{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T01:32:13Z","timestamp":1787794333715,"version":"build-2784847793"},"reference-count":67,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T00:00:00Z","timestamp":1740096000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T00:00:00Z","timestamp":1740096000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Struct Mol Biol"],"published-print":{"date-parts":[[2025,6]]},"DOI":"10.1038\/s41594-024-01465-6","type":"journal-article","created":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T05:13:27Z","timestamp":1740114807000},"page":"1069-1080","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["CTCF\/RAD21 organize the ground state of chromatin\u2013nuclear speckle association"],"prefix":"10.1038","volume":"32","author":[{"given":"Ruofan","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelby","family":"Roseman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allison P.","family":"Siegenfeld","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1905-8686","authenticated-orcid":false,"given":"Zachary","family":"Gardner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2187-1027","authenticated-orcid":false,"given":"Son C.","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khoa A.","family":"Tran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric F.","family":"Joyce","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajan","family":"Jain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian B.","family":"Liau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian D.","family":"Krantz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6418-6615","authenticated-orcid":false,"given":"Katherine A.","family":"Alexander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5398-4400","authenticated-orcid":false,"given":"Shelley L.","family":"Berger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,2,21]]},"reference":[{"key":"1465_CR1","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1016\/j.cell.2018.05.024","volume":"174","author":"SA Quinodoz","year":"2018","unstructured":"Quinodoz, S. A. et al. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744\u2013757.e24 (2018).","journal-title":"Cell"},{"key":"1465_CR2","doi-asserted-by":"publisher","first-page":"976","DOI":"10.3390\/biology2030976","volume":"2","author":"M Morimoto","year":"2013","unstructured":"Morimoto, M. & Boerkoel, C. F. The role of nuclear bodies in gene expression and disease. Biology 2, 976\u20131033 (2013).","journal-title":"Biology"},{"key":"1465_CR3","doi-asserted-by":"publisher","first-page":"a000646","DOI":"10.1101\/cshperspect.a000646","volume":"3","author":"DL Spector","year":"2011","unstructured":"Spector, D. L. & Lamond, A. I. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 3, a000646 (2011).","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"1465_CR4","doi-asserted-by":"publisher","first-page":"16069","DOI":"10.1038\/nmicrobiol.2016.69","volume":"1","author":"A Mor","year":"2016","unstructured":"Mor, A. et al. Influenza virus mRNA trafficking through host nuclear speckles. Nat. Microbiol. 1, 16069 (2016).","journal-title":"Nat. Microbiol."},{"key":"1465_CR5","doi-asserted-by":"publisher","first-page":"e201904046","DOI":"10.1083\/jcb.201904046","volume":"219","author":"J Kim","year":"2019","unstructured":"Kim, J., Venkata, N. C., Gonzalez, G. A. H., Khanna, N. & Belmont, A. S. Gene expression amplification by nuclear speckle association. J. Cell Biol. 219, e201904046 (2019).","journal-title":"J. Cell Biol."},{"key":"1465_CR6","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1083\/jcb.200803174","volume":"182","author":"JM Brown","year":"2008","unstructured":"Brown, J. M. et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell Biol. 182, 1083\u20131097 (2008).","journal-title":"J. Cell Biol."