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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2016-01-27
  • AnnouncementXML: Submission_2016-03-16_06:18:28.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: A.H. Smits
  • Title: Active DNA demethylation during the vertebrate phylotypic period
  • Description: The vertebrate body plan and organs are shaped during a highly conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of thousands of enhancers during the phylotypic period in zebrafish, Xenopus and mouse. These dynamic enhancers are linked to essential developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. Phylotypic stage-specific binding of Tet proteins to (hydroxy)methylated DNA, and enrichment of hydroxymethylcytosine on these enhancers, implicated active DNA demethylation in this process. Furthermore, loss of function of Tet1/2/3 in zebrafish caused reduced chromatin accessibility and increased methylation levels specifically on these enhancers, indicative of DNA methylation being an upstream regulator of phylotypic enhancer function. Overall, our study reveals a novel regulatory module associated with the most conserved phase of vertebrate embryogenesis and uncovers an ancient developmental role for the Tet dioxygenases.
  • SpeciesList: scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
  • ModificationList: monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
  • Instrument: Q Exactive; LTQ Orbitrap Velos

Dataset History

VersionDatetimeStatusChangeLog Entry
02014-07-22 06:45:41ID requested
12016-01-27 08:46:55announced
22016-03-16 06:18:29announcedUpdated publication reference for PubMed record(s): 26928226.

Publication List

  1. Bogdanović O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen M, Gómez-Skarmeta JL, Lister R, Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet, 48(4):417-26(2016) [pubmed]

Keyword List

  1. curator keyword: Biological
  2. submitter keyword: Zebrafish, Development, DNA methylation, DNA interactors, proteome

Contact List

    Michiel Vermeulen
    • contact affiliation: Department of Medical Oncology and Department of Molecular Cancer Research, Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht, the Netherlands
    • contact email: M.Vermeulen-3@umcutrecht.nl
    • lab head:
    A.H. Smits
    • contact affiliation: Radboud University Nijmegen
    • contact email: a.smits@ncmls.ru.nl
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
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