-page":"gkaf415","DOI":"10.1093\/nar\/gkaf415","volume":"53","author":"G Fettweis","year":"2025","unstructured":"Fettweis, G. et al. Transcription factors form a ternary complex with NIPBL\/MAU2 to localize cohesin at enhancers. Nucleic Acids Res. 53, gkaf415 (2025).","journal-title":"Nucleic Acids Res."},{"key":"2688_CR11","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1101\/gad.343475.120","volume":"35","author":"Y Zhu","year":"2021","unstructured":"Zhu, Y., Denholtz, M., Lu, H. & Murre, C. Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization. Genes Dev. 35, 65\u201381 (2021).","journal-title":"Genes Dev."},{"key":"2688_CR12","doi-asserted-by":"publisher","first-page":"eabj8360","DOI":"10.1126\/sciadv.abj8360","volume":"8","author":"L Rinaldi","year":"2022","unstructured":"Rinaldi, L. et al. The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation. Sci. Adv. 8, eabj8360 (2022).","journal-title":"Sci. Adv."},{"key":"2688_CR13","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1126\/science.aar7831","volume":"360","author":"M Ganji","year":"2018","unstructured":"Ganji, M. et al. Real-time imaging of DNA loop extrusion by condensin. Science 360, 102\u2013105 (2018).","journal-title":"Science"},{"key":"2688_CR14","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1126\/science.aaz4475","volume":"366","author":"Y Kim","year":"2019","unstructured":"Kim, Y., Shi, Z., Zhang, H., Finkelstein, I. J. & Yu, H. Human cohesin compacts DNA by loop extrusion. Science 366, 1345\u20131349 (2019).","journal-title":"Science"},{"key":"2688_CR15","doi-asserted-by":"publisher","first-page":"1338","DOI":"10.1126\/science.aaz3418","volume":"366","author":"IF Davidson","year":"2019","unstructured":"Davidson, I. F. et al. DNA loop extrusion by human cohesin. Science 366, 1338\u20131345 (2019).","journal-title":"Science"},{"key":"2688_CR16","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1016\/j.cell.2024.12.020","volume":"188","author":"R Barth","year":"2025","unstructured":"Barth, R. et al. SMC motor proteins extrude DNA asymmetrically and can switch directions. Cell 188, 749\u2013763 (2025).","journal-title":"Cell"},{"key":"2688_CR17","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/s41586-022-04730-0","volume":"606","author":"BJH Dequeker","year":"2022","unstructured":"Dequeker, B. J. H. et al. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature 606, 197\u2013203 (2022).","journal-title":"Nature"},{"key":"2688_CR18","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1038\/s41588-023-01364-4","volume":"55","author":"S Zhang","year":"2023","unstructured":"Zhang, S., Ubelmesser, N., Barbieri, M. & Papantonis, A. Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion. Nat. Genet. 55, 832\u2013840 (2023).","journal-title":"Nat. Genet."},{"key":"2688_CR19","doi-asserted-by":"publisher","first-page":"2856","DOI":"10.1016\/j.molcel.2023.07.006","volume":"83","author":"H Zhang","year":"2023","unstructured":"Zhang, H. et al. CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Mol. Cell 83, 2856\u20132871 (2023).","journal-title":"Mol. Cell"},{"key":"2688_CR20","doi-asserted-by":"publisher","first-page":"2316","DOI":"10.1016\/j.bpj.2020.10.014","volume":"119","author":"A Maji","year":"2020","unstructured":"Maji, A., Padinhateeri, R. & Mitra, M. K. The accidental ally: nucleosome barriers can accelerate cohesin-mediated loop formation in chromatin. Biophys. J. 119, 2316\u20132325 (2020).","journal-title":"Biophys. J."},{"key":"2688_CR21","doi-asserted-by":"publisher","first-page":"4788","DOI":"10.1016\/j.bpj.2022.10.044","volume":"121","author":"A Attou","year":"2022","unstructured":"Attou, A., Zulske, T. & Wedemann, G. Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions. Biophys. J. 121, 4788\u20134799 (2022).","journal-title":"Biophys. J."},{"key":"2688_CR22","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2210480120","volume":"120","author":"EJ Banigan","year":"2023","unstructured":"Banigan, E. J. et al. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proc. Natl Acad. Sci. USA 120, e2210480120 (2023).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2688_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18377-w","volume":"11","author":"B Nabet","year":"2020","unstructured":"Nabet, B. et al. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat. Commun. 11, 4687 (2020).","journal-title":"Nat. Commun."},{"key":"2688_CR24","doi-asserted-by":"publisher","first-page":"9742","DOI":"10.1073\/pnas.0910668107","volume":"107","author":"N Ahmadiyeh","year":"2010","unstructured":"Ahmadiyeh, N. et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc. Natl Acad. Sci. USA 107, 9742\u20139746 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2688_CR25","doi-asserted-by":"publisher","first-page":"2502","DOI":"10.1038\/nprot.2013.150","volume":"8","author":"S Wang","year":"2013","unstructured":"Wang, S. et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat. Protoc. 8, 2502\u20132515 (2013).","journal-title":"Nat. Protoc."