Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model.

Bryan J. Matthews,David J. Waxman,Tisha Melia,Terry Furey

doi:10.1371/journal.pgen.1009588

Abstract

Sex differences in gene expression are widespread in the liver, where many autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57BL/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose their sex-biased expression in CAST/EiJ mouse liver. To elucidate the observed strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of the sex differences in expression between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-dependent gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs apparently lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.

Highlights

Many vertebrate tissues, including non-reproductive tissues, show significant sex differences in their gene expression profiles, metabolic and physiological properties, and patterns of disease susceptibility [1,2,3]
H3K27ac ChIPseq data for male and female B6 and CAST mouse liver are available under accession number GSE130909
DNase-seq data for male and female B6 and CAST mouse liver are available under accession number

Summary

Introduction

Many vertebrate tissues, including non-reproductive tissues, show significant sex differences in their gene expression profiles, metabolic and physiological properties, and patterns of disease susceptibility [1,2,3]. Hundreds of genes are expressed in a sex-dependent manner, including protein-coding genes [13], miRNAs [14,15] and lncRNA genes [16,17,18]. These sex differences in expression contribute to sex differences in chemical sensing and metabolism [19,20,21], response to injury [22,23], and susceptibility to disease [24,25,26,27]. Major dysregulation of hepatic sex-biased genes occurs upon loss of the GH receptor-activated proximal transcriptional regulator STAT5 [9,37,38] or its downstream targets, notably the transcriptional repressors Bcl6 [39,40] and Cux2 [41]

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Results

Discussion

Conclusion