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

Tisha Melia,David J Waxman,Gregory S Barsh

doi:10.1371/journal.pone.0242665

Abstract

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 long non-coding RNA 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.

Highlights

Sex differences in mammalian gene expression are not limited to reproductive tissues, and occur somatic tissues [1], most notably the liver, as seen in mouse [2,3,4], rat [5, 6] and human [7, 8]
Sex-biased gene expression was highly variable across the eight Diversity Outbred (DO) founder strains (Fig 1A), with sex bias lost in at least one strain for 96% of the genes examined, and only 20 genes showing sex-biased expression in all 8 strains
Principal component analysis (PCA) based on the expression levels of all sex-specific genes revealed that the largest variance (PC1) corresponds to the sex of each liver, as expected, while the second component (PC2) clustered the individual liver samples based on the evolutionary distance between strains (Fig 1C)

Summary

Introduction

Sex differences in mammalian gene expression are not limited to reproductive tissues, and occur somatic tissues [1], most notably the liver, as seen in mouse [2,3,4], rat [5, 6] and human [7, 8]. Growth hormone (GH) is a key regulator of sex-biased gene expression [25, 26] and acts via its sex-dependent pattern of pituitary secretion: pulsatile in males and nearly continuous in females in both rodents and humans [27,28,29]. These sex differential plasma GH profiles, in turn, induce the sex-differential activation of the JAK2/STAT5 signaling pathway in hepatocytes. Sex differences are evident in the liver epigenome, including extensive sex differences in open chromatin regions (DNase I hypersensitive sites; DHS) [33, 34], chromatin marks [4, 35, 36], DNA methylation [37,38,39] and 3D genomic interactions and organization [40] associated with the transcription of sex-specific genes

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Discussion

Conclusion