Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice

Sex-specific transcription characterizes hundreds of genes in mouse liver, many implicated in sex-differential drug and lipid metabolism and disease susceptibility. While the regulation of liver sex differences by growth hormone-activated STAT5 is well established, little is known about autosomal genetic factors regulating the sex-specific liver transcriptome. Here we show, using genotyping and expression data from a large population of Diversity Outbred mice, that genetic factors work in tandem with growth hormone to control the individual variability of hundreds of sex-biased genes, including many lncRNA genes. Significant associations between single nucleotide polymorphisms and sex-specific gene expression were identified as expression quantitative trait loci (eQTLs), many of which showed strong sex-dependent associations. Remarkably, autosomal genetic modifiers of sex-specific genes were found to account for more than 200 instances of gain or loss of sex-specificity across eight Diversity Outbred mouse founder strains. Sex-biased STAT5 binding sites and open chromatin regions with strain-specific variants were significantly enriched at eQTL regions regulating correspondingly sex-specific genes, supporting the proposed functional regulatory nature of the eQTL regions identified. Binding of the male-biased, growth hormone-regulated repressor BCL6 was most highly enriched at trans-eQTL regions controlling female-specific genes. Co-regulated gene clusters defined by overlapping eQTLs included sets of highly correlated genes from different chromosomes, further supporting trans-eQTL action. These findings elucidate how an unexpectedly large number of autosomal factors work in tandem with growth hormone signaling pathways to regulate the individual variability associated with sex differences in liver metabolism and disease. Author summaryMale-female differences in liver gene expression confer sex differences in many biological processes relevant to health and disease, including lipid and drug metabolism and liver disease susceptibility. While the role of hormonal factors, most notably growth hormone, in regulating hepatic sex differences is well established, little is known about how autosomal genetic factors impact sex differences on an individual basis. Here, we harness the power of mouse genetics provided by the Diversity Outbred mouse model to discover significant genome-wide associations between genetic variants and sex-specific liver gene expression. Remarkably, we found that autosomal expression quantitative trait loci with a strong sex-bias account for the loss or gain of sex-specific expression of more than 200 autosomal genes seen across eight founder mice strains. Genetic associations with sex-specific genes were enriched for sex-biased and growth hormone-dependent regulatory regions harboring strain-specific genetic variants. Co-regulated gene clusters identified by overlapping regulatory regions included highly correlated genes from different chromosomes. These findings reveal the extensive regulatory role played by autosomal genetic variants, working in tandem with growth hormone signaling pathways, in the transcriptional control of sex-biased genes, many of which have been implicated in sex differential outcomes in liver metabolism and disease susceptibility.