{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T09:28:30Z","timestamp":1793525310980,"version":"4.5.0"},"reference-count":76,"publisher":"Elsevier BV","issue":"23","license":[{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP17K16293"],"award-info":[{"award-number":["JP17K16293"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP23K07262"],"award-info":[{"award-number":["JP23K07262"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP16H06279 (PAGS)"],"award-info":[{"award-number":["JP16H06279 (PAGS)"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP22H04925 (PAGS)"],"award-info":[{"award-number":["JP22H04925 (PAGS)"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP20K08176"],"award-info":[{"award-number":["JP20K08176"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Biology"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1016\/j.jmb.2026.170040","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T15:50:16Z","timestamp":1790610616000},"page":"170040","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["TAD Boundary Disruption in Xq27\u2013q28 Deletions Rewires 3D Chromatin Architecture and May Predispose to Primary Skewed X Chromosome Inactivation"],"prefix":"10.1016","volume":"438","author":[{"given":"Kimiko","family":"Katoh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroyo","family":"Nishide","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6413-0100","authenticated-orcid":false,"given":"Yu","family":"Hamaguchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minami","family":"Soga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaori","family":"Aiba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kagayaki","family":"Kato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Motosuke","family":"Tsutsumi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2295-0659","authenticated-orcid":false,"given":"Joe","family":"Sakamoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8955-3132","authenticated-orcid":false,"given":"Elena","family":"Solovieva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6102-1495","authenticated-orcid":false,"given":"Tomomi","family":"Nemoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takumi","family":"Era","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michiaki","family":"Hamada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ikuo","family":"Uchiyama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5693-2227","authenticated-orcid":false,"given":"Nobuaki","family":"Wakamatsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6397-373X","authenticated-orcid":false,"given":"Masato","family":"Asai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmb.2026.170040_b0005","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/190372a0","article-title":"Gene action in the X chromosome of the mouse (Mus musculus L.)","volume":"190","author":"Lyon","year":"1961","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0010","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/0092-8674(92)90520-M","article-title":"The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus","volume":"71","author":"Brown","year":"1992","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0015","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/s41580-021-00438-7","article-title":"Gene regulation in time and space during X chromosome inactivation","volume":"23","author":"Loda","year":"2022","journal-title":"Nature Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jmb.2026.170040_b0020","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.ceb.2020.11.004","article-title":"Xist-mediated chromatin changes that establish silencing of an entire X chromosome in mammals","volume":"70","author":"Boeren","year":"2021","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.jmb.2026.170040_b0025","doi-asserted-by":"crossref","DOI":"10.1016\/j.gde.2022.101927","article-title":"A lifelong duty: how Xist maintains the inactive X chromosome","volume":"75","author":"Jacobson","year":"2022","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.jmb.2026.170040_b0030","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.ajhg.2009.05.003","article-title":"X chromosome inactivation is initiated in human preimplantation embryos","volume":"84","author":"van den Berg","year":"2009","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0035","doi-asserted-by":"crossref","DOI":"10.1016\/j.gde.2023.102096","article-title":"Modeling X chromosome inactivation and reactivation during human development","volume":"82","author":"Khan","year":"2023","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.jmb.2026.170040_b0040","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.cell.2023.11.033","article-title":"XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells","volume":"187","author":"Dror","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0045","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1038\/s41594-024-01325-3","article-title":"XIST dampens X chromosome activity in a SPEN-dependent manner during early human development","volume":"31","author":"Alfeghaly","year":"2024","journal-title":"Nature Struct. Mol. Biol."},{"key":"10.1016\/j.jmb.2026.170040_b0050","doi-asserted-by":"crossref","DOI":"10.1126\/science.1237973","article-title":"The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome","volume":"341","author":"Engreitz","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.jmb.2026.170040_b0055","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nature12719","article-title":"High-resolution Xist binding maps reveal two-step spreading during X chromosome inactivation","volume":"504","author":"Simon","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0060","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1016\/j.cell.2024.12.004","article-title":"A biophysical basis for the spreading behavior and limited diffusion of Xist","volume":"188","author":"Ding","year":"2025","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0065","doi-asserted-by":"crossref","DOI":"10.1002\/bies.202200105","article-title":"Causality in transcription and genome