Figure 2

Sex impacts global distribution of CpG methylation on the X chromosome. (A) Histogram plot representing frequency distribution of methylation level (mCG/CG) across CpG sites with depth of at least 10x on the X chromosome. Number of CpGs included: B6 Female, 787,051; B6 Male, 793,002; C3 Female, 773,057; C3 Male, 787,158. (B) Histogram plot representing frequency distribution of methylation level (mCG/CG) across CpG sites with depth of at least 10x on a representative autosome, chromosome 3. Number of CpGs included: B6 Female, 1,055,125; B6 Male, 1,049,035; C3 Female, 1,014,511; C3 Male, 1,019,177. (C) Number of differentially methylated regions (DMRs) on chromosomes X and 3 that distinguish male from female animals using two different tools, DSS and Metilene. DMRs are partitioned by direction, indicating regions with greater methylation level in female mice (F > M) or regions with greater methylation level in male mice (M > F). (D) Number of DMRs on chromosomes X and 3 that distinguish B6 from C3 animals. DMRs are partitioned by direction, indicating regions with greater methylation level in B6 mice (B6 > C3) or regions with greater methylation level in C3 mice (C3 > B6). (E) Boxplots of CG weighted methylation levels at sex-specific DMRs (using DSS) on the X chromosome for B6 male, C3 male, B6 female, and C3 female mice. Methylation levels at F > M DMRs are significantly less than methylation levels at M > F DMRs, regardless of sex (Mann-Whitney U-test). (F) Percentage of sex-specific DMRs (using DSS) on the X chromosome that overlap intergenic regions, TSS, or intragenic (non-TSS) regions. (G) Percentage of sex-specific DMRs (using DSS) on the X chromosome that overlap CpG island regions or non-CpG island regions. Percentages were calculated based on total DMR count for each type (F > M, M > F, random genomic null region set). ChrX, chromosome X; Chr3, chromosome 3.