Tissue-specific epigenetic and genetic regulation of sexual dimorphism

Sexual dimorphism evolves from sex-specific selective pressures and is often mediated by tissue-specific differential gene expression, although the mechanisms are not fully understood. Here, we investigate the role of DNA methylation as a potential regulator of tissue-specific sex-biased gene expression in the house sparrow (Passer domesticus). We found that both gene expression and DNA methylation show a strong tissue-specific pattern, and that samples clustered by tissue type, except in gonadal tissue, where there was a strong sex-specific clustering. Sex-biased gene expression and sex-biased DNA methylation patterns were more enriched on the Z-chromosome than on the autosomes, and most sex-biased genes were tissue-specific, with the majority of sex bias occurring in the gonads. As expected, we detected a strong negative correlation between DNA methylation levels and gene expression levels around the transcription start site (TSS). In gonads, sex-biased DNA methylation accounted for 14% of the sex differences in gene expression. These findings highlight heterogeneous methylation and expression patterns among tissues and thus the importance of choosing the correct tissue for studies aiming to gain insights into the evolution of sexually dimorphic traits. Understanding these genetic mechanisms is vital for comprehending the evolutionary potential of sexes, their ecological roles and for informing conservation efforts. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.