{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T09:57:21Z","timestamp":1790675841978,"version":"4.1.0"},"reference-count":114,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":17,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK015602"],"award-info":[{"award-number":["DK015602"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["BioEssays"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Transcription and three\u2010dimensional (3D) genome organization are closely coupled, but their precise relationship remains unresolved. Evidence from perturbation, imaging, and modeling studies suggests that transcription is not strictly required for the establishment of large\u2010scale genome features such as compartments and topologically associating domains (TADs). Instead, transcription seems to exert more prominent effects at finer spatial scales, where it influences enhancer\u2013promoter interactions, local chromatin loops, and microcompartments. RNA molecules, polymerase\u2010driven supercoiling, and R\u2010loop formation may further modulate chromatin organization at the gene level. At the same time, many architectural proteins and transcriptional regulators operate with functional overlap, complicating efforts to disentangle cause and consequence. Together, these observations suggest that genome architecture provides a relatively stable framework for regulated gene expression, while transcription and associated factors refine chromatin organization in a context\u2010dependent manner. Understanding how these processes are integrated will require systematic, multi\u2010scale perturbations across different biological and biochemical systems.<\/jats:p>","DOI":"10.1002\/bies.70182","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T08:34:47Z","timestamp":1789720487000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcription and Three\u2010Dimensional Genome Organization: Cause, Consequence, or Coordination?"],"prefix":"10.1002","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-2471-9355","authenticated-orcid":false,"given":"Dagyeong","family":"Yang","sequence":"first","affiliation":[{"name":"Nuclear Organization and Gene Expression Section Laboratory of Biochemistry and Genetics National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health  Bethesda Maryland USA"},{"name":"Program in Computational Biology Bioinformatics, and Genomics University of Maryland  College Park Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4894-0037","authenticated-orcid":false,"given":"Elissa P.","family":"Lei","sequence":"additional","affiliation":[{"name":"Nuclear Organization and Gene Expression Section Laboratory of Biochemistry and Genetics National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health  Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1181369"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11082"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.05.004"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.11.021"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.15252\/embj.201798004"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature24281"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.15252\/embj.201798083"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.09.043"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature12644"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.09.030"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22822"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22989"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576\u2010025\u201000859\u20106"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1518552112"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.04.085"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.09.026"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41594\u2010022\u201000890\u20109"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aaw1668"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010021\u201021366\u20102"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2012.08.031"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.01.010"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.03.024"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010017\u201002525\u2010w"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2017.07.022"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb\u20102014\u201015\u20105\u2010r82"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt325"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1242059"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2024.10.017"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010022\u201001117\u20109"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2025.101002"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.02.023"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201948068"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010020\u201002067\u20103"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abg8205"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2018.06.003"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010026\u201069105\u20109"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010020\u201015607\u2010z"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010021\u201000878\u2010z"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010021\u201000816\u2010z"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature13417"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010026\u201002503\u20103"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010024\u201049727\u20107"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2025.10.013"},{"key":"e_1_2_10_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010023\u201001391\u20101"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201038429\u20101"},{"key":"e_1_2_10_47_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.advenzreg.2010.10.001"},{"key":"e_1_2_10_48_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201042274\u20107"},{"key":"e_1_2_10_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.07.006"},{"key":"e_1_2_10_50_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13578\u2010026\u201001531\u20100"},{"key":"e_1_2_10_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature09380"},{"key":"e_1_2_10_52_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf415"},{"key":"e_1_2_10_53_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13072\u2010025\u201000598\u20102"},{"key":"e_1_2_10_54_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004153"},{"key":"e_1_2_10_55_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