Identification of germline differentially methylated CGIs from DNA methylome profiles.

<p>(A) Venn-like diagram of two groups of CGIs, namely, oocyte-methylated CGIs (light pink) and sperm-methylated CGIs (light blue) and two groups of gDMRs, namely, oocyte-methylated gDMRs (red) and sperm-methylated gDMRs (blue). (B) The genomic distribution of 1329 oocyte-methylated (left) and 349 sperm-methylated gDMRs (right). The gDMRs were classified into 5 genomic locations; promoter (within 500-bp upstream from the first exon) or first exon, last exon, other exon, intron, and intergenic region. (C) The locations of the intragenic 1045 oocyte-methylated (left) and 229 sperm-methylated gDMRs (right). The gDMRs were classified into 5 gene group locations; the genes were divided into 5 percentile groups according to their expression levels in wild-type oocytes and sperm, as shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002440#pgen-1002440-g003" target="_blank">Figure 3</a>. (D) Histograms of the methylation levels of the gDMRs in blastocysts. The number of newly identified oocyte-specific, sperm-specific methylated gDMRs, and known ICRs are shown in black, red, and blue, respectively. (E) Bisulfite sequencing at the <i>Gpr1</i> gDMR in mouse blastocysts. (<i>Top</i>) Schematic representation of paternally-expressed <i>Gpr1</i>. The gene and gDMRs are shown in blue and green, respectively, and CpG sites are represented by vertical bars. (<i>Bottom</i>) Methylated and unmethylated CpGs are indicated by open and closed circles, respectively. The maternal and paternal alleles were distinguished by three polymorphisms between C57BL/6N and JF1 mice (G/A at 63,247,064; T/A at 63,247,072; and TA/AG at 63,247,089–63,247,090 on chromosome 1). (F) Histograms of the methylation levels of the demethylation-resistant oocyte-methylated gDMRs in <i>Dnmt3L^−/−</i> oocytes. The number of newly identified oocyte-specific, sperm-specific methylated gDMRs, and known ICRs are shown in black, red, and blue, respectively.