Sex differences in DNA methylation on sex chromosomes and chromatin accessibility patterns of MHMs. (A) Differences in DNA methylation between male and female X Chromosomes in human brains (5mC [%] [M-F]). (B) Differences in DNA methylation between male and female Z Chromosomes in the white-throated sparrow. (C) Differences in DNA methylation between male and female Z Chromosomes in chicken. Two regions with extreme sex differences in DNA methylation (MHM1 and MHM2) are highlighted. For A–C, methylation values were plotted using a 10-kb window size with a 2-kb step size. (D) A zoomed-in view of the MHM loci. Methylation levels (5mC [%]) for males (blue) and females (red) are shown in the upper lines. Lower lines (orange) depict sex differences in DNA methylation. (E) Both MHMs (shaded areas) display increased chromatin accessibility in females compared with males. ATAC-seq reads were merged per sex and normalized to fragment pileup per million reads for direct comparison between sexes. For either CD4+ T cells (Foissac et al. 2019) or forelimb (E4.5) (Sackton et al. 2019), the two loci contained significantly female-biased peaks, tested using bdgdiff from the MACS2 program (Zhang et al. 2008). The vast majority of tissue/cell types with available data show similar patterns (Supplemental Fig. S5).