folding: Insights from X inactivation","volume":"44","author":"Bauer","year":"2022","journal-title":"Bioessays"},{"key":"10.1016\/j.jmb.2026.170040_b0070","doi-asserted-by":"crossref","first-page":"1864","DOI":"10.1101\/gr.133751.111","article-title":"Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations","volume":"22","author":"Pinter","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.jmb.2026.170040_b0075","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","article-title":"Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions","volume":"161","author":"Lupianez","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0080","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nature19800","article-title":"Formation of new chromatin domains determines pathogenicity of genomic duplications","volume":"538","author":"Franke","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0085","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/BF00276593","article-title":"X-autosome translocations: cytogenetic characteristics and their consequences","volume":"61","author":"Mattei","year":"1982","journal-title":"Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0090","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1055\/s-2001-15395","article-title":"Ring X and other structural X chromosome abnormalities: X inactivation and phenotype","volume":"19","author":"Leppig","year":"2001","journal-title":"Semin. Reprod. Med."},{"key":"10.1016\/j.jmb.2026.170040_b0095","doi-asserted-by":"crossref","DOI":"10.1007\/s12041-021-01314-1","article-title":"X chromosome inactivation: implications in human disease","volume":"100","author":"Pereira","year":"2021","journal-title":"J. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0100","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1007\/BF00196232","article-title":"Unusual X chromosome inactivation in a mentally retarded girl with an interstitial deletion Xq27: implications for the fragile X syndrome","volume":"84","author":"Schmidt","year":"1990","journal-title":"Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0105","first-page":"289","article-title":"Hunter disease (mucopolysaccharidosis type II) associated with unbalanced inactivation of the X chromosomes in a karyotypically normal girl","volume":"49","author":"Clarke","year":"1991","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0110","first-page":"1108","article-title":"Myotubular myopathy in a girl with a deletion at Xq27-q28 and unbalanced X inactivation assigns the MTM1 gene to a 600-kb region","volume":"56","author":"Dahl","year":"1995","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0115","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/(SICI)1098-1004(1996)7:3<266::AID-HUMU12>3.0.CO;2-0","article-title":"A 5-megabase familial deletion removes the IDS and FMR-1 genes in a male Hunter patient","volume":"7","author":"Birot","year":"1996","journal-title":"Hum. Mutat."},{"key":"10.1016\/j.jmb.2026.170040_b0120","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1471-2350-14-49","article-title":"Deletion Xq27.3q28 in female patient with global developmental delays and skewed X-inactivation","volume":"14","author":"Marshall","year":"2013","journal-title":"BMC Med. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0125","doi-asserted-by":"crossref","first-page":"101","DOI":"10.3389\/fgene.2020.00101","article-title":"Skewed X chromosome inactivation and compensatory upregulation of escape genes precludes major clinical symptoms in a female with a large Xq deletion","volume":"11","author":"Santos-Reboucas","year":"2020","journal-title":"Front. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0130","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1002\/humu.24058","article-title":"Clinical and molecular genetic characterization of two female patients harboring the Xq27.3q28 deletion with different ratios of X chromosome inactivation","volume":"41","author":"Katoh","year":"2020","journal-title":"Hum. Mutat."},{"key":"10.1016\/j.jmb.2026.170040_b0135","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/j.tjog.2025.05.007","article-title":"Prenatal diagnosis of a familial Xq27.1-q28 deletion with an asymptomatic mother carrier and no abnormality in the female fetus","volume":"64","author":"Chen","year":"2025","journal-title":"Taiwan. J. Obstet. Gynecol."},{"key":"10.1016\/j.jmb.2026.170040_b0140","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1086\/507565","article-title":"X chromosome-inactivation patterns of 1,005 phenotypically unaffected females","volume":"79","author":"Amos-Landgraf","year":"2006","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0145","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/s41431-018-0291-3","article-title":"Skewed X-inactivation is common in the general female population","volume":"27","author":"Shvetsova","year":"2019","journal-title":"Eur. J. Hum. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0150","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1002\/ajmg.1320510429","article-title":"X inactivation pattern in interstitial deletions of the fragile X region","volume":"51","author":"Schmidt","year":"1994","journal-title":"Am. J. Med. Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0155","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41586-019-1812-0","article-title":"Key role for CTCF in establishing chromatin structure in human embryos","volume":"576","author":"Chen","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0160","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.stem.2016.10.006","article-title":"Human naive pluripotent stem cells model X chromosome dampening and X inactivation","volume":"20","author":"Sahakyan","year":"2017","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0165","doi-asserted-by":"crossref","first-page":"2748","DOI":"10.1242\/dev.146811","article-title":"Epigenetic resetting of human pluripotency","volume":"144","author":"Guo","year":"2017","journal-title":"Development"},{"key":"10.1016\/j.jmb.2026.170040_b0170","doi-asserted-by":"crossref","first-page":"3881","DOI":"10.1038\/s41596-023-00898-5","article-title":"EpiTyping: analysis of epigenetic aberrations in parental imprinting and X chromosome inactivation using RNA-seq","volume":"18","author":"Sarel-Gallily","year":"2023","journal-title":"Nature Protoc."