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

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dc.citation.articleNumber3303
dc.citation.journalTitleNature Communications
dc.citation.volumeNumber14
dc.contributor.authorHarris, Hannah L.
dc.contributor.authorGu, Huiya
dc.contributor.authorOlshansky, Moshe
dc.contributor.authorWang, Ailun
dc.contributor.authorFarabella, Irene
dc.contributor.authorEliaz, Yossi
dc.contributor.authorKalluchi, Achyuth
dc.contributor.authorKrishna, Akshay
dc.contributor.authorJacobs, Mozes
dc.contributor.authorCauer, Gesine
dc.contributor.authorPham, Melanie
dc.contributor.authorRao, Suhas S. P.
dc.contributor.authorDudchenko, Olga
dc.contributor.authorOmer, Arina
dc.contributor.authorMohajeri, Kiana
dc.contributor.authorKim, Sungjae
dc.contributor.authorNichols, Michael H.
dc.contributor.authorDavis, Eric S.
dc.contributor.authorGkountaroulis, Dimos
dc.contributor.authorUdupa, Devika
dc.contributor.authorAiden, Aviva Presser
dc.contributor.authorCorces, Victor G.
dc.contributor.authorPhanstiel, Douglas H.
dc.contributor.authorNoble, William Stafford
dc.contributor.authorNir, Guy
dc.contributor.authorDi Pierro, Michele
dc.contributor.authorSeo, Jeong-Sun
dc.contributor.authorTalkowski, Michael E.
dc.contributor.authorAiden, Erez Lieberman
dc.contributor.authorRowley, M. Jordan
dc.contributor.orgCenter for Theoretical Biological Physics
dc.date.accessioned2023-07-21T16:14:05Z
dc.date.available2023-07-21T16:14:05Z
dc.date.issued2023
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.
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.
dc.identifier.digitals41467-023-38429-1
dc.identifier.doihttps://doi.org/10.1038/s41467-023-38429-1
dc.identifier.urihttps://hdl.handle.net/1911/115015
dc.language.isoeng
dc.publisherSpringer Nature
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.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleChromatin alternates between A and B compartments at kilobase scale for subgenic organization
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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