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Series GSE67974 Query DataSets for GSE67974
Status Public on Dec 15, 2015
Title Embryonic transcription is controlled by maternally defined chromatin state
Organism Xenopus tropicalis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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.
Overall design 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
Contributor(s) Hontelez S, Veenstra GC
Citation(s) 26679111
Submission date Apr 16, 2015
Last update date May 15, 2019
Contact name Saartje Hontelez
Organization name Radboud University
Department Molecular developmental biology
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (2)
GPL15472 Illumina HiSeq 2000 (Xenopus (Silurana) tropicalis)
GPL20082 Illumina HiSeq 1500 (Xenopus (Silurana) tropicalis)
Samples (72)
GSM1659896 H3K4me1_stage9
GSM1659897 H3K4me1_stage10.5
GSM1659898 H3K4me1_stage12
BioProject PRJNA281501
SRA SRP057395

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Supplementary file Size Download File type/resource
GSE67974_RAW.tar 4.4 Gb (http)(custom) TAR (of BED, BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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