},{"key":"1465_CR7","doi-asserted-by":"publisher","first-page":"1666","DOI":"10.1016\/j.molcel.2021.03.006","volume":"81","author":"KA Alexander","year":"2021","unstructured":"Alexander, K. A. et al. p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol. Cell 81, 1666\u20131681.e6 (2021).","journal-title":"Mol. Cell"},{"key":"1465_CR8","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1038\/s41586-024-07429-6","volume":"629","author":"P Bhat","year":"2024","unstructured":"Bhat, P. et al. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature 629, 1165\u20131173 (2024).","journal-title":"Nature"},{"key":"1465_CR9","doi-asserted-by":"publisher","first-page":"4025","DOI":"10.1083\/jcb.201807108","volume":"217","author":"Y Chen","year":"2018","unstructured":"Chen, Y. et al. Mapping 3D genome organization relative to nuclear compartments using TSA-seq as a cytological ruler. J. Cell Biol. 217, 4025\u20134048 (2018).","journal-title":"J. Cell Biol."},{"key":"1465_CR10","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1101\/gr.266239.120","volume":"31","author":"L Zhang","year":"2021","unstructured":"Zhang, L. et al. TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. Genome Res. 31, 251\u2013264 (2021).","journal-title":"Genome Res."},{"key":"1465_CR11","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02253-3","volume":"22","author":"Y Wang","year":"2021","unstructured":"Wang, Y. et al. SPIN reveals genome-wide landscape of nuclear compartmentalization. Genome Biol. 22, 36 (2021).","journal-title":"Genome Biol."},{"key":"1465_CR12","doi-asserted-by":"publisher","unstructured":"Roseman, S. A. et al. DNA methylation insulates genic regions from CTCF loops near nuclear speckles. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.07.26.550645 (2024).","DOI":"10.1101\/2023.07.26.550645"},{"key":"1465_CR13","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1038\/s41586-019-1910-z","volume":"578","author":"Y Li","year":"2020","unstructured":"Li, Y. et al. The structural basis for cohesin\u2013CTCF-anchored loops. Nature 578, 472\u2013476 (2020).","journal-title":"Nature"},{"key":"1465_CR14","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nature12644","volume":"503","author":"F Jin","year":"2013","unstructured":"Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290\u2013294 (2013).","journal-title":"Nature"},{"key":"1465_CR15","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/bioinformatics\/btv562","volume":"32","author":"B Gel","year":"2016","unstructured":"Gel, B. et al. regioneR: an R\/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics 32, 289\u2013291 (2016).","journal-title":"Bioinformatics"},{"key":"1465_CR16","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1016\/j.cell.2017.11.008","volume":"171","author":"AS Weintraub","year":"2017","unstructured":"Weintraub, A. S. et al. YY1 is a structural regulator of enhancer\u2013promoter loops. Cell 171, 1573\u20131588.e28 (2017).","journal-title":"Cell"},{"key":"1465_CR17","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/cdd.2017.174","volume":"25","author":"KD Sullivan","year":"2018","unstructured":"Sullivan, K. D., Galbraith, M. D., Andrysik, Z. & Espinosa, J. M. Mechanisms of transcriptional regulation by p53. Cell Death Differ. 25, 133\u2013143 (2018).","journal-title":"Cell Death Differ."},{"key":"1465_CR18","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1016\/S0955-0674(97)80068-3","volume":"9","author":"M Karin","year":"1997","unstructured":"Karin, M., Liu, Z. & Zandi, E. AP-1 function and regulation. Curr. Opin. Cell Biol. 9, 240\u2013246 (1997).","journal-title":"Curr. Opin. Cell Biol."},{"key":"1465_CR19","doi-asserted-by":"publisher","first-page":"e60579","DOI":"10.7554\/eLife.60579","volume":"9","author":"\u0130A Ilik","year":"2020","unstructured":"Ilik, \u0130. A. et al. SON and SRRM2 are essential for nuclear speckle formation. eLife 9, e60579 (2020).","journal-title":"eLife"},{"key":"1465_CR20","doi-asserted-by":"publisher","unstructured":"Alexander, K. A. et al. Nuclear speckles regulate functional programs in cancer. Nat. Cell Biol. https:\/\/doi.org\/10.1038\/s41556-024-01570-0 (2025).","DOI":"10.1038\/s41556-024-01570-0"},{"key":"1465_CR21","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1038\/s41593-021-00879-5","volume":"24","author":"SH Ahanger","year":"2021","unstructured":"Ahanger, S. H. et al. Distinct nuclear compartment-associated genome architecture in the developing mammalian brain. Nat. Neurosci. 