Monodelphis domestica Epigenomics

Hypermethylation at CpG islands associated with gene promoters is a late, stabilizing step that maintains transcriptional silence on the inactive X chromosome of eutherian mammals. In contrast to eutherians, there are limited genome wide data on DNA methylation from other vertebrates. Previous studies of single genes in various marsupial models revealed no differential DNA methylation of promoters between the sexes, leading to the conclusion that it plays no role in marsupial X-inactivation. Using reduced representation bisulfite sequencing, we analysed CpG methylation to generate male and female methylation profiles in four representative vertebrates (mouse, gray short-tailed opossum, platypus and chicken). Platypus and chicken displayed no large-scale differential DNA methylation between the sexes on the autosomes or the sex chromosomes. As expected, in female mice, we observed hypermethylation at transcription start sites of genes subject to X-inactivation. In opossum there was no differential DNA methylation detected between the sexes at transcription start sites of genes subject to X-inactivation. However, regions flanking transcription start sites (especially 1.25-3.75 kb upstream) of these genes were hypomethylated. For genes subject to X-inactivation, our data demonstrate that the difference between DNA methylation level at transcription start sites and their flaking regions is consistent between eutherian and marsupial mammals, which we propose has a silencing effect in both groups. Our study is the first genome wide analysis of DNA methylation from matched tissue in male and female chicken, platypus and opossum. It provides the first evidence for a regulatory role of DNA methylation in marsupial X-inactivation.