Dosage compensation and sexual conflict in female heterogametic methylomes

DNA methylation (DNAm) suppresses gene expression and contributes to dosage compensation in mammals but whether DNAm plays a similar role in female ZW chromosome heterogametic species remains unresolved. We assessed chromosome-level DNAm using whole genome bisulphite sequencing in two avian species, zebra finches and jackdaws. Dosage compensation by DNAm would result in higher and more variable DNAm level in males relative to females on the Z chromosome. However, we found that the level of DNAm and its variance on the Z chromosome was lower in males. Moreover, male Z chromosome-based gene promoters were more frequently hypomethylated compared to females, indicating absence of upregulation on a gene-by-gene basis across the female Z chromosome. We suggest our findings reveal mitigation of an intra-genomic sexual conflict, with females suppressing expression of Z chromosome-based genes that benefit male but not female fitness. W was the most methylated chromosome, but hypermethylation on the W chromosome was mostly confined to intergenic regions, presumably resulting in the downregulation of transposable elements known to comprise a large part of the W chromosome. Thus, DNAm is involved in the development of sex-dependent phenotypes, but dosage compensation is achieved through other mechanisms.