24, 1235\u20131242 (2021).","journal-title":"Nat. Neurosci."},{"key":"1465_CR22","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1016\/j.cell.2020.07.032","volume":"182","author":"J-H Su","year":"2020","unstructured":"Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B. & Zhuang, X. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell 182, 1641\u20131659.e26 (2020).","journal-title":"Cell"},{"key":"1465_CR23","doi-asserted-by":"publisher","first-page":"14.23.1","DOI":"10.1002\/0471142727.mb1423s105","volume":"105","author":"BJ Beliveau","year":"2014","unstructured":"Beliveau, B. J., Apostolopoulos, N. & Wu, C. Visualizing genomes with oligopaint FISH probes. Curr. Protoc. Mol. Biol. 105, 14.23.1\u201314.23.20 (2014).","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"1465_CR24","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":"1465_CR25","doi-asserted-by":"publisher","first-page":"2020","DOI":"10.1073\/pnas.1911708117","volume":"117","author":"EM Pugacheva","year":"2020","unstructured":"Pugacheva, E. M. et al. CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention. Proc. Natl Acad. Sci. USA 117, 2020\u20132031 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1465_CR26","doi-asserted-by":"publisher","unstructured":"Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R. & Darzacq, X. CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife https:\/\/doi.org\/10.7554\/eLife.25776 (2017).","DOI":"10.7554\/eLife.25776"},{"key":"1465_CR27","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1126\/science.1256904","volume":"346","author":"PJ Huis in \u2018t Veld","year":"2014","unstructured":"Huis in \u2018t Veld, P. J. et al. Characterization of a DNA exit gate in the human cohesin ring. Science 346, 968\u2013972 (2014).","journal-title":"Science"},{"key":"1465_CR28","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28377-7","volume":"13","author":"JHI Haarhuis","year":"2022","unstructured":"Haarhuis, J. H. I. et al. A Mediator\u2013cohesin axis controls heterochromatin domain formation. Nat. Commun. 13, 754 (2022).","journal-title":"Nat. Commun."},{"key":"1465_CR29","doi-asserted-by":"publisher","first-page":"144966","DOI":"10.1016\/j.gene.2020.144966","volume":"758","author":"H Cheng","year":"2020","unstructured":"Cheng, H., Zhang, N. & Pati, D. Cohesin subunit RAD21: from biology to disease. Gene 758, 144966 (2020).","journal-title":"Gene"},{"key":"1465_CR30","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1038\/s41586-023-06340-w","volume":"620","author":"DS Park","year":"2023","unstructured":"Park, D. S. et al. High-throughput Oligopaint screen identifies druggable 3D genome regulators. Nature 620, 209\u2013217 (2023).","journal-title":"Nature"},{"key":"1465_CR31","doi-asserted-by":"publisher","first-page":"5924","DOI":"10.1128\/MCB.00560-08","volume":"28","author":"A Zhou","year":"2008","unstructured":"Zhou, A., Ou, A. C., Cho, A., Benz, E. J. & Huang, S.-C. Novel splicing factor RBM25 modulates Bcl-x pre-mRNA 5\u2032 splice site selection. Mol. Cell. Biol. 28, 5924\u20135936 (2008).","journal-title":"Mol. Cell. Biol."},{"key":"1465_CR32","doi-asserted-by":"publisher","first-page":"5775","DOI":"10.1016\/j.cell.2021.10.014","volume":"184","author":"SA Quinodoz","year":"2021","unstructured":"Quinodoz, S. A. et al. RNA promotes the formation of spatial compartments in the nucleus. Cell 184, 5775\u20135790.e30 (2021).","journal-title":"Cell"},{"key":"1465_CR33","doi-asserted-by":"publisher","first-page":"1937","DOI":"10.1161\/CIRCULATIONAHA.118.036726","volume":"139","author":"DP Lee","year":"2019","unstructured":"Lee, D. P. et al. Robust CTCF-based chromatin architecture underpins epigenetic changes in the heart failure stress\u2013gene response. Circulation 139, 1937\u20131956 (2019).","journal-title":"Circulation"},{"key":"1465_CR34","doi-asserted-by":"publisher","first-page":"1670","DOI":"10.1111\/febs.16362","volume":"290","author":"JA Horsfield","year":"2023","unstructured":"Horsfield, J. A. Full circle: a brief history of cohesin and the regulation of gene expression. FEBS J. 290, 1670\u20131687 (2023).","journal-title":"FEBS J."