Regulation of Chromatin Accessibility by the Farnesoid X Receptor Is Essential for Circadian and Bile Acid Homeostasis In Vivo

SIMPLE SUMMARY: The Farnesoid X Receptor (FXR) is a nuclear receptor that regulates the expression of several genes involved in the metabolism of bile acids (BAs) which is essential for normal liver function. In this study, we used the CRISPR/Cas9 system to generate a novel FXR knockout mouse model and demonstrate that FXR deletion in hepatocytes is associated with a global reduction in chromatin accessibility. The loss of chromatin accessibility was predominantly localized to promoter-associated transcription factor motifs, such as the NFγ/CBP and the KLF/SP1 family of pioneer transcription factors. Importantly, we demonstrate that the loss of FXR mediated chromatin accessibility contributes to dysregulation in bile acid and circadian homeostasis in hepatocytes. ABSTRACT: The Farnesoid X Receptor (FXR) belongs to the nuclear receptor superfamily and is an essential bile acid (BA) receptor that regulates the expression of genes involved in the metabolism of BAs. FXR protects the liver from BA overload, which is a major etiology of hepatocellular carcinoma. Herein, we investigated the changes in gene expression and chromatin accessibility in hepatocytes by performing RNA-seq in combination with the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) using a novel FXR knockout mouse model (Fxr(ex5Δ): Nr1h4(ex5Δ/ex5Δ)) generated through CRISPR/Cas9. Consistent with previous Fxr knockout models, we found that Fxr(ex5Δ) mice develop late-onset HCC associated with increased serum and hepatic BAs. FXR deletion was associated with a dramatic loss of chromatin accessibility, primarily at promoter-associated transcription factor binding sites. Importantly, several genes involved in BA biosynthesis and circadian rhythm were downregulated following loss of FXR, also displayed reduced chromatin accessibility at their promoter regions. Altogether, these findings suggest that FXR helps to maintain a transcriptionally active state by regulating chromatin accessibility through its binding and recruitment of transcription factors and coactivators.