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GEO Series: GSE67974

Title: Embryonic transcription is controlled by maternally defined chromatin state

Summary

During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of embryonic epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using α-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3 and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300-recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences.


Contributors: Saartje Hontelez, GertJan Veenstra

Experiment Type: We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA

Experiment Reagents: alpha-amanitin.

Article: XB-ART-51677, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
Pol II WE - NF11 GSM1974230  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 polr2a Ab8
   Pol II WE + alpha amanitin - NF11 GSM1974229  ChIP-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical alpha-amanitin NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 polr2a Ab8
WE - NF11 GSM1974232  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
   WE + alpha amanitin - NF11 DEG GSM1974231  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical alpha-amanitin NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
H3K27me3 WE - NF11 GSM1659936  GSM1974226  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 H3f3a Ab24
   H3K27me3 WE + alpha amanitin - NF11 GSM1659935  GSM1974225  ChIP-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical alpha-amanitin NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 H3f3a Ab24
H3K4me3 WE - NF11 GSM1659905  GSM1974224  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 Tri-Methyl H3f3a Ab19
   H3K4me3 WE + alpha amanitin - NF11 GSM1659904  GSM1974223  ChIP-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical alpha-amanitin NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 Tri-Methyl H3f3a Ab19
input WE - NF29/30 GSM1659955  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30  
   H3K27me3 WE - NF29/30 GSM1659939  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 H3f3a Ab24
   H3K36me3 WE - NF29/30 GSM1659919  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 H3f3a Ab30
   H3K4me1 WE - NF29/30 GSM1659900  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 methyl-H3f3a Ab13
   H3K4me3 WE - NF29/30 GSM1659908  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 Tri-Methyl H3f3a Ab19
   H3K9ac WE - NF29/30 GSM1659914  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 h3f3a Ab32
   H3K9me2 WE - NF29/30 GSM1659944  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 h3f3a Ab31
   H3K9me3 WE - NF29/30 GSM1659949  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 H3f3a Ab26
   H4K20me3 WE - NF29/30 GSM1659954  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 Hist1h4a Ab1
   Pol II WE - NF29/30 GSM1659931  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 polr2a Ab8
   ep300 WE - NF29/30 GSM1659926  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30 ep300 Ab1
ep300 WE - NF11 GSM1659923  GSM1974228  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 ep300 Ab1
   ep300 WE + alpha amanitin - NF11 GSM1659922  GSM1974227  ChIP-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical alpha-amanitin NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 ep300 Ab1
H3K27me3 WE - NF10.5 GSM1659934  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 H3f3a Ab24
H3K27me3 WE - NF12 GSM1659937  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 H3f3a Ab24
H3K27me3 WE - NF16 GSM1659938  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 H3f3a Ab24
H3K27me3 WE - NF8 GSM1659932  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8 H3f3a Ab24
H3K27me3 WE - NF9 GSM1659933  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 H3f3a Ab24
H3K36me3 WE - NF10.5 GSM1659916  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 H3f3a Ab30
H3K36me3 WE - NF12 GSM1659917  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 H3f3a Ab30
H3K36me3 WE - NF16 GSM1659918  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 H3f3a Ab30
H3K36me3 WE - NF9 GSM1659915  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 H3f3a Ab30
H3K4me1 WE - NF10.5 GSM1659897  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 methyl-H3f3a Ab13
H3K4me1 WE - NF12 GSM1659898  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 methyl-H3f3a Ab13
H3K4me1 WE - NF16 GSM1659899  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 methyl-H3f3a Ab13
H3K4me1 WE - NF9 GSM1659896  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 methyl-H3f3a Ab13
H3K4me3 WE - NF10.5 GSM1659903  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 Tri-Methyl H3f3a Ab19
H3K4me3 WE - NF12 GSM1659906  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 Tri-Methyl H3f3a Ab19
H3K4me3 WE - NF16 GSM1659907  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 Tri-Methyl H3f3a Ab19
H3K4me3 WE - NF8 GSM1659901  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8 Tri-Methyl H3f3a Ab19
H3K4me3 WE - NF9 GSM1659902  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Tri-Methyl H3f3a Ab19
H3K9ac WE - NF10.5 GSM1659911  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 h3f3a Ab32
H3K9ac WE - NF12 GSM1659912  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 h3f3a Ab32
H3K9ac WE - NF16 GSM1659913  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 h3f3a Ab32
H3K9ac WE - NF8 GSM1659909  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8 h3f3a Ab32
H3K9ac WE - NF9 GSM1659910  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 h3f3a Ab32
H3K9me2 WE - NF10.5 GSM1659941  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 h3f3a Ab31
H3K9me2 WE - NF12 GSM1659942  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 h3f3a Ab31
H3K9me2 WE - NF16 GSM1659943  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 h3f3a Ab31
H3K9me2 WE - NF9 GSM1659940  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 h3f3a Ab31
H3K9me3 WE - NF10.5 GSM1659946  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 H3f3a Ab26
H3K9me3 WE - NF12 GSM1659947  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 H3f3a Ab26
H3K9me3 WE - NF16 GSM1659948  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 H3f3a Ab26
H3K9me3 WE - NF9 GSM1659945  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 H3f3a Ab26
H4K20me3 WE - NF10.5 GSM1659951  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 Hist1h4a Ab1
H4K20me3 WE - NF12 GSM1659952  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 Hist1h4a Ab1
H4K20me3 WE - NF16 GSM1659953  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 Hist1h4a Ab1
H4K20me3 WE - NF9 GSM1659950  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Hist1h4a Ab1
Pol II WE - NF10.5 GSM1659928  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 polr2a Ab8
Pol II WE - NF12 GSM1659929  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 polr2a Ab8
Pol II WE - NF16 GSM1659930  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 polr2a Ab8
Pol II WE - NF9 GSM1659927  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 polr2a Ab8
WE - NF10.5 GSM1677167  Bisulfite-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
WE - NF9 GSM1875285  Bisulfite-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
ep300 WE - NF10.5 GSM1659921  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 ep300 Ab1
ep300 WE - NF12 GSM1659924  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 ep300 Ab1
ep300 WE - NF16 GSM1659925  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 ep300 Ab1
ep300 WE - NF9 GSM1659920  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 ep300 Ab1
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