},{"key":"2688_CR26","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1038\/s41586-019-1318-9","volume":"571","author":"EJ Adams","year":"2019","unstructured":"Adams, E. J. et al. FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes. Nature 571, 408\u2013412 (2019).","journal-title":"Nature"},{"key":"2688_CR27","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.ejca.2016.01.002","volume":"57","author":"D Obinata","year":"2016","unstructured":"Obinata, D. et al. Abhydrolase domain containing 2, an androgen target gene, promotes prostate cancer cell proliferation and migration. Eur. J. Cancer 57, 39\u201349 (2016).","journal-title":"Eur. J. Cancer"},{"key":"2688_CR28","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1038\/nature03649","volume":"435","author":"CS Lee","year":"2005","unstructured":"Lee, C. S., Friedman, J. R., Fulmer, J. T. & Kaestner, K. H. The initiation of liver development is dependent on Foxa transcription factors. Nature 435, 944\u2013947 (2005).","journal-title":"Nature"},{"key":"2688_CR29","doi-asserted-by":"publisher","first-page":"13809","DOI":"10.1074\/jbc.M414122200","volume":"280","author":"H Wan","year":"2005","unstructured":"Wan, H. et al. Compensatory roles of Foxa1 and Foxa2 during lung morphogenesis. J. Biol. Chem. 280, 13809\u201313816 (2005).","journal-title":"J. Biol. Chem."},{"key":"2688_CR30","doi-asserted-by":"publisher","first-page":"2052","DOI":"10.1053\/j.gastro.2009.08.059","volume":"137","author":"DZ Ye","year":"2009","unstructured":"Ye, D. Z. & Kaestner, K. H. Foxa1 and Foxa2 control the differentiation of goblet and enteroendocrine L- and D-cells in mice. Gastroenterology 137, 2052\u20132062 (2009).","journal-title":"Gastroenterology"},{"key":"2688_CR31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-37544-3","volume":"14","author":"Z Wei","year":"2023","unstructured":"Wei, Z. et al. MYC reshapes CTCF-mediated chromatin architecture in prostate cancer. Nat. Commun. 14, 1787 (2023).","journal-title":"Nat. Commun."},{"key":"2688_CR32","doi-asserted-by":"publisher","first-page":"100681","DOI":"10.1016\/j.xpro.2021.100681","volume":"2","author":"D Wu","year":"2021","unstructured":"Wu, D., Wang, L. & Huang, H. Protocol to apply spike-in ChIP\u2013seq to capture massive histone acetylation in human cells. STAR Protoc. 2, 100681 (2021).","journal-title":"STAR Protoc."},{"key":"2688_CR33","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"2688_CR34","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP\u2013seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"2688_CR35","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010).","journal-title":"Mol. Cell"},{"key":"2688_CR36","doi-asserted-by":"crossref","first-page":"D87","DOI":"10.1093\/nar\/gkaa516","volume":"48","author":"O Fornes","year":"2020","unstructured":"Fornes, O. et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, D87\u2013D92 (2020).","journal-title":"Nucleic Acids Res."},{"key":"2688_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/srep34962","volume":"6","author":"M Fournier","year":"2016","unstructured":"Fournier, M. et al. FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells. Sci. Rep. 6, 34962 (2016).","journal-title":"Sci. Rep."},{"key":"2688_CR38","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.cell.2017.09.026","volume":"171","author":"SSP Rao","year":"2017","unstructured":"Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171, 305\u2013320 (2017).","journal-title":"Cell"},{"key":"2688_CR39","doi-asserted-by":"publisher","DOI":"10.1038\/srep16803","volume":"5","author":"L Mannini","year":"2015","unstructured":"Mannini, L. et al. Mutant cohesin affects RNA polymerase II regulation in Cornelia de Lange syndrome. Sci. Rep. 5, 16803 (2015).","journal-title":"Sci. Rep."},{"key":"2688_CR40","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1534\/genetics.117.202291","volume":"207","author":"I Boudaoud","year":"2017","unstructured":"Boudaoud, I. et al. Connected gene communities underlie transcriptional changes in Cornelia de Lange syndrome. Genetics 207, 139\u2013151 (2017).","journal-title":"Genetics"},{"key":"2688_CR41","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1016\/j.molcel.2015.04.001","volume":"58","author":"C Estaras","year":"2015","unstructured":"Estaras, C., Benner, C. & Jones, K. A. SMADs and YAP compete to control elongation of beta-catenin:LEF-1-recruited RNAPII during hESC differentiation. Mol. Cell 58, 780\u2013793 (2015).","journal-title":"Mol. Cell"},{"key":"2688_CR42","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.1016\/j.cell.2014.11.013","volume":"159","author":"J Qian","year":"2014","unstructured":"Qian, J. et al. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell 159, 1524\u20131537 (2014).","journal-title":"Cell"},{"key":"2688_CR43","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"EP Consortium","year":"2012","unstructured":"Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57\u201374 (2012).","journal-title":"Nature"},{"key":"2688_CR44","doi-asserted-by":"publisher","first-page":"1735","DOI":"10.1158\/1055-9965.EPI-19-0066","volume":"28","author":"A Booms","year":"2019","unstructured":"Booms, A., Coetzee, G. A. & Pierce, S. E. MCF-7 as a model for functional analysis of breast cancer risk variants. Cancer Epidemiol. Biomarkers Prev. 28, 1735\u20131745 (2019).","journal-title":"Cancer Epidemiol. Biomarkers Prev."