Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

• DOI: 10.1371/journal.pgen.1002440
• Publication Date: 2012-01-06T08:47:27Z
• Authors: Hisato Kobayashi; Takayuki Sakurai; Misaki Imai; Nozomi Takahashi; Atsushi Fukuda; Obata Yayoi; Shun Sato; Kazuhiko Nakabayashi; Kenichiro Hata; Yusuke Sotomaru; Yutaka Suzuki; Tomohiro Kono
• Keywords: Genomic Imprinting; RNA-Directed DNA Methylation; Illumina Methylation Assay; Differentially methylated regions; Bisulfite sequencing; Methylated DNA immunoprecipitation; CpG site; Epigenomics

Genome-wide dynamic changes in DNA methylation are indispensable for germline development and genomic imprinting mammals. Here, we report single-base resolution methylome transcriptome maps of mouse germ cells, generated using whole-genome shotgun bisulfite sequencing cDNA (mRNA-seq). Oocyte genomes showed a significant positive correlation between mRNA transcript levels the transcribed region. Sperm had nearly complete coverage methylation, except CpG-rich regions, negative gene expression promoter methylation. Thus, these revealed that oocytes sperms widely different extent distribution Furthermore, comparison oocyte sperm methylomes identified more than 1,600 CpG islands differentially methylated (germline gDMRs), addition to known control regions (ICRs). About half sequences appear be at least partially resistant global demethylation occurs during preimplantation development. In absence Dnmt3L, neither most oocyte-methylated gDMRs nor intragenic was observed. There also genome-wide hypomethylation, partial particular retrotransposons, while maintaining expression, oocytes. Along with identification many Dnmt3L-dependent present results suggest can divided into 2 types: which is required maternal imprinting, Dnmt3L-independent might essential endogenous retroviral silencing. The data provide entirely new perspectives on evaluation epigenetic markers cells.