{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T12:16:37Z","timestamp":1774008997652,"version":"3.50.1"},"posted":{"date-parts":[[2026,3,17]]},"group-title":"Molecular Biology","reference-count":71,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T00:00:00Z","timestamp":1773705600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The human genome organizes into several thousand chromatin packing domains that couple euchromatin and heterochromatin into unified nanoscale volumes. Prior work suggested these domains form by transcriptionally driven loops that guide packing domain assembly. Here, we study the process of transcriptionally driven domain formation and maintenance. By pairing auxin-inducible degron technology with nanoscopic imaging, transcriptomics, and Hi-C, we show that Pol-II regulates conformationally defined interphase chromatin packing domains. Pol-II facilitates nascent domain generation and maintains mature domain integrity through the process of generating transcriptional loops. Mechanistically, Pol-II maintains the packing of intronic and intergenic chromatin within domains by transcribing exons within gene bodies. Consequently, polymerase loss disrupts genome connectivity,\n                  <jats:italic>in situ<\/jats:italic>\n                  packing domains, and gene expression, genome-wide. Our findings suggest chromatin packing domains and RNA synthesis are tightly coupled to optimize transcriptional responses in human cells.\n                <\/jats:p>","DOI":"10.64898\/2026.03.15.711889","type":"posted-content","created":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T03:50:13Z","timestamp":1773805813000},"source":"Crossref","is-referenced-by-count":0,"title":["Gene transcription and chromatin packing domains form a self- organizing system"],"prefix":"10.64898","author":[{"given":"Lucas M","family":"Carter","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"},{"name":"Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wing Shun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruyi","family":"Gong","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Acosta","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niyati","family":"Pandya","sequence":"additional","affiliation":[{"name":"Stanley Manne Children\u2019s Research Institute, Ann & Robert H. Lurie Children\u2019s Hospital, Chicago, IL, USA"},{"name":"Northwestern University Feinberg School of Medicine, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcelo A","family":"Carignano","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily Pujadas","family":"Liwag","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"},{"name":"Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kunlun","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiffany","family":"Kuo","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"},{"name":"Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle","family":"MacQuarrie","sequence":"additional","affiliation":[{"name":"Stanley Manne Children\u2019s Research Institute, Ann & Robert H. Lurie Children\u2019s Hospital, Chicago, IL, USA"},{"name":"Northwestern University Feinberg School of Medicine, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masato T.","family":"Kanemaki","sequence":"additional","affiliation":[{"name":"National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan"},{"name":"Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan"},{"name":"Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luay","family":"Almassalha","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"},{"name":"Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Northwestern University, Chicago, Il, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vadim","family":"Backman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026032003150467000_2026.03.15.711889v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2019.02.003"},{"key":"2026032003150467000_2026.03.15.711889v1.2","doi-asserted-by":"publisher","DOI":"10.1101\/2024.09.17.613111"},{"key":"2026032003150467000_2026.03.15.711889v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1275-3"},{"key":"2026032003150467000_2026.03.15.711889v1.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.1181369"},{"key":"2026032003150467000_2026.03.15.711889v1.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.aag0025"},{"key":"2026032003150467000_2026.03.15.711889v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-16028-2"},{"key":"2026032003150467000_2026.03.15.711889v1.7","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adq6652"},{"key":"2026032003150467000_2026.03.15.711889v1.8","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202509964"},{"key":"2026032003150467000_2026.03.15.711889v1.9","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aba8811"},{"key":"2026032003150467000_2026.03.15.711889v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2021.06.009"},{"key":"2026032003150467000_2026.03.15.711889v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48698-z"},{"key":"2026032003150467000_2026.03.15.711889v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19532-z"},{"key":"2026032003150467000_2026.03.15.711889v1.13","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201811090"},{"key":"2026032003150467000_2026.03.15.711889v1.14","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abe4310"},{"key":"2026032003150467000_2026.03.15.711889v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.111730"},{"key":"2026032003150467000_2026.03.15.711889v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.11.021"},{"key":"2026032003150467000_2026.03.15.711889v1.17","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02067-3"},{"key":"2026032003150467000_2026.03.15.711889v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.09.026"},{"key":"2026032003150467000_2026.03.15.711889v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.05.004"},{"key":"2026032003150467000_2026.03.15.711889v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01223-8"},{"key":"2026032003150467000_2026.03.15.711889v1.21","doi-asserted-by":"publisher","DOI":"10.1101\/2024.03.02.582972"},{"key":"2026032003150467000_2026.03.15.711889v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-08602-5"},{"key":"2026032003150467000_2026.03.15.711889v1.23","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-023-01391-1"},{"key":"2026032003150467000_2026.03.15.711889v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-09890-3"},{"key":"2026032003150467000_2026.03.15.711889v1.25","doi-asserted-by":"publisher","DOI":"10.1021\/cr60292a002"},{"key":"2026032003150467000_2026.03.15.711889v1.26","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.82.16.5328"},{"issue":"2","key":"2026032003150467000_2026.03.15.711889v1.27","first-page":"1904","article-title":"Actinomycin