<<< Full experiment listing


PXD001164 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleActive DNA demethylation during the vertebrate phylotypic period
DescriptionThe 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterA.H. Smits
SpeciesList scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive; LTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog 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
Bogdanovi, ć 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, G, ó, mez-Skarmeta JL, Lister R, Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet, 48(4):417-26(2016) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Zebrafish, Development, DNA methylation, DNA interactors, proteome
Contact List
Michiel Vermeulen
contact affiliationDepartment of Medical Oncology and Department of Molecular Cancer Research, Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht, the Netherlands
contact emailM.Vermeulen-3@umcutrecht.nl
lab head
A.H. Smits
contact affiliationRadboud University Nijmegen
contact emaila.smits@ncmls.ru.nl
dataset submitter
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/01/PXD001164
PRIDE project URI
Repository Record List
[ + ]