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Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2016,8,2]]},"abstract":"<jats:title>Significance<\/jats:title>\n                  <jats:p>\n                    In human females, one of the two X chromosomes is inactive (Xi) and adopts an unusual 3D conformation. The Xi chromosome contains superloops, large chromatin loops that are often anchored at the macrosatellite repeat\n                    <jats:italic>DXZ4<\/jats:italic>\n                    , and is partitioned into two large intervals, called superdomains, whose boundary lies at\n                    <jats:italic>DXZ4<\/jats:italic>\n                    . Here, we use spatial proximity mapping, microscopy, and genome editing to study the Xi. We find that superloops and superdomains are conserved across humans, macaque, and mouse. By mapping proximity between three or more loci, we show that superloops tend to occur simultaneously. Deletion of\n                    <jats:italic>DXZ4<\/jats:italic>\n                    from the human Xi disrupts superloops, eliminates superdomains, and alters chromatin modifications. Finally, we show that a model in which CCCTC-binding factor (CTCF) and cohesin extrude chromatin can explain the formation of superloops and superdomains.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1609643113","type":"journal-article","created":{"date-parts":[[2016,7,18]],"date-time":"2016-07-18T22:18:28Z","timestamp":1468880308000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":285,"title":["Deletion of\n                    <i>DXZ4<\/i>\n                    on the human inactive X chromosome alters higher-order genome architecture"],"prefix":"10.1073","volume":"113","author":[{"given":"Emily M.","family":"Darrow","sequence":"first","affiliation":[{"name":"Department of Biological Science, Florida State University, Tallahassee, FL 32306;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam H.","family":"Huntley","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"},{"name":"John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02139;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Dudchenko","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Center for Theoretical Biological Physics, Rice University, Houston, TX 77030;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena K.","family":"Stamenova","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02139;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neva C.","family":"Durand","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuo","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Biological Science, Florida State University, Tallahassee, FL 32306;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Su-Chen","family":"Huang","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian L.","family":"Sanborn","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Center for Theoretical Biological Physics, Rice University, Houston, TX 77030;"},{"name":"Department of Computer Science, Stanford University, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ido","family":"Machol","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Shamim","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew P.","family":"Seberg","sequence":"additional","affiliation":[{"name":"Department of Biological Science, Florida State University, Tallahassee, FL 32306;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric S.","family":"Lander","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02139;"},{"name":"Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139;"},{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA 02115;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian P.","family":"Chadwick","sequence":"additional","affiliation":[{"name":"Department of Biological Science, Florida State University, Tallahassee, FL 32306;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erez Lieberman","family":"Aiden","sequence":"additional","affiliation":[{"name":"The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA 02139;"},{"name":"Center for Theoretical Biological Physics, Rice University, Houston, TX 77030;"},{"name":"Department of Computer Science, Rice University, Houston, TX 77005;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2016,7,18]]},"reference":[{"key":"e_1_3_4_1_2","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 MF","year":"1961","unstructured":"MF Lyon, Gene action in the X-chromosome of the mouse (Mus musculus L.). 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Cell 71, 527\u2013542 (1992).","journal-title":"Cell"},{"key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1139\/bcb-2015-0016","article-title":"The making of a Barr body: The mosaic of factors that eXIST on the mammalian inactive X chromosome","volume":"94","author":"Dixon-McDougall T","year":"2016","unstructured":"T Dixon-McDougall, C Brown, The making of a Barr body: The mosaic of factors that eXIST on the mammalian inactive X chromosome. Biochem Cell Biol 94, 56\u201370 (2016).","journal-title":"Biochem Cell Biol"},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/nature03479","article-title":"X-inactivation profile reveals extensive variability in X-linked gene expression in females","volume":"434","author":"Carrel L","year":"2005","unstructured":"L Carrel, HF Willard, X-inactivation profile reveals extensive variability in X-linked gene expression in females. 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Mol Cell 40, 397\u2013409 (2010).","journal-title":"Mol Cell"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"465","DOI":"10.4161\/nucl.2.5.17862","article-title":"A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at \u2265 20 Mb genomic length scales","volume":"2","author":"Teller K","year":"2011","unstructured":"K Teller, , A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at \u2265 20 Mb genomic length scales. Nucleus 2, 465\u2013477 (2011).","journal-title":"Nucleus"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao SS","year":"2014","unstructured":"SS Rao, , A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665\u20131680 (2014).","journal-title":"Cell"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/ng0592-137","article-title":"A novel GC-rich human macrosatellite VNTR in Xq24 is differentially methylated on active and inactive X chromosomes","volume":"1","author":"Giacalone J","year":"1992","unstructured":"J Giacalone, J Friedes, U Francke, A novel GC-rich human macrosatellite VNTR in Xq24 is differentially methylated on active and inactive X chromosomes. 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Genome Biol 16, 152 (2015).","journal-title":"Genome Biol"},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"aab2276","DOI":"10.1126\/science.aab2276","article-title":"Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation","volume":"349","author":"Minajigi A","year":"2015","unstructured":"A Minajigi, , Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. 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