Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

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dc.citation.articleNumber3303en_US
dc.citation.journalTitleNature Communicationsen_US
dc.citation.volumeNumber14en_US
dc.contributor.authorHarris, Hannah L.en_US
dc.contributor.authorGu, Huiyaen_US
dc.contributor.authorOlshansky, Mosheen_US
dc.contributor.authorWang, Ailunen_US
dc.contributor.authorFarabella, Ireneen_US
dc.contributor.authorEliaz, Yossien_US
dc.contributor.authorKalluchi, Achyuthen_US
dc.contributor.authorKrishna, Akshayen_US
dc.contributor.authorJacobs, Mozesen_US
dc.contributor.authorCauer, Gesineen_US
dc.contributor.authorPham, Melanieen_US
dc.contributor.authorRao, Suhas S. P.en_US
dc.contributor.authorDudchenko, Olgaen_US
dc.contributor.authorOmer, Arinaen_US
dc.contributor.authorMohajeri, Kianaen_US
dc.contributor.authorKim, Sungjaeen_US
dc.contributor.authorNichols, Michael H.en_US
dc.contributor.authorDavis, Eric S.en_US
dc.contributor.authorGkountaroulis, Dimosen_US
dc.contributor.authorUdupa, Devikaen_US
dc.contributor.authorAiden, Aviva Presseren_US
dc.contributor.authorCorces, Victor G.en_US
dc.contributor.authorPhanstiel, Douglas H.en_US
dc.contributor.authorNoble, William Stafforden_US
dc.contributor.authorNir, Guyen_US
dc.contributor.authorDi Pierro, Micheleen_US
dc.contributor.authorSeo, Jeong-Sunen_US
dc.contributor.authorTalkowski, Michael E.en_US
dc.contributor.authorAiden, Erez Liebermanen_US
dc.contributor.authorRowley, M. Jordanen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2023-07-21T16:14:05Zen_US
dc.date.available2023-07-21T16:14:05Zen_US
dc.date.issued2023en_US
dc.description.abstractNuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF’s RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.en_US
dc.identifier.citationHarris, Hannah L., Gu, Huiya, Olshansky, Moshe, et al.. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization." <i>Nature Communications,</i> 14, (2023) Springer Nature: https://doi.org/10.1038/s41467-023-38429-1.en_US
dc.identifier.digitals41467-023-38429-1en_US
dc.identifier.doihttps://doi.org/10.1038/s41467-023-38429-1en_US
dc.identifier.urihttps://hdl.handle.net/1911/115015en_US
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of Fair Use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleChromatin alternates between A and B compartments at kilobase scale for subgenic organizationen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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