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Series GSE125318 Query DataSets for GSE125318
Status Public on Dec 18, 2019
Title Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Around implantation, the epiblast transits from naïve to primed pluripotency, before giving rise to the three germ layers. How chromatin is reconfigured during this developmental window remains poorly understood. We performed a genome-wide investigation of chromatin landscapes during this period. We find that enhancers in ectoderm are already pre-accessible in embryonic day 6.5 (E6.5) Epi when cells enter a primed pluripotent state. Unexpectedly, strong H3K4me3 emerges at developmental gene promoters in E6.5 epiblast and positively correlates with H3K27me3, thus establishing bivalency. These genes also show enhanced spatial interactions. Both the strong bivalency and spatial clustering are virtually absent in preimplantation embryos and are markedly reduced in fate-committed lineages. Finally, we show that KMT2B is essential for establishing bivalent H3K4me3 at E6.5 but becomes partially dispensable later. Its deficiency leads to impaired activation of developmental genes and subsequent embryonic lethality. Thus, our data characterize lineage-specific chromatin reconfiguration and a unique chromatin state for primed pluripotency.
Overall design To determine the dynamics of chromatin states during gastrulation in mouse early embryos, male (DBA2) and female (C57BL/6N) were mated and multiple lineages were separated from embryos, including epiblast (Epi) and visceral endoderm (VE) at embryonic day 6.5 (E6.5), ectoderm (Ect), primitive streak (PS), mesoderm (Mes) and endoderm (End) at E7.5. We then conducted miniATAC-seq and STAR ChIP-seq for H3K4me3, H3K27ac, and H3K27me3 in these tissues. We also performed RNA-seq, ChIP-seq, MethylC-seq, and sisHi-C in E6.5Epi and/or E8.5 head tissues to determine the chromatin configuration in embryos upon loss of Kmt2b.
Contributor(s) Xiang Y, Zhang Y, Xie W
Citation(s) 31844322
Submission date Jan 18, 2019
Last update date Mar 18, 2020
Contact name Wei Xie
Organization name Tsinghua University
Department School of Life Science
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (104)
GSM3568840 RNA_E65Epi_Kmt2b_KO_rep1
GSM3568841 RNA_E65Epi_Kmt2b_KO_rep2
GSM3568842 RNA_E65Epi_Kmt2b_KO_rep3
BioProject PRJNA515849
SRA SRP180192

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125318_ATAC_bed.tar.gz 245.6 Mb (ftp)(http) TAR
GSE125318_ChIP_bed.tar.gz 1.5 Gb (ftp)(http) TAR
GSE125318_E65Epi_Kmt2b_KO_rep1.hic 883.1 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_KO_rep2.hic 780.0 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_KO_rep3.hic 803.2 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_WT_rep1.hic 808.5 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_WT_rep2.hic 723.9 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_WT_rep3.hic 819.1 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_WT_rep4.hic 614.7 Mb (ftp)(http) HIC
GSE125318_E65Epi_Kmt2b_WT_rep5.hic 665.0 Mb (ftp)(http) HIC
GSE125318_Kmt2b.RNA.FPKM.txt.gz 561.5 Kb (ftp)(http) TXT
GSE125318_MethylC_E65Epi_Kmt2b_KO_mCG.bed.gz 80.6 Mb (ftp)(http) BED
GSE125318_MethylC_E85_head_Kmt2b_KO_mCG.bed.gz 84.3 Mb (ftp)(http) BED
GSE125318_MethylC_E85_head_Kmt2b_WT_mCG.bed.gz 85.0 Mb (ftp)(http) BED
GSE125318_Tet12.RNA.FPKM.txt.gz 662.6 Kb (ftp)(http) TXT
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