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GEO Series: GSE41161

Title: Principles of nucleation of H3K27 methylation during embryonic development

Summary

During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 K27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here, we report on H3K27me3 deposition dynamics in Xenopus embryos, on sequence elements that initiate deposition during pluripotency, and the sequence characteristics that segregate Polycomb-regulated domains from the rest of the genome. Strikingly, although PRC2 binds widely to active enhancers, H3K27me3 is only deposited at a small subset of these sites. Using a Support Vector Machine algorithm these sequences can be predicted accurately on basis of DNA sequence alone, with a sequence signature conserved between humans, frog and fish. The results suggest a genetic-default model in which genomic sequence constrains Polycomb regulation.


Contributors: Gert Jan Veenstra, Simon van Heeringen, Robert Akkers, Ila van Kruijsbergen, Lars Hanssen, Nilofar Sharifi, Gert-Jan Veenstra, M. Asif Arif

Experiment Type: ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development

Article: XB-ART-47807, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
input WE - NF29/30 GSM1009604  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30  
   H3K27me3 WE - NF29/30 GSM1009596  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 H3f3a Ab24
   H3K4me3 WE - NF29/30 GSM1009592  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 Tri-Methyl H3f3a Ab19
   Pol II WE - NF29/30 GSM1009600  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 Polr2a Ab7
Ezh2 WE - NF9 GSM1009601  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Ezh2 Ab1
H3K27me3 WE - NF12 GSM1009594  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 H3f3a Ab24
H3K27me3 WE - NF16 GSM1009595  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 H3f3a Ab24
H3K27me3 WE - NF9 GSM1009593  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 H3f3a Ab24
H3K4me1 WE - NF9 GSM1009603  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 h3f3a Ab29
H3K4me3 WE - NF12 GSM1009590  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 Tri-Methyl H3f3a Ab19
H3K4me3 WE - NF16 GSM1009591  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 Tri-Methyl H3f3a Ab19
H3K4me3 WE - NF9 GSM1009589  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Tri-Methyl H3f3a Ab19
Jarid2 WE - NF9 GSM1009602  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 jarid2 Ab1
Pol II WE - NF12 GSM1009598  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 Polr2a Ab7
Pol II WE - NF16 GSM1009599  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 Polr2a Ab7
Pol II WE - NF9 GSM1009597  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Polr2a Ab7
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