CTCF looping is established during gastrulation in medaka embryos

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dc.citation.firstpage968en_US
dc.citation.journalTitleGenome Researchen_US
dc.citation.lastpage980en_US
dc.citation.volumeNumber31en_US
dc.contributor.authorNakamura, Ryoheien_US
dc.contributor.authorMotai, Yuichien_US
dc.contributor.authorKumagai, Masahikoen_US
dc.contributor.authorWike, Candice L.en_US
dc.contributor.authorNishiyama, Haruyoen_US
dc.contributor.authorNakatani, Yoichiroen_US
dc.contributor.authorDurand, Neva C.en_US
dc.contributor.authorKondo, Kaorien_US
dc.contributor.authorKondo, Takashien_US
dc.contributor.authorTsukahara, Tatsuyaen_US
dc.contributor.authorShimada, Atsukoen_US
dc.contributor.authorCairns, Bradley R.en_US
dc.contributor.authorAiden, Erez Liebermanen_US
dc.contributor.authorMorishita, Shinichien_US
dc.contributor.authorTakeda, Hiroyukien_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2022-01-21T16:23:58Zen_US
dc.date.available2022-01-21T16:23:58Zen_US
dc.date.issued2021en_US
dc.description.abstractChromatin looping plays an important role in genome regulation. However, because ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation) are extremely challenging in mammalian early embryos, the developmental stage at which cohesin-mediated loops form remains unknown. Here, we study early development in medaka (the Japanese killifish, Oryzias latipes) at 12 time points before, during, and after gastrulation (the onset of cell differentiation) and characterize transcription, protein binding, and genome architecture. We find that gastrulation is associated with drastic changes in genome architecture, including the formation of the first loops between sites bound by the insulator protein CTCF and a large increase in the size of contact domains. In contrast, the binding of the CTCF is fixed throughout embryogenesis. Loops form long after genome-wide transcriptional activation, and long after domain formation seen in mouse embryos. These results suggest that, although loops may play a role in differentiation, they are not required for zygotic transcription. When we repeated our experiments in zebrafish, loops did not emerge until gastrulation, that is, well after zygotic genome activation. We observe that loop positions are highly conserved in synteny blocks of medaka and zebrafish, indicating that the 3D genome architecture has been maintained for >110–200 million years of evolution.en_US
dc.identifier.citationNakamura, Ryohei, Motai, Yuichi, Kumagai, Masahiko, et al.. "CTCF looping is established during gastrulation in medaka embryos." <i>Genome Research,</i> 31, (2021) Cold Spring Harbor Laboratory Press: 968-980. https://doi.org/10.1101/gr.269951.120.en_US
dc.identifier.digitalGenomeRes-2021-Nakamura-968-80en_US
dc.identifier.doihttps://doi.org/10.1101/gr.269951.120en_US
dc.identifier.urihttps://hdl.handle.net/1911/111930en_US
dc.language.isoengen_US
dc.publisherCold Spring Harbor Laboratory Pressen_US
dc.rightsThis article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.en_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/.en_US
dc.titleCTCF looping is established during gastrulation in medaka embryosen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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