},{"key":"1465_CR35","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1038\/s41590-018-0184-1","volume":"19","author":"S Cuartero","year":"2018","unstructured":"Cuartero, S. et al. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat. Immunol. 19, 932\u2013941 (2018).","journal-title":"Nat. Immunol."},{"key":"1465_CR36","doi-asserted-by":"publisher","first-page":"e34915","DOI":"10.1371\/journal.pone.0034915","volume":"7","author":"JM Moore","year":"2012","unstructured":"Moore, J. M. et al. Loss of maternal CTCF is associated with peri-implantation lethality of Ctcf null embryos. PLoS ONE 7, e34915 (2012).","journal-title":"PLoS ONE"},{"key":"1465_CR37","doi-asserted-by":"publisher","first-page":"e1006985","DOI":"10.1371\/journal.pgen.1006985","volume":"13","author":"M Gomez-Velazquez","year":"2017","unstructured":"Gomez-Velazquez, M. et al. CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart. PLoS Genet. 13, e1006985 (2017).","journal-title":"PLoS Genet."},{"key":"1465_CR38","doi-asserted-by":"publisher","first-page":"6605","DOI":"10.1093\/nar\/20.24.6605","volume":"20","author":"RP Birkenbihl","year":"1992","unstructured":"Birkenbihl, R. P. & Subramani, S. Cloning and characterization of rad21 an essential gene of Schizosaccharomyces pombe involved in DNA double-strand-break repair. Nucleic Acids Res. 20, 6605\u20136611 (1992).","journal-title":"Nucleic Acids Res."},{"key":"1465_CR39","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.e24 (2017).","journal-title":"Cell"},{"key":"1465_CR40","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1016\/j.cell.2017.05.004","volume":"169","author":"EP Nora","year":"2017","unstructured":"Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930\u2013944.e22 (2017).","journal-title":"Cell"},{"key":"1465_CR41","doi-asserted-by":"publisher","first-page":"6699","DOI":"10.1093\/nar\/gkz462","volume":"47","author":"J Hyle","year":"2019","unstructured":"Hyle, J. et al. Acute depletion of CTCF directly affects MYC regulation through loss of enhancer\u2013promoter looping. Nucleic Acids Res. 47, 6699\u20136713 (2019).","journal-title":"Nucleic Acids Res."},{"key":"1465_CR42","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"1465_CR43","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.molcel.2010.10.006","volume":"40","author":"K Richter","year":"2010","unstructured":"Richter, K., Haslbeck, M. & Buchner, J. The heat shock response: life on the verge of death. Mol. Cell 40, 253\u2013266 (2010).","journal-title":"Mol. Cell"},{"key":"1465_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-08949-w","volume":"10","author":"J Li","year":"2019","unstructured":"Li, J. et al. An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis. Nat. Commun. 10, 1535 (2019).","journal-title":"Nat. Commun."},{"key":"1465_CR45","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1002\/wrna.1235","volume":"5","author":"X Lu","year":"2014","unstructured":"Lu, X., Ng, H. & Bubulya, P. A. The role of SON in splicing, development, and disease. Wiley Interdiscip. Rev. RNA 5, 637\u2013646 (2014).","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"1465_CR46","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1016\/j.ajhg.2012.04.019","volume":"90","author":"MA Deardorff","year":"2012","unstructured":"Deardorff, M. A. et al. RAD21 mutations cause a human cohesinopathy. Am. J. Hum. Genet. 90, 1014\u201327 (2012).","journal-title":"Am. J. Hum. Genet."