Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

Abstract

We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-related differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation, and disease. To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse livers and in livers of male mice feminized by continuous infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-related differences. Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male livers. We also identified broad genomic regions (up to ϳ100 kb) showing sex-dependent hypersensitivity and similar patterns of GH responses. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100 kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism and several new candidates for further investigation. This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions. Sexual dimorphism in gene expression is common in mammalian somatic tissues (23) and has broad implications for human health. Sex differences in gene expression may contribute to differences between men and women in the prevalence, extent, and progression of disease, including autoimmune diseases (54), kidney disease (37), cardiovascular disease (45), and liver diseases, such as hepatocellular carcinoma (9, 58). In addition, sex-related differences in pharmacokinetics and pharmacodynamics are common and may affect drug response (52). Sex-related differences in gene expression have been widely studied in liver, where they affect Ͼ1,000 transcripts (5, 51, 57) and impact physiological and pathophysiological functions ranging from lipid and fatty acid metabolism to xenobiotic metabolism and disease susceptibility (52). In the liver, sexrelated differences in gene expression are primarily determined by growth hormone (GH) signaling (3, 21), which shows important sex-related differences that reflect the sex-related differences in plasma GH profiles seen in many species, including rats, mice, and humans (53).The underlying mechanisms of sexual dimorphism in mammalian tissues have been only partly elucidated at the molecular level. In the male rat liver, intermittent plasma GH pulses repeatedly activate the latent cytoplasmic transcription factor STAT5b, whose activity is essential for sex-related differences in the liver (5). The more continuous, female-like pattern of pituitary GH secretion can be mimicked by continuous GH infusion in mal...

Decreased expression of Small glutamine-rich tetratricopeptide repeat-containing protein (SGT) correlated with prognosis of Hepatocellular carcinoma

“…SGTB expression did not correlate with age, metastasis, tumor size, cirrhosis, the level of AFP, but notably correlated with gender, histological grade (P<0.001) and HBsAg (P=0.002) ( Table 1). Although the sgtb gene is considered as weakly female specific in mouse liver in some research [14], we haven't find the discrepancy between the male and female human paracancerous liver tissues.…”

Activation of DNA Damage Response Signaling by Condensed Chromatin

“…Damage-induced chromatin changes were dampened in both the expansion and compaction phases after overexpression of the Set1/Ash2 methyltransferase ASH2L (Fig. 1B), which globally increases the H3 lysine 4 methyl mark that is implicated in transcriptional activation and mediates chromatin expansion through recruitment of chromatin modifiers (Boyle et al, 2008; Chambeyron and Bickmore, 2004; Consortium et al, 2007; Ling et al, 2010; Luco et al, 2010; Santos-Rosa et al, 2002; Shimada et al, 2006). In agreement with recent findings (Khurana et al, 2014) we conclude that the DNA damage response involves initial expansion of chromatin followed by a phase of chromatin condensation.…”

Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone

“…The enrichment of sex-specific lincRNAs for nearby and correspondingly sex-biased binding by GH-dependent transcriptional activators and the inverse pattern of sex-biased binding by GH-dependent repressors indicate a role for these TFs in the proximal regulation of sex-specific lincRNA transcription, in addition to their established roles in regulating expression of sex-specific protein-coding genes (52)(53)(54)(55). One such GH-regulated TF, STAT5, is a key GH-responsive factor whose deletion in male mouse liver leads to widespread disruption of sex-specific coding-gene expression (57) and sex-specific lincRNA expression ( Fig.…”

“…We investigated whether sex-specific lincRNA genes are enriched for nearby sites of sex-dependent chromatin accessibility, which bind TFs in a sex-dependent manner (54)(55)(56) and can be detected as sex-biased DHS (52). We found that the stringent (i.e., GH-regulated) male-specific lincRNAs are significantly enriched for nearby (within 10 kb) male-biased DHS (P ϭ 5.77eϪ11) and depleted of female-biased DHS.…”

“…In the liver, sex-biased gene expression is regulated by the sex-dependent patterns of pituitary growth hormone (GH) release (39): pulsatile GH release in males versus persistent (nearly continuous) GH release in females (45)(46)(47). The resulting sex differences in plasma GH profiles activate the TF STAT5 (48) by JAK2-catalyzed tyrosine phosphorylation (49) in a dynamic, sex-differential manner (50,51), which is linked to downstream sex differences in liver chromatin accessibility and epigenetic (histone) marks (52,53). These sex-differential chromatin states are associated with sex differences in the binding of STAT5 and other GH-regulated TFs (54)(55)(56), which together regulate the sex-biased transcription of ϳ1,000 liver-expressed genes (57)(58)(59).…”