Fig. 1

DNA methylation profiles of the X and Y chromosome. All plots show raw (non-normalized) data after probe filtering. A Density plot of X and Y chromosome beta values by sex. XX sample beta value densities are shown in blue, XY sample beta value densities are shown in dashed green. B Difference in DNAme between XX and XY samples at all CpGs along the X chromosome in the filtered dataset, difference in DNAme β values between the sexes (XX-XY) is plotted on the Y axis, hg19 X chromosome coordinates are plotted along the x axis. Blue highlights indicate PAR1 (chrX:60001–2699520), the X-transposed region (chrX:88400000–92000000), and PAR2 (chrX:154931044–155260560). C Difference in DNAme between XX and XY samples along the X chromosome using hg19 chrX coordinates. Plots are separated into CpGs associated with CpG island (CGI) promoter or gene body regions, blue highlights indicate PAR1, the X-transposed region, and PAR2