Comparative developmental genomics of sex-biased gene expression in early embryogenesis across mammals

Mammalian gonadal sex is determined by the presence or absence of a Y chromosome. In males, the Y chromosome initiates male gonadogenesis and the subsequent production of male-specific hormones defines the male state of each cell in the organism. In females, the lack of a Y chromosome and the presence of two X chromosomes triggers the development of female gonads, hormones, and cellular identity. However, sex chromosome-linked genes encoding dosage-sensitive transcription and epigenetic factors are expressed well before gonad formation and have the potential to establish sex-biased expression. Here, we apply a comparative bioinformatics analysis on published single-cell datasets from mouse and human during very early embryogenesis–from two-cell to preimplantation stages–to characterize sex-specific signals and to assess the degree of conservation among early-acting sex-specific genes and pathways. Clustering and regression analyses of gene expression across samples reveal that sex initially plays a significant role in overall gene expression patterns at the earliest stages of embryogenesis. In addition, gene expression signals from male and female gametes during fertilization may still be present. Although these transcriptional sex effects rapidly diminish, the sex-biased expression of epigenetic enzymes has the potential to establish sex-specific patterns that persist beyond preimplantation. Sex-biased genes appear to form sex-specific protein-protein interaction networks across preimplantation stages in both mammals. While the distribution of sex-differentially expressed genes (sexDEGs) in early embryonic stages are similar in mice and humans, the genes involved are generally different. Non-negative matrix factorization (NMF) on male and female transcriptomes generated clusters of genes with similar expression patterns across sex and developmental stages including post-fertilization, epigenetic, and preimplantation ontologies conserved between mouse and human. This comparative study uncovers much earlier than expected sex-specific signals in mouse and human embryos that pre-date hormonal signaling from the gonads. These early signals are diverged with respect to orthologs yet conserved in terms of function with important implications in the use of genetic models for sex-specific disease.