GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

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)

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)

More...

GSM1845258	ChIP-Seq growing oocyte 7days K4Me3
GSM1845259	ChIP-Seq growing oocyte 10days K4Me3
GSM1845260	ChIP-Seq growing oocyte 14days K4Me3

GSM1845261	ChIP-Seq GV 8weeks K4Me3
GSM1845262	ChIP-Seq MII oocyte K4Me3 rep1
GSM1845263	ChIP-Seq MII oocyte K4Me3 rep2
GSM1845264	ChIP-Seq PN5 zygote K4Me3 rep1
GSM1845265	ChIP-Seq PN5 zygote K4Me3 rep2
GSM1845266	ChIP-Seq 2-cell early K4Me3 rep1
GSM1845267	ChIP-Seq 2-cell early K4Me3 rep2
GSM1845268	ChIP-Seq 2-cell late K4Me3 rep1
GSM1845269	ChIP-Seq 2-cell late K4Me3 rep2
GSM1845270	ChIP-Seq 4-cell K4Me3 rep1
GSM1845271	ChIP-Seq 4-cell K4Me3 rep2
GSM1845272	ChIP-Seq 8-cell K4Me3 rep1
GSM1845273	ChIP-Seq 8-cell K4Me3 rep2
GSM1845274	ChIP-Seq ICM K4Me3 rep1
GSM1845275	ChIP-Seq ICM K4Me3 rep2
GSM1845276	ChIP-Seq epiblast E6.5 K4Me3
GSM1845277	ChIP-Seq cortex K4Me3
GSM1845280	ChIP-Seq 2cell alpha-amanitin K4Me3
GSM1845281	ChIP-Seq 2cell aphidicolin K4Me3
GSM1845282	ChIP-Seq MII oocyte commercial antibody K4Me3
GSM1845283	ChIP-Seq PN5 zygote histone H3
GSM1845284	ChIP-Seq 5000 mESC K4Me3
GSM1845285	ChIP-Seq 2000 mESC K4Me3
GSM1845286	ChIP-Seq 500 mESC K4Me3 rep1
GSM1845287	ChIP-Seq 200 mESC K4Me3 rep1
GSM1845288	ChIP-Seq 500 mESC commercial antibody K4Me3
GSM1845289	ChIP-Seq 1000 mESC K27Me3
GSM1845290	ChIP-Seq 500 mESC K27Ac
GSM1845291	ChIP-Seq oocyte K4Me3 zebrafish
GSM1845292	RNA-Seq Growing_oocyte_10days
GSM1845293	RNA-Seq Growing_oocyte_14days
GSM1845294	RNA-Seq GV_8weeks
GSM1845295	RNA-Seq MII_oocyte_rep1
GSM1845296	RNA-Seq MII_oocyte_rep2
GSM1845297	RNA-Seq zygote_PN5_rep1
GSM1845298	RNA-Seq zygote_PN5_rep2
GSM1845299	RNA-Seq 2cell_early_rep1
GSM1845300	RNA-Seq 2cell_early_rep2
GSM1845301	RNA-Seq 2cell_late_rep1
GSM1845302	RNA-Seq 2cell_late_rep2
GSM1845303	RNA-Seq 4cell_rep1
GSM1845304	RNA-Seq 4cell_rep2
GSM1845305	RNA-Seq 8cell_rep1
GSM1845306	RNA-Seq 8cell_rep2
GSM1845307	RNA-Seq ICM rep1
GSM1845308	RNA -seq ICM rep2
GSM1845312	RNA-Seq PN5 zygote alpha-amanitin
GSM1845313	RNA-Seq 2cell alpha-amanitin
GSM1845314	RNA-Seq 2cell aphidicolin rep1
GSM1845315	RNA-Seq 2cell aphidicolin rep2
GSM2101161	ChIP-Seq Maternal pronucleus of PN3 zygote K4Me3
GSM2101162	ChIP-Seq Paternal pronucleus of PN3 zygote K4Me3
GSM2101163	ChIP-Seq sperm K4Me3 rep1
GSM2205867	ChIP-Seq sperm K4Me3 rep2

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

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 Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |