Epigenetic landscape of hormone-independent sexual dimorphism and characterization of canine XIST

Sexual dimorphism in dogs (Canis lupus familiaris) manifests through pronounced differences in morphology, physiology, and disease susceptibility. Despite early neutering, the persistence of sex-specific differences highlights the need to investigate factors beyond sex hormones that contribute to these characteristics. We collected whole blood tissue from spayed female (n = 4) and castrated male (n = 4) beagles and performed whole genome bisulfite sequencing (WGBS) and RNA seq. To investigate hormone-independent sex dimorphism of DNA methylation in neutered dogs, we investigated differentially methylated genes (DMGs) between sexes and candidate molecular pathways. Furthermore, we analyzed sex-related correlations between gene expression and methylation levels. Sex-related differentially methylated genes, independent of hormone influence, are associated with oncogenic signaling and neuronal pathways. Differences in methylation status between the sexes were significantly associated with alterations in gene expression, indicating that methylation plays a regulatory role in gene transcription. Identification of canine XIST, previously annotated as LOC102156855, suggests a conserved mechanism of X-chromosome inactivation across species and a sex-specific epigenetic imprint on the genome, which is maintained independent of sex hormones. These findings enrich the understanding of sex-specific biology in dogs and highlight the intricate interplay between epigenetic modifications and gene expression in determining sex-specific phenotypes and disease susceptibilities.