Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse

Abstract

Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. To better understand the impact of the Y chromosome on autosomal DNA methylation patterns and its contribution to sex bias in methylation, we identified Y chromosome dependent differentially methylated regions (yDMRs) using whole-genome bisulfite sequencing methylation data from livers of mice with different combinations of sex-chromosome complement and gonadal sex. Nearly 90% of the autosomal yDMRs mapped to transposable elements (TEs) and most of them had lower methylation in XY compared to XX or XO mice. Follow-up analyses of four reporter autosomal yDMRs showed that Y-dependent methylation levels were consistent across most somatic tissues but varied in strains with different origins of the Y chromosome, suggesting that genetic variation in the Y chromosome influenced methylation levels of autosomal regions. Mice lacking the q-arm of the Y chromosome (B6.NPYq-2) as well as mice with a loss-of-function mutation in Kdm5d showed no differences in methylation levels compared to wild type mice. In conclusion, the Y-linked modifier of TE methylation is likely to reside on the short arm of Y chromosome and further studies are required to identify this gene.

Loss of Chromosome Y in Neuroblastoma Is Associated With High‐Risk Disease, 11q‐Deletion, and Telomere Maintenance

“…The genetic mechanisms predisposing to LoY are proposed to be shared by that of genomic instability [37] and defects in detecting and eliminating aneuploidy cause mis‐segregation and facilitate clonal expansion of LoY cells [38]. However, LoY has also been linked to demethylation of transposable elements [39], thereby affecting genome stability. If LoY in NB tumors reflect genomic instability, then LoY could serve as a biomarker for high‐risk NB disease.…”