},{"key":"10.1016\/j.jmb.2026.170040_b0175","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109032","article-title":"Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome","volume":"35","author":"Brenes","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0180","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109215","article-title":"Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation","volume":"35","author":"Bansal","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0185","doi-asserted-by":"crossref","first-page":"2516","DOI":"10.1038\/s41467-022-30259-x","article-title":"Preventing erosion of X chromosome inactivation in human embryonic stem cells","volume":"13","author":"Cloutier","year":"2022","journal-title":"Nature Commun."},{"key":"10.1016\/j.jmb.2026.170040_b0190","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.stem.2015.03.016","article-title":"Erosion of X chromosome inactivation in human pluripotent cells initiates with XACT coating and depends on a specific heterochromatin landscape","volume":"16","author":"Vallot","year":"2015","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0195","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109233","article-title":"Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening","volume":"35","author":"Khan","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0200","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature11049","article-title":"Spatial partitioning of the regulatory landscape of the X-inactivation centre","volume":"485","author":"Nora","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0205","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature18589","article-title":"Structural organization of the inactive X chromosome in the mouse","volume":"535","author":"Giorgetti","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0210","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/s41556-025-01823-6","article-title":"Escape from X inactivation is directly modulated by Xist noncoding RNA","volume":"28","author":"Hauth","year":"2026","journal-title":"Nature Cell Biol."},{"key":"10.1016\/j.jmb.2026.170040_b0215","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2025.115351","article-title":"B cell stimulation changes the structure and higher-order organization of the inactive X chromosome","volume":"44","author":"Sierra","year":"2025","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0220","doi-asserted-by":"crossref","first-page":"8991","DOI":"10.1038\/s41467-024-53449-1","article-title":"Population variability in X chromosome inactivation across 10 mammalian species","volume":"15","author":"Werner","year":"2024","journal-title":"Nature Commun."},{"key":"10.1016\/j.jmb.2026.170040_b0225","doi-asserted-by":"crossref","DOI":"10.1242\/dev.167833","article-title":"Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development","volume":"145","author":"Boroviak","year":"2018","journal-title":"Development"},{"key":"10.1016\/j.jmb.2026.170040_b0230","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2026.117124","article-title":"A single-cell CRISPR screen defines a gene regulatory network governing human pluripotency in primed and naive cells","volume":"45","author":"Keshet","year":"2026","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0235","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyab034","article-title":"Bayesian modeling of skewed X inactivation in genetically diverse mice identifies a novel Xce allele associated with copy number changes","volume":"218","author":"Sun","year":"2021","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2026.170040_b0240","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109222","article-title":"Deletion of lncRNA XACT does not change expression dosage of X-linked genes, but affects differentiation potential in hPSCs","volume":"35","author":"Motosugi","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0245","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/nature24265","article-title":"Landscape of X chromosome inactivation across human tissues","volume":"550","author":"Tukiainen","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0250","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1126\/science.1163802","article-title":"The air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin","volume":"322","author":"Nagano","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.jmb.2026.170040_b0255","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1008268","article-title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","volume":"15","author":"Andergassen","year":"2019","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0260","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nature09872","article-title":"Eutherian mammals use diverse strategies to initiate X chromosome inactivation during development","volume":"472","author":"Okamoto","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0265","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.cell.2007.11.019","article-title":"Induction of pluripotent stem cells from adult human fibroblasts by defined factors","volume":"131","author":"Takahashi","year":"2007","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0270","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1016\/j.stemcr.2019.10.009","article-title":"Wnt inhibition facilitates RNA-mediated reprogramming of human somatic cells to naive pluripotency","volume":"13","author":"Bredenkamp","year":"2019","journal-title":"Stem Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0275","doi-asserted-by":"crossref","DOI":"10.1242\/dev.172916","article-title":"Capacitation of human naive pluripotent stem cells for multi-lineage differentiation","volume":"146","author":"Rostovskaya","year":"2019","journal-title":"Development"},{"key":"10.1016\/j.jmb.2026.170040_b0280","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1016\/j.celrep.2015.04.039","article-title":"A