Genomic analysis of hepatic farnesoid X receptor (FXR) binding sites reveals altered binding in obesity and direct gene repression by FXR

Abstract

The nuclear bile acid receptor, Farnesoid X Receptor (FXR), is an important transcriptional regulator of liver metabolism. Despite recent advances in understanding its functions, how FXR regulates genomic targets and whether the transcriptional regulation by FXR is altered in obesity remain largely unknown. Here, we analyzed hepatic genome-wide binding sites of FXR in normal and dietary obese mice by chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. A total of 15,263 and 5,272 FXR binding sites were identified in livers of normal and obese mice, respectively, after a short one hour treatment with the synthetic FXR agonist, GW4064. Of these sites, 7,440 and 2,344 were detected uniquely in normal and obese mice. FXR binding sites were localized mostly in intergenic and intron regions at an IR1 motif in both groups, but also clustered within 1 kb of transcription start sites. FXR binding sites were detected near previously unknown target genes with novel functions, including diverse cellular signaling pathways, apoptosis, autophagy, hypoxia, inflammation, RNA processing, metabolism of amino acids, and transcriptional regulators. Further analyses of randomly selected genes from both normal and obese mice suggested more FXR binding sites are likely functionally inactive in obesity. Surprisingly, occupancies of FXR, RXRα, RNA polymerase II, and epigenetic gene activation and repression histone marks, and mRNA levels of genes examined, suggested that direct gene repression by agonist-activated FXR is common. Comparison of genomic FXR binding sites in normal and obese mice further suggested that FXR transcriptional signaling is altered in dietary obese mice, which may underlie aberrant metabolism and liver function in obesity. (HEPATOLOGY 2012.)