Single Nucleus MultiOmics Links Novel Transcription Factor Motifs to Murine Hepatic Sex Differences in Chromatin Accessibility and Metabolic Dysfunction-Associated Steatotic Liver Disease

Abstract

The liver exhibits striking sexual dimorphism in gene expression that impacts drug and lipid metabolism and disease susceptibility, with males showing substantially higher predisposition to metabolic dysfunction-associated steatotic liver disease (MASLD) and its complications including hepatocellular carcinoma. These sex differences are primarily controlled by sexually dimorphic pituitary growth hormone (GH) secretion patterns; however, the underlying transcriptional and epigenetic regulatory networks remain only partially understood. Here, we generated paired single-nucleus chromatin accessibility (snATAC-seq) and gene expression (snRNA-seq) profiles from 46,188 liver nuclei isolated from male, female and continuous GH-infused male mice to comprehensively map the epigenetic basis of hepatic sexual dimorphism. We identified 127,957 accessible chromatin regions genome-wide, including thousands of novel regions enriched specifically in non-parenchymal cells. Sex-biased differentially accessible chromatin regions (DARs) were almost exclusively hepatocyte-localized, and continuous GH infusion feminized their accessibility, demonstrating that plasma GH patterns alone are sufficient to reprogram sex-biased hepatocyte chromatin landscapes. Correlation-based peak-to-gene linkage analysis mapped these DARs to sex-biased gene targets and revealed that regulatory interactions are constrained by topologically associated domain boundaries. Motif enrichment analysis identified both established regulators (STAT5, CUX2, BCL6) and novel transcription factors (TFs) at sex-biased DARs. ATAC-seq footprinting revealed novel TF motifs predicted to be occupied at DARs linked to sex-biased genes implicated in MASLD, providing mechanistic insights into the male bias in fatty liver disease. Further, motif co-occurrence analysis revealed TF clusters likely cooperating to regulate sex-dependent gene expression programs. We also identified stringently cell type-specific regulatory regions with cell type-specific TF motifs that define the regulatory architecture underlying hepatocyte and non-parenchymal cell identities. This comprehensive multiOmic atlas elucidates TF networks controlling sex-dependent liver gene expression and serves as a foundational resource for understanding molecular mechanisms underlying sex disparities in MASLD and other liver diseases.