Molecular analyses of avian sex chromosomes and sex chromosome-like autosomes

Abstract

Sex chromosomes have originated multiple times throughout eukaryotes. In species with the XY sex-determination system, dosage compensation (a process that balances expression of sex-linked genes between sexes) is often efficient, and its epigenetic basis has been well studied. However, the extent of epigenetic differentiation between sexes in female-heterogametic systems (ZW), which generally lack complete compensation, is poorly understood. Here, I examined the genome-wide DNA methylation landscapes between males and females in mammalian and avian species. In contrast to the X chromosome in mammals, birds display highly similar methylation patterns between sexes on the Z chromosome. Despite this, in chicken and potentially other species in the Galloanserae lineage, two extremely localized regions with pronounced methylation differentiation were observed, including a previously identified locus (referred to as ‘male hypermethylated [MHM1]’) and a novel locus (referred to as ‘MHM2’). The two MHM loci bear remarkably similar molecular features and potential function in reducing male-to-female expression ratios of their neighboring genes. Therefore, DNA methylation is employed to solve dose problems for genes potentially essential to females, at least twice in the evolutionary history of the Galloanserae lineage. In the white-throated sparrow, a pair of autosomes that are distinguished by chromosomal inversions resemble sex chromosomes. In this species, two plumage morphs that mate almost exclusively with each other display striking behavioral differences: within the same sex, birds of the white-striped morph (ZAL2/ZAL2m) display more territorial aggression and less nestling provision than birds of the tan-striped morph (ZAL2/ZAL2). A detailed genomic comparison between a tan bird and a rare ZAL2m homozygote revealed subtle nucleotide differences between ZAL2 and ZAL2m as well as weak degeneration of the non-recombining ZAL2m chromosome. Nevertheless, a large proportion of genes exhibit allelic differential expression in the brain. Intriguingly, similar to the evolutionary path taken by sex chromosomes across many taxa, dosage compensation evolved as a mechanism to re-balance expression between morphs in this nascent autosomal system. Last, I examined the DNA methylation landscape of the white-throated sparrow. Differences in DNA methylation between chicks and adults are pervasive across the genome, with hypermethylation in adults consistent with the overexpression of DNA methyltransferases. Functional enrichment analysis revealed that the observed changes in methylation are likely involved in development. In contrast to the widespread age effects, morph influences are most prominent on the ZAL2/ZAL2m chromosomes. Notably, allelic differences in DNA methylation and allelic differences in gene expression are significantly linked. Taken together, these findings offer new insights into the epigenetic regulation of gene expression in avian sex chromosomes and sex chromosome-like autosomes.