2210480120"},{"key":"e_1_2_10_56_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22063"},{"key":"e_1_2_10_57_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010026\u201002516\u2010y"},{"key":"e_1_2_10_58_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.07.047"},{"key":"e_1_2_10_59_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.343475.120"},{"key":"e_1_2_10_60_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abj8360"},{"key":"e_1_2_10_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010023\u201001364\u20104"},{"key":"e_1_2_10_62_1","doi-asserted-by":"publisher","DOI":"10.15252\/embj.201695402"},{"key":"e_1_2_10_63_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2024.102920"},{"key":"e_1_2_10_64_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41556\u2010022\u201000847\u20106"},{"key":"e_1_2_10_65_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add4920"},{"key":"e_1_2_10_66_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms19030884"},{"key":"e_1_2_10_67_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010023\u201001649\u20108"},{"key":"e_1_2_10_68_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adn2955"},{"key":"e_1_2_10_69_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000138"},{"key":"e_1_2_10_70_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005969"},{"key":"e_1_2_10_71_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.09.032"},{"key":"e_1_2_10_72_1","doi-asserted-by":"publisher","DOI":"10.64898\/2026.02.06.704447"},{"key":"e_1_2_10_73_1","doi-asserted-by":"publisher","DOI":"10.64898\/2026.03.17.712299"},{"key":"e_1_2_10_74_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580\u2010019\u20100114\u20106"},{"key":"e_1_2_10_75_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.06.001"},{"key":"e_1_2_10_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2024.102208"},{"key":"e_1_2_10_77_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003\u2010023\u201004819\u2010w"},{"key":"e_1_2_10_78_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010023\u201005961\u20105"},{"key":"e_1_2_10_79_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.02.007"},{"key":"e_1_2_10_80_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2025.02.002"},{"key":"e_1_2_10_81_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13072\u2010025\u201000618\u20101"},{"key":"e_1_2_10_82_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2023.03.017"},{"key":"e_1_2_10_83_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2025.100778"},{"key":"e_1_2_10_84_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41594\u2010022\u201000821\u20108"},{"key":"e_1_2_10_85_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.76539"},{"key":"e_1_2_10_86_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abn6583"},{"key":"e_1_2_10_87_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010022\u201001232\u20107"},{"key":"e_1_2_10_88_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010025\u201002406\u20109"},{"key":"e_1_2_10_89_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1183"},{"key":"e_1_2_10_90_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi7178"},{"key":"e_1_2_10_91_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010022\u201004680\u20107"},{"key":"e_1_2_10_92_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.07.008"},{"key":"e_1_2_10_93_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.21926"},{"key":"e_1_2_10_94_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.352648.125"},{"key":"e_1_2_10_95_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010021\u201000888\u2010x"},{"key":"e_1_2_10_96_1","doi-asserted-by":"publisher","DOI":"10.1242\/dev.186536"},{"issue":"12","key":"e_1_2_10_97_1","first-page":"1743","article-title":"A Novel Sequence\u2010Specific DNA Binding Protein Which Interacts With Three Regularly Spaced Direct Repeats of the CCCTC\u2010Motif in the 5\u2032\u2010Flanking Sequence of the Chicken c\u2010myc Gene","volume":"5","author":"Lobanenkov V. V.","year":"1990","journal-title":"Oncogene"},{"key":"e_1_2_10_98_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.16.6.2802"},{"key":"e_1_2_10_99_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092\u20108674(00)81967\u20104"},{"key":"e_1_2_10_100_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2416384122"},{"key":"e_1_2_10_101_1","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202255146"},{"key":"e_1_2_10_102_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2019.02.001"},{"key":"e_1_2_10_103_1","doi-asserted-by":"publisher","DOI":"10.1038\/emboj.2013.111"},{"key":"e_1_2_10_104_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010021\u201024407\u2010y"},{"key":"e_1_2_10_105_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2004.11.004"},{"key":"e_1_2_10_106_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092\u20108674(95)90008\u2010X"},{"key":"e_1_2_10_107_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010025\u201021036\u2010z"},{"key":"e_1_2_10_108_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.120.303144"},{"key":"e_1_2_10_109_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.66668"},{"key":"e_1_2_10_110_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.192682.115"},{"key":"e_1_2_10_111_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature07388"},{"key":"e_1_2_10_112_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.03.002"},{"key":"e_1_2_10_113_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010023\u201001442\u20107"},{"key":"e_1_2_10_114_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.277567.122"},{"key":"e_1_2_10_115_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010021\u201025418\u20105"}],"container-title":["BioEssays"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/bies.70182","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/bies.70182","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/bies.70182","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T09:15:19Z","timestamp":1790673319000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/bies.70182"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":114,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["10.1002\/bies.70182"],"URL":"https:\/\/doi.org\/10.1002\/bies.70182","archive":["Portico"],"relation":{},"ISSN":["0265-9247","1521-1878"],"issn-type":[{"value":"0265-9247","type":"print"},{"value":"1521-1878","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"2026-04-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-02","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-18","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70182"}}