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Series GSE34864 Query DataSets for GSE34864
Status Public on Mar 28, 2012
Title A unique regulatory phase of DNA methylation in the early mammalian embryo
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and to date no base-resolution maps exist to support and refine it. Here, we generated genome-scale DNA methylation maps in mouse gametes and through post-implantation embryogenesis. We find that the oocyte already exhibits global hypomethylation, most prominently at specific subfamilies of LINE-1 and LTR-containing retro-elements, which are disparate between gametes and resolve to lower methylation values in zygote. Surprisingly, the oocyte contributes a unique set of Differentially Methylated Regions (DMRs), including many CpG Island promoter regions, that are maintained in the early embryo but are lost at the onset of embryonic specification and absent in somatic cells. In contrast, sperm contributed methylation includes retrotransposons that become completely methylated after the blastocyst stage. Our data provide a complete genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic and before returning to the canonical somatic pattern.
Overall design Comparison of DNA methylation patterns in mouse gametes and through embryogenesis using Reduced Representation Bisulfite Sequencing (RRBS)
Contributor(s) Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A
Citation(s) 22456710
Submission date Jan 04, 2012
Last update date Jul 06, 2022
Contact name Michelle M Chan
Organization name UCSF
Lab Weissman Lab
Street address 1700 4th St.
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (76)
GSM856495 oocytes-BDF1-1
GSM856496 oocytes-BDF1-2
GSM856497 oocytes-ICR-3
Reanalyzed by GSE171332
SRA SRP010119
BioProject PRJNA150129

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
GSE34864_RAW.tar 523.0 Mb (http)(custom) TAR (of TXT)
GSE34864_README.txt 878 b (ftp)(http) TXT
GSE34864_mousePMD100bpMe.txt.gz 93.8 Mb (ftp)(http) TXT
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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