},{"key":"1465_CR47","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1002\/humu.9478","volume":"28","author":"G Borck","year":"2007","unstructured":"Borck, G. et al. Incidence and clinical features of X\u2010linked Cornelia de Lange syndrome due to SMC1L1 mutations. Hum. Mutat. 28, 205\u2013206 (2007).","journal-title":"Hum. Mutat."},{"key":"1465_CR48","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1086\/424698","volume":"75","author":"LA Gillis","year":"2004","unstructured":"Gillis, L. A. et al. NIPBL mutational analysis in 120 Individuals with Cornelia de Lange Syndrome and evaluation of genotype\u2013phenotype correlations. Am. J. Hum. Genet. 75, 610\u2013623 (2004).","journal-title":"Am. J. Hum. Genet."},{"key":"1465_CR49","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1038\/s41576-018-0031-0","volume":"19","author":"AD Kline","year":"2018","unstructured":"Kline, A. D. et al. Diagnosis and management of Cornelia de Lange syndrome: first international consensus statement. Nat. Rev. Genet. 19, 649\u2013666 (2018).","journal-title":"Nat. Rev. Genet."},{"key":"1465_CR50","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1002\/ajmg.a.30919","volume":"138A","author":"M Kaur","year":"2005","unstructured":"Kaur, M. et al. Precocious sister chromatid separation (PSCS) in Cornelia de Lange syndrome. Am. J. Med. Genet. A 138A, 27\u201331 (2005).","journal-title":"Am. J. Med. Genet. A"},{"key":"1465_CR51","doi-asserted-by":"publisher","first-page":"1478","DOI":"10.1093\/hmg\/ddm098","volume":"16","author":"MG Vrouwe","year":"2007","unstructured":"Vrouwe, M. G. et al. Increased DNA damage sensitivity of Cornelia de Lange syndrome cells: evidence for impaired recombinational repair. Hum. Mol. Genet. 16, 1478\u20131487 (2007).","journal-title":"Hum. Mol. Genet."},{"key":"1465_CR52","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1038\/nrm3454","volume":"13","author":"S Kervestin","year":"2012","unstructured":"Kervestin, S. & Jacobson, A. NMD: a multifaceted response to premature translational termination. Nat. Rev. Mol. Cell Biol. 13, 700\u2013712 (2012).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"1465_CR53","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/j.gene.2015.08.063","volume":"575","author":"M Haase","year":"2016","unstructured":"Haase, M. & Fitze, G. HSP90AB1: helping the good and the bad. Gene 575, 171\u2013186 (2016).","journal-title":"Gene"},{"key":"1465_CR54","doi-asserted-by":"publisher","first-page":"4188","DOI":"10.1128\/MCB.20.12.4188-4198.2000","volume":"20","author":"ML Whitfield","year":"2000","unstructured":"Whitfield, M. L. et al. Stem-loop binding protein, the protein that binds the 3\u2032 end of histone mRNA, is cell cycle regulated by both translational and posttranslational mechanisms. Mol. Cell. Biol. 20, 4188\u20134198 (2000).","journal-title":"Mol. Cell. Biol."},{"key":"1465_CR55","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s13072-019-0289-2","volume":"12","author":"S Hu","year":"2019","unstructured":"Hu, S., Lv, P., Yan, Z. & Wen, B. Disruption of nuclear speckles reduces chromatin interactions in active compartments. Epigenetics Chromatin 12, 43 (2019).","journal-title":"Epigenetics Chromatin"},{"key":"1465_CR56","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1146\/annurev-genom-083115-022339","volume":"17","author":"M Merkenschlager","year":"2016","unstructured":"Merkenschlager, M. & Nora, E. P. CTCF and cohesin in genome folding and transcriptional gene regulation. Annu. Rev. Genom. Hum. Genet. 17, 17\u201343 (2016).","journal-title":"Annu. Rev. Genom. Hum. Genet."},{"key":"1465_CR57","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1042\/EBC20180069","volume":"63","author":"L Braccioli","year":"2019","unstructured":"Braccioli, L. & Wit de, E. CTCF: a Swiss-army knife for genome organization and transcription regulation. Essays Biochem. 63, 157\u2013165 (2019).","journal-title":"Essays Biochem."},{"key":"1465_CR58","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1016\/j.ajhg.2016.06.029","volume":"99","author":"J-H Kim","year":"2016","unstructured":"Kim, J.