Integrated chromatin and transcriptomic profiling reveals sex-specific mechanisms of gene regulation in hepatic nutrient responses

The three-dimensional organizing of the genome plays an important role in cellular function. Alterations between open and closed chromatin states contributes to DNA binding, collaborative transcriptional activities and informs post-transcriptional processing. The liver is the primary site orchestrating metabolic control, needing to mount a rapid adaptive response to environmental challenges. Here, we leveraged ATAC-seq to interrogate the chromatin architecture in liver under different dietary cues. We mapped over 120,000 nucleosome peaks, revealing a remarkably preserved hepatic chromatin landscape across feeding conditions. Stringent analysis of nucleosome rearrangements, unexpectedly, nominated sex as the most dominant factor segregating changes in chromatin accessibility. Lipid-rich diet led to a more accessible chromatin confirmation at promoter regions in female mice along with enrichment of promoter binding CCAAT-binding domain proteins. Male liver exhibited stronger binding for nutrient sensing nuclear receptors. Integrative analysis with gene expression and lipid composition corroborates a role for chromatin states in informing functional differences in metabolic traits. We uncouple the influence of gonadal and sex-chromosomal factors using the Four Core Genotype mouse model. Leveraging our framework, we provide mechanistic evidence underlying the regulation for the critical sex-dimorphic GWAS gene, Pnpla3. In summary, we provide a comprehensive epigenetic resource in murine liver that uncovers the complexity of chromatin dynamics in response to diet and sex. Overall design: Wild-type mice were obtained from The Jackson Laboratory and were fed ad libitum on either a standard chow diet, Western diet (WD: Research Diets, D12079B), or high-fat diet (HFD: Research Diets, D12492). For the ATAC-seq experiments, mice were subjected to diet treatments for 2 weeks. 75,000 nuclei were extracted and centrifuged at 500 g for 5 min at 4°C and used for the transposition reaction. ATAC-Seq libraries were constructed using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described (Buenrostro et al. 2015). We performed size selection usign AMPure XP magnetic beads. Libraries were sequenced at the Broad Stem Cell Research Center Sequencing Core (BSCRC) at UCLA.