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Series GSE163620 Query DataSets for GSE163620
Status Public on Nov 26, 2021
Title The conservation and divergence of epigenitic reprogramming during mammalian early development
Organisms Sus scrofa; Bos taurus; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Other
Methylation profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To explore how parental epigenetic information is transmitted to the next generation across mammals, we systematically investigated the epigenomes of oocytes and early embryos among human, bovine, porcine, rat, and mouse. This unprecedented dataset revealed strikingly diverse, species-specific innovation of epigenetic transition. In oocytes, DNA methylation is restricted to active gene bodies in rodents, allowing methylation of maternal imprints but not intergenic paternal imprints. Strikingly, hypermethylation also occurs in non-transcribed regions in porcine and bovine, where paternal imprints instead reside in hypomethylated, megabase-long “CpG continents (CGCs)”. Despite the presence of H3K4me3 and H3K27me3 domains in non-human oocytes, only rodent H3K27me3 survives beyond genome activation, supporting H3K27me3-mediated imprinting. Coincidently, regulatory elements are segregated away from H3K27me3 domains, the ectopic invasion of which leads to aberrant embryonic transcription. Finally, human does not fully resemble any of the rest species. Hence, mammals invent diverse epigenetic inheritance and reprogramming which center around a delicate balance in establishing imprints while protecting other regulatory regions.
 
Overall design DNA methylomes, H3K4me3, H3K27me3, H3K36me2, H3K36me3 are profiled and analyzed in the gametes and preimplantation embryos among five mammalian species, including human, bovine, porcine, rat and mouse.
 
Contributor(s) Lu X, Zhang Y, Xie W
Citation(s) 34818044
Submission date Dec 21, 2020
Last update date Nov 27, 2021
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
 
Platforms (4)
GPL21273 HiSeq X Ten (Mus musculus)
GPL22918 HiSeq X Ten (Sus scrofa)
GPL24230 HiSeq X Ten (Bos taurus)
Samples (188)
GSM4982814 bovine_FGO_DNAme_rep1
GSM4982815 porcine_FGO_DNAme_rep1
GSM4982816 porcine_FGO_DNAme_rep2
Relations
BioProject PRJNA686960
SRA SRP298725

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
GSE163620_RAW.tar 194.2 Mb (http)(custom) TAR (of BW)
GSE163620_evolution_processed_data_files.tar.gz 3.8 Gb (ftp)(http) TAR
GSE163620_mouseEed_Ctrl_MII_H3K4me3_merge.bw 69.9 Mb (ftp)(http) BW
GSE163620_mouseEed_mCKO_MII_H3K4me3_merge.bw 75.3 Mb (ftp)(http) BW
GSE163620_pig_PG_Mo_4rep_merged_fpkm_ens2GeneName.txt.gz 401.3 Kb (ftp)(http) TXT
GSE163620_pig_PG_Mo_H3K27me3_CR.bw 36.2 Mb (ftp)(http) BW
GSE163620_pig_PG_Mo_H3K4me3_CR.bw 53.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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