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Series GSE71434 Query DataSets for GSE71434
Status Public on Sep 15, 2016
Title Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
Organisms Danio rerio; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Histone modifications are considered as fundamental epigenetic regulators that control many crucial cellular processes 1. However, whether these marks can be passed on from gametes to the next generation in mammals is a long-standing question that remains unclear. By developing a highly sensitive approach, STAR ChIP-seq, we provided a panoramic view of the landscape of H3K4me3, a histone hallmark for transcription initiation 2, from developing gametes to postimplantation embryos. Interestingly, we found that upon fertilization, extensive reprogramming occurred on the paternal genome, as few H3K4me3 peaks were observed in zygotes before they reappeared after major zygotic genome activation at the late 2-cell stage. On the maternal genome, we unexpectedly found a non-canonical form of H3K4me3 (ncH3K4me3) in full-grown and mature oocytes, which exists as broad peaks at promoters and a large number of distal loci. Such broad H3K4me3 peaks are in striking contrast to typical sharp H3K4me3 peaks restricted in CpG rich regions of promoters. Interestingly, ncH3K4me3 in oocytes overlaps almost exclusively with partially methylated DNA domains (PMDs). It is then inherited in preimplantation embryos before being erased in the late 2-cell embryos, when canonical H3K4me3 starts to be established. The removal of ncH3K4me3 requires zygotic transcription but is independent of DNA replication mediated passive dilution. Finally, downregulation of H3K4me3 in full-grown oocytes by overexpressing an H3K4me3 demethylase KDM5B is associated with defects in genome silencing. Taken together, these data unveiled inheritance and highly dynamic reprogramming of the epigenome in early mammalian development.
Overall design Mouse preimplantation embryos were obtained from crosses of C57BL/6N and PWK. A newly developed ChIP-seq approach (STAR ChIP-seq) and RNA-seq were performed in these embryos at variou stages in preimplantation development.

Please note that [1] 'PN5 zygote histone H3' sample represents input files for PN5_K4me3 sample, using H3 antibody.
[2] both separate (for each replicate sample, i.e. sample supplementary file) and combined processed bed file (for all replicates, i.e. Series supplementary file) have been provided.
Contributor(s) Zhang B, Zheng H, Huang B, Li W, Xie W
Citation(s) 27626382
Submission date Jul 28, 2015
Last update date May 15, 2019
Contact name Bingjie Zhang
Organization name Tsinghua University
Street address 30 Shuangqing Rd
City Beijing
State/province Beijing
ZIP/Postal code 100190
Country China
Platforms (2)
GPL18171 Illumina HiSeq 1500 (Danio rerio)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (57)
GSM1845258 ChIP-Seq growing oocyte 7days K4Me3
GSM1845259 ChIP-Seq growing oocyte 10days K4Me3
GSM1845260 ChIP-Seq growing oocyte 14days K4Me3
BioProject PRJNA292073
SRA SRP062106

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
GSE71434_2cell_APH_maternal_K4me3.bed.gz 18.2 Mb (ftp)(http) BED
GSE71434_2cell_APH_paternal_K4me3.bed.gz 8.9 Mb (ftp)(http) BED
GSE71434_2cell_amanitin_maternal_K4me3.bed.gz 18.0 Mb (ftp)(http) BED
GSE71434_2cell_amanitin_paternal_K4me3.bed.gz 9.2 Mb (ftp)(http) BED
GSE71434_2cell_early_K4me3.bed.gz 71.3 Mb (ftp)(http) BED
GSE71434_2cell_early_K4me3_broadpeak.bed.gz 382.9 Kb (ftp)(http) BED
GSE71434_2cell_early_maternal_K4me3.bed.gz 33.2 Mb (ftp)(http) BED
GSE71434_2cell_early_maternal_broadpeak.bed.gz 327.3 Kb (ftp)(http) BED
GSE71434_2cell_early_paternal_K4me3.bed.gz 18.8 Mb (ftp)(http) BED
GSE71434_2cell_early_paternal_broadpeak.bed.gz 87.6 Kb (ftp)(http) BED
GSE71434_2cell_late_K4me3.bed.gz 67.0 Mb (ftp)(http) BED
GSE71434_2cell_late_K4me3_broadpeak.bed.gz 346.9 Kb (ftp)(http) BED
GSE71434_2cell_late_maternal_K4me3.bed.gz 25.6 Mb (ftp)(http) BED
GSE71434_2cell_late_maternal_broadpeak.bed.gz 134.3 Kb (ftp)(http) BED
GSE71434_2cell_late_paternal_K4me3.bed.gz 14.7 Mb (ftp)(http) BED
GSE71434_2cell_late_paternal_broadpeak.bed.gz 156.8 Kb (ftp)(http) BED
GSE71434_4cell_K4me3.bed.gz 54.6 Mb (ftp)(http) BED
GSE71434_4cell_K4me3_broadpeak.bed.gz 310.2 Kb (ftp)(http) BED
GSE71434_4cell_maternal_K4me3.bed.gz 20.4 Mb (ftp)(http) BED
GSE71434_4cell_maternal_broadpeak.bed.gz 211.1 Kb (ftp)(http) BED
GSE71434_4cell_paternal_K4me3.bed.gz 11.5 Mb (ftp)(http) BED
GSE71434_4cell_paternal_broadpeak.bed.gz 170.9 Kb (ftp)(http) BED
GSE71434_8cell_K4me3.bed.gz 53.9 Mb (ftp)(http) BED
GSE71434_8cell_K4me3_broadpeak.bed.gz 268.3 Kb (ftp)(http) BED
GSE71434_8cell_maternal_K4me3.bed.gz 18.6 Mb (ftp)(http) BED
GSE71434_8cell_maternal_broadpeak.bed.gz 165.4 Kb (ftp)(http) BED
GSE71434_8cell_paternal_K4me3.bed.gz 14.1 Mb (ftp)(http) BED
GSE71434_8cell_paternal_broadpeak.bed.gz 144.6 Kb (ftp)(http) BED
GSE71434_FPKM_inhibition.txt.gz 390.3 Kb (ftp)(http) TXT
GSE71434_FPKM_stage.txt.gz 762.8 Kb (ftp)(http) TXT
GSE71434_ICM_K4me3.bed.gz 50.5 Mb (ftp)(http) BED
GSE71434_ICM_K4me3_broadpeak.bed.gz 206.6 Kb (ftp)(http) BED
GSE71434_ICM_maternal_K4me3.bed.gz 14.7 Mb (ftp)(http) BED
GSE71434_ICM_maternal_broadpeak.bed.gz 141.1 Kb (ftp)(http) BED
GSE71434_ICM_paternal_K4me3.bed.gz 11.8 Mb (ftp)(http) BED
GSE71434_ICM_paternal_broadpeak.bed.gz 125.6 Kb (ftp)(http) BED
GSE71434_MII_oocyte_K4me3.bed.gz 64.0 Mb (ftp)(http) BED
GSE71434_MII_oocyte_K4me3_broadpeak.bed.gz 685.1 Kb (ftp)(http) BED
GSE71434_PN5_zygote_K4me3.bed.gz 71.0 Mb (ftp)(http) BED
GSE71434_PN5_zygote_K4me3_broadpeak.bed.gz 485.7 Kb (ftp)(http) BED
GSE71434_RAW.tar 2.9 Gb (http)(custom) TAR (of BED)
GSE71434_sperm_K4me3.bed.gz 74.4 Mb (ftp)(http) BED
GSE71434_sperm_K4me3_broadpeak.bed.gz 143.2 Kb (ftp)(http) BED
GSE71434_zygote_maternal_K4me3.bed.gz 29.6 Mb (ftp)(http) BED
GSE71434_zygote_maternal_broadpeak.bed.gz 479.7 Kb (ftp)(http) BED
GSE71434_zygote_paternal_K4me3.bed.gz 12.0 Mb (ftp)(http) BED
GSE71434_zygote_paternal_broadpeak.bed.gz 12.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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