Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

Dna methylation is an epigenetic modification that plays a crucial role in normal mammalian development,retrotransposon silencing,and cellular reprogramming. although methylation mainly occurs on the cytosine in a cg site,non-cg methylation is prevalent in pluripotent stem cells,brain,and oocytes. we previously identified non-cg methylation in several cg-rich regions in mouse germinal vesicle oocytes (gvos),but the overall distribution of non-cg methylation and the enzymes responsible for this modification are unknown. using amplification-free whole-genome bisulfite sequencing,which can be used with minute amounts of dna,we constructed the base-resolution methylome maps of gvos,non-growing oocytes (ngos),and mutant gvos lacking the dna methyltransferase dnmt1,dnmt3a,dnmt3b,or dnmt3l. we found that nearly two-thirds of all methylcytosines occur in a non-cg context in gvos. the distribution of non-cg methylation closely resembled that of cg methylation throughout the genome and showed clear enrichment in gene bodies. compared to ngos,gvos were over four times more methylated at non-cg sites,indicating that non-cg methylation accumulates during oocyte growth. lack of dnmt3a or dnmt3l resulted in a global reduction in both cg and non-cg methylation,showing that non-cg methylation depends on the dnmt3a-dnmt3l complex. dnmt3b was dispensable. of note,lack of dnmt1 resulted in a slight decrease in cg methylation,suggesting that this maintenance enzyme plays a role in non-dividing oocytes. dnmt1 may act on cg sites that remain hemimethylated in the de novo methylation process. our results provide a basis for understanding the mechanisms and significance of non-cg methylation in mammalian oocytes. © 2013 shirane et al.