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Series GSE56650 Query DataSets for GSE56650
Status Public on Sep 11, 2014
Title Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed during early embryogenesis to establish full developmental potential. Previous studies have suggested that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes subsequent passive demethylation via DNA replication during cleavage. Active demethylation is known to depend on 5mC oxidation by Tet dioxygenases and excision of oxidized bases by thymine DNA glycosylase (TDG). Here we show that both maternal and paternal genomes undergo widespread active and passive demethylation in zygotes before the first mitotic division. Passive demethylation was blocked by the replication inhibitor aphidicolin, and active demethylation was abrogated by deletion of Tet3 in both pronuclei. At actively demethylated loci, 5mCs were processed to unmodified cytosines. Surprisingly, the demethylation process was unaffected by the deletion of TDG from the zygote, suggesting the existence of other demethylation mechanisms downstream of Tet3-mediated oxidation.
Overall design The dataset includes RRBS anlysis of 2 MII oocyte samples, 3 WT female pronuclei samples PN3-4 stage, 2 Tet3 KO female pronuclei samples and 2 Aphidicolin treated female pronuclei samples. Also as male counterpart, a Sperm sample, 2 WT male pronuclei samples PN3-4 stage, 2 Tet3 KO male pronuclei samples and 2 Aphidicolin treated male pronuclei samples were included.
Contributor(s) Guo F, Li X, Liang D, Li T, Zhu P, Guo H, Wu X, Wen L, Gu T, Hu B, Walsh CP, Li J, Tang F, Xu G
Citation(s) 25220291
Submission date Apr 09, 2014
Last update date May 15, 2019
Contact name Xianlong Li
Organization name Peking University
Department Biodynamic Optical Imaging Center, College of Life Sciences
Street address 5, Yiheyuan Rd., Haidian District
City Beijing
ZIP/Postal code 100871
Country China
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (16)
GSM1366370 Oocyte_1
GSM1366371 Oocyte_2
GSM1366372 FemalePN_WT_2
BioProject PRJNA244161
SRA SRP041060

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Supplementary file Size Download File type/resource
GSE56650_RAW.tar 625.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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