-H. et al. De novo mutations in SON disrupt RNA splicing of genes essential for brain development and metabolism, causing an intellectual-disability syndrome. Am. J. Hum. Genet. 99, 711\u2013719 (2016).","journal-title":"Am. J. Hum. Genet."},{"key":"1465_CR59","doi-asserted-by":"publisher","first-page":"1774","DOI":"10.1016\/j.gim.2022.04.011","volume":"24","author":"S Cuinat","year":"2022","unstructured":"Cuinat, S. et al. Loss-of-function variants in SRRM2 cause a neurodevelopmental disorder. Genet. Med. 24, 1774\u20131780 (2022).","journal-title":"Genet. Med."},{"key":"1465_CR60","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/s41586-020-2832-5","volume":"586","author":"J Kaplanis","year":"2020","unstructured":"Kaplanis, J. et al. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 586, 757\u2013762 (2020).","journal-title":"Nature"},{"key":"1465_CR61","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/978-1-4939-9674-2_11","volume":"2038","author":"SC Nguyen","year":"2019","unstructured":"Nguyen, S. C. & Joyce, E. F. Programmable chromosome painting with Oligopaints. Methods Mol. Biol. 2038, 167\u2013180 (2019).","journal-title":"Methods Mol. Biol."},{"key":"1465_CR62","doi-asserted-by":"publisher","first-page":"1174","DOI":"10.1016\/j.molcel.2019.01.006","volume":"73","author":"J Petrovic","year":"2019","unstructured":"Petrovic, J. et al. Oncogenic notch promotes long-range regulatory interactions within hyperconnected 3D cliques. Mol. Cell 73, 1174\u20131190.e12 (2019).","journal-title":"Mol. Cell"},{"key":"1465_CR63","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1186\/s12859-021-04344-9","volume":"22","author":"DR Stirling","year":"2021","unstructured":"Stirling, D. R. et al. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics 22, 433 (2021).","journal-title":"BMC Bioinformatics"},{"key":"1465_CR64","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":"1465_CR65","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1007\/978-1-4939-0512-6_5","volume":"1150","author":"S Xu","year":"2014","unstructured":"Xu, S., Grullon, S., Ge, K. & Peng, W. Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells. Methods Mol. Biol. 1150, 97\u2013111 (2014).","journal-title":"Methods Mol. Biol."},{"key":"1465_CR66","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders, S., Pyl, P. T. & Huber, W. HTSeq\u2014a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166\u2013169 (2015).","journal-title":"Bioinformatics"},{"key":"1465_CR67","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1038\/nbt.2931","volume":"32","author":"D Risso","year":"2013","unstructured":"Risso, D., Ngai, J., Speed, T. P. & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896\u2013902 (2013).","journal-title":"Nat. Biotechnol."}],"container-title":["Nature Structural & Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41594-024-01465-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-024-01465-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-024-01465-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,16]],"date-time":"2025-06-16T18:02:09Z","timestamp":1750096929000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41594-024-01465-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,21]]},"references-count":67,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,6]]}},"alternative-id":["1465"],"URL":"https:\/\/doi.org\/10.1038\/s41594-024-01465-6","relation":{},"ISSN":["1545-9993","1545-9985"],"issn-type":[{"value":"1545-9993","type":"print"},{"value":"1545-9985","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,21]]},"assertion":[{"value":"29 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 December 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 February 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"B.B.L. has received research funding from Eisai and AstraZeneca and is a shareholder and member of the scientific advisory board of Light Horse Therapeutics. The remaining authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}