},{"key":"2688_CR45","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.molcel.2013.08.037","volume":"52","author":"J Gertz","year":"2013","unstructured":"Gertz, J. et al. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol. Cell 52, 25\u201336 (2013).","journal-title":"Mol. Cell"},{"key":"2688_CR46","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1016\/j.cell.2013.07.034","volume":"154","author":"J Yan","year":"2013","unstructured":"Yan, J. et al. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 154, 801\u2013813 (2013).","journal-title":"Cell"},{"key":"2688_CR47","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1016\/j.molcel.2018.07.012","volume":"71","author":"X Lyu","year":"2018","unstructured":"Lyu, X., Rowley, M. J. & Corces, V. G. Architectural proteins and pluripotency factors cooperate to orchestrate the transcriptional response of hESCs to temperature stress. Mol. Cell 71, 940\u2013955 (2018).","journal-title":"Mol. Cell"},{"key":"2688_CR48","doi-asserted-by":"publisher","first-page":"1336","DOI":"10.1038\/ng.3930","volume":"49","author":"KJ Kron","year":"2017","unstructured":"Kron, K. J. et al. TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer. Nat. Genet. 49, 1336\u20131345 (2017).","journal-title":"Nat. Genet."},{"key":"2688_CR49","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1038\/msb.2011.54","volume":"7","author":"J Rozowsky","year":"2011","unstructured":"Rozowsky, J. et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol. Syst. Biol. 7, 522 (2011).","journal-title":"Mol. Syst. Biol."},{"key":"2688_CR50","doi-asserted-by":"publisher","first-page":"1134","DOI":"10.1016\/j.molcel.2018.05.022","volume":"70","author":"NJ Petela","year":"2018","unstructured":"Petela, N. J. et al. Scc2 is a potent activator of cohesin\u2019s ATPase that promotes loading by binding Scc1 without Pds5. Mol. Cell 70, 1134\u20131148 (2018).","journal-title":"Mol. Cell"},{"key":"2688_CR51","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1101\/gr.243832.118","volume":"29","author":"M Pherson","year":"2019","unstructured":"Pherson, M., Misulovin, Z., Gause, M. & Dorsett, D. Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila. Genome Res. 29, 602\u2013612 (2019).","journal-title":"Genome Res."},{"key":"2688_CR52","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SS Rao","year":"2014","unstructured":"Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665\u20131680 (2014).","journal-title":"Cell"},{"key":"2688_CR53","doi-asserted-by":"publisher","first-page":"D882","DOI":"10.1093\/nar\/gkz1062","volume":"48","author":"Y Luo","year":"2020","unstructured":"Luo, Y. et al. New developments on the encyclopedia of DNA elements (ENCODE) data portal. Nucleic Acids Res. 48, D882\u2013D889 (2020).","journal-title":"Nucleic Acids Res."},{"key":"2688_CR54","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1016\/j.celrep.2015.02.004","volume":"10","author":"M Vietri Rudan","year":"2015","unstructured":"Vietri Rudan, M. et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 10, 1297\u20131309 (2015).","journal-title":"Cell Rep."},{"key":"2688_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-49684-1","volume":"15","author":"J Zhang","year":"2024","unstructured":"Zhang, J. et al. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment. Nat. Commun. 15, 5524 (2024).","journal-title":"Nat. Commun."},{"key":"2688_CR56","doi-asserted-by":"publisher","first-page":"5596","DOI":"10.1093\/nar\/gkae198","volume":"52","author":"M Puerto","year":"2024","unstructured":"Puerto, M. et al. The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization. Nucleic Acids Res. 52, 5596\u20135609 (2024).","journal-title":"Nucleic Acids Res."},{"key":"2688_CR57","doi-asserted-by":"publisher","first-page":"e59889","DOI":"10.7554\/eLife.59889","volume":"9","author":"L Costantino","year":"2020","unstructured":"Costantino, L., Hsieh, T. S., Lamothe, R., Darzacq, X. & Koshland, D. Cohesin residency determines chromatin loop patterns. Elife 9, e59889 (2020).","journal-title":"Elife"},{"key":"2688_CR58","doi-asserted-by":"publisher","unstructured":"Zhang, X., Jia, T., Wei, Z., He, H. H. & Guo, H. vhang072\/FOXA1_NIPBL_3D-genome custom code. Zenodo https:\/\/doi.org\/10.5281\/zenodo.20635221 (2026).","DOI":"10.5281\/zenodo.20635221"}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41588-026-02688-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-026-02688-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-026-02688-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T22:02:48Z","timestamp":1786053768000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41588-026-02688-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,16]]},"references-count":58,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8]]}},"alternative-id":["2688"],"URL":"https:\/\/doi.org\/10.1038\/s41588-026-02688-7","relation":{},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,16]]},"assertion":[{"value":"15 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}