primary role for the Tsix lncRNA in maintaining random X chromosome inactivation","volume":"11","author":"Gayen","year":"2015","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0285","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.cell.2016.08.009","article-title":"Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos","volume":"167","author":"Petropoulos","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0290","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.stem.2014.07.002","article-title":"Systematic identification of culture conditions for induction and maintenance of naive human pluripotency","volume":"15","author":"Theunissen","year":"2014","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0295","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1016\/j.stem.2020.06.002","article-title":"Overcoming autocrine FGF signaling-induced heterogeneity in naive human ESCs enables modeling of random X chromosome inactivation","volume":"27","author":"An","year":"2020","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0300","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jmb.2026.170040_b0305","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jmb.2026.170040_b0310","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","author":"Soneson","year":"2015","journal-title":"F1000Res"},{"key":"10.1016\/j.jmb.2026.170040_b0315","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nature Biotechnol."},{"key":"10.1016\/j.jmb.2026.170040_b0320","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1016\/j.stem.2016.06.011","article-title":"Molecular criteria for defining the naive human pluripotent state","volume":"19","author":"Theunissen","year":"2016","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0325","doi-asserted-by":"crossref","first-page":"3284","DOI":"10.1016\/j.cell.2024.05.010","article-title":"Capturing totipotency in human cells through spliceosomal repression","volume":"187","author":"Li","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0330","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1016\/j.stemcr.2019.04.004","article-title":"Enhancer chromatin and 3D genome architecture changes from naive to primed human embryonic stem cell states","volume":"12","author":"Battle","year":"2019","journal-title":"Stem Cell Rep."},{"key":"10.1016\/j.jmb.2026.170040_b0335","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1038\/s41588-019-0479-7","article-title":"Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells","volume":"51","author":"Zhang","year":"2019","journal-title":"Nature Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0340","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.molcel.2020.03.003","article-title":"Ultrastructural details of mammalian chromosome architecture","volume":"78","author":"Krietenstein","year":"2020","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2026.170040_b0345","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/nature14450","article-title":"Condensin-driven remodelling of X chromosome topology during dosage compensation","volume":"523","author":"Crane","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2026.170040_b0350","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gkaf1109","article-title":"The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture","volume":"54","author":"Yu","year":"2026","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2026.170040_b0355","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/s41588-022-01065-4","article-title":"Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale","volume":"54","author":"Zhou","year":"2022","journal-title":"Nature Genet."},{"key":"10.1016\/j.jmb.2026.170040_b0360","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jmb.2026.170040_b0365","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1159\/000357962","article-title":"Microdeletions including FMR1 in three female patients with intellectual disability - further delineation of the phenotype and expression studies","volume":"5","author":"Zink","year":"2014","journal-title":"Mol. Syndromol."},{"key":"10.1016\/j.jmb.2026.170040_b0370","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1002\/mgg3.425","article-title":"Hemophilia B in a female with intellectual disability caused by a deletion of Xq26.3q28 encompassing the F9","volume":"6","author":"Stoof","year":"2018","journal-title":"Mol. Genet. Genomic Med."},{"key":"10.1016\/j.jmb.2026.170040_b0375","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1089\/cell.2020.0012","article-title":"Generation of induced pluripotent stem cells from a female patient with a Xq27.3-q28 deletion to establish disease models and identify therapies","volume":"22","author":"Watanabe","year":"2020","journal-title":"Cell. Reprogram."},{"key":"10.1016\/j.jmb.2026.170040_b0380","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/s41556-025-01658-1","article-title":"alpha-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells","volume":"27","author":"Van Nerum","year":"2025","journal-title":"Nature Cell Biol."}],"container-title":["Journal of Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283626004134?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283626004134?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T09:02:14Z","timestamp":1793523734000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022283626004134"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,12]]},"references-count":76,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["S0022283626004134"],"URL":"https:\/\/doi.org\/10.1016\/j.jmb.2026.170040","relation":{},"ISSN":["0022-2836"],"issn-type":[{"value":"0022-2836","type":"print"}],"subject":[],"published":{"date-parts":[[2026,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"TAD Boundary Disruption in Xq27\u2013q28 Deletions Rewires 3D Chromatin Architecture and May Predispose to Primary Skewed X Chromosome Inactivation","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmb.2026.170040","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"170040"}}