PXD001164-3

PXD001164 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:06:39.996.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	A.H. Smits
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-07-22 06:45:41	ID requested
1	2016-01-27 08:46:55	announced
2	2016-03-16 06:18:29	announced	Updated publication reference for PubMed record(s): 26928226.
⏵ 3	2024-10-22 04:06:40	announced	2024-10-22: Updated project metadata.

10.1038/ng.3522;

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]

curator keyword: Biological

submitter keyword: Zebrafish, DNA interactors, Development, DNA methylation, proteome

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

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

• PRIDE
  1. PXD001164
     1. Label: PRIDE project
     2. Name: Active DNA demethylation during the vertebrate phylotypic period