D Inhibits Cell Proliferations and Promotes Apoptosis in Osteosarcoma Cells","volume":"8","year":"2015","journal-title":"Int J Clin Exp Med"},{"key":"2026032003150467000_2026.03.15.711889v1.28","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.85.5.1417"},{"key":"2026032003150467000_2026.03.15.711889v1.29","first-page":"290","article-title":"[Actinomycin D and its mechanisms of action]","volume":"59","year":"2005","journal-title":"Postepy Hig Med Dosw (Online)"},{"key":"2026032003150467000_2026.03.15.711889v1.30","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae069"},{"key":"2026032003150467000_2026.03.15.711889v1.31","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.1040760202"},{"key":"2026032003150467000_2026.03.15.711889v1.32","doi-asserted-by":"publisher","DOI":"10.4161\/trns.2.3.16172"},{"key":"2026032003150467000_2026.03.15.711889v1.33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1608198113"},{"key":"2026032003150467000_2026.03.15.711889v1.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.03.023"},{"key":"2026032003150467000_2026.03.15.711889v1.35","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae478"},{"key":"2026032003150467000_2026.03.15.711889v1.36","doi-asserted-by":"publisher","DOI":"10.1101\/gr.220640.117"},{"key":"2026032003150467000_2026.03.15.711889v1.37","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abg8205"},{"key":"2026032003150467000_2026.03.15.711889v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.03.002"},{"key":"2026032003150467000_2026.03.15.711889v1.39","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqab040"},{"key":"2026032003150467000_2026.03.15.711889v1.40","doi-asserted-by":"publisher","DOI":"10.1126\/science.adv0134"},{"key":"2026032003150467000_2026.03.15.711889v1.41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx1123"},{"key":"2026032003150467000_2026.03.15.711889v1.42","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqaa073"},{"key":"2026032003150467000_2026.03.15.711889v1.43","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2017.00139"},{"key":"2026032003150467000_2026.03.15.711889v1.44","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2021.08.018"},{"key":"2026032003150467000_2026.03.15.711889v1.45","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-019-1100-5"},{"key":"2026032003150467000_2026.03.15.711889v1.46","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04570-y"},{"key":"2026032003150467000_2026.03.15.711889v1.47","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2497-0"},{"key":"2026032003150467000_2026.03.15.711889v1.48","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02812-w"},{"key":"2026032003150467000_2026.03.15.711889v1.49","doi-asserted-by":"publisher","DOI":"10.1101\/2024.06.08.598009"},{"key":"2026032003150467000_2026.03.15.711889v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39387-4"},{"key":"2026032003150467000_2026.03.15.711889v1.51","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aax6232"},{"key":"2026032003150467000_2026.03.15.711889v1.52","doi-asserted-by":"publisher","DOI":"10.1038\/srep41061"},{"key":"2026032003150467000_2026.03.15.711889v1.53","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2014.02.019"},{"key":"2026032003150467000_2026.03.15.711889v1.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2019.11.007"},{"key":"2026032003150467000_2026.03.15.711889v1.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.07.002"},{"key":"2026032003150467000_2026.03.15.711889v1.56","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2288-x"},{"key":"2026032003150467000_2026.03.15.711889v1.57","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2026032003150467000_2026.03.15.711889v1.58","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"2026032003150467000_2026.03.15.711889v1.59","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku365"},{"key":"2026032003150467000_2026.03.15.711889v1.60","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-323"},{"key":"2026032003150467000_2026.03.15.711889v1.61","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"2026032003150467000_2026.03.15.711889v1.62","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-3578-9_16"},{"key":"2026032003150467000_2026.03.15.711889v1.63","unstructured":"Broad Institute. Picard Toolkit, 2019. https:\/\/broadinstitute.github.io\/picard\/."},{"key":"2026032003150467000_2026.03.15.711889v1.64","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137"},{"key":"2026032003150467000_2026.03.15.711889v1.65","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu202"},{"key":"2026032003150467000_2026.03.15.711889v1.66","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2019"},{"key":"2026032003150467000_2026.03.15.711889v1.67","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2010.02.013"},{"key":"2026032003150467000_2026.03.15.711889v1.68","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09717-6"},{"key":"2026032003150467000_2026.03.15.711889v1.69","doi-asserted-by":"publisher","DOI":"10.1101\/2024.03.28.587095"},{"key":"2026032003150467000_2026.03.15.711889v1.70","doi-asserted-by":"publisher","DOI":"10.1364\/OL.400231"},{"key":"2026032003150467000_2026.03.15.711889v1.71","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2021.100865"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.03.15.711889","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T10:15:13Z","timestamp":1774001713000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.03.15.711889"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,17]]},"references-count":71,"URL":"https:\/\/doi.org\/10.64898\/2026.03.15.711889","relation":{},"subject":[],"published":{"date-parts":[[2026,3,17]]},"subtype":"preprint"}}