Hepatocyte Nuclear Factor 4 Alpha and Farnesoid X Receptor Co-regulates Gene Transcription in Mouse Livers on a Genome-Wide Scale

Farnesoid X receptor (Fxr) is a ligand-activated nuclear receptor critical for liver function. Reports indicate that the functions of Fxr in the liver may overlap with those of hepatocyte nuclear factor 4 alpha (Hnf4 alpha), but studies of their precise genome-wide interaction to regulate gene transcription in the liver are lacking. Thus, we compared the genome-wide binding of Fxr and Hnf4 alpha in the liver of mice and characterized their cooperative activity on binding to and activating target gene transcription. Genome-wide ChIP-Seq data of Fxr and Hnf4 alpha in mouse liver were analyzed by MACS, BEDTools, and DAVID. Co-immunoprecipitation, ChIP-qPCR, and luciferase assays were done to test for protein-protein interaction and cooperative binding. ChIP-seq analysis showed nearly 50% binding sites of Fxr and Hnf4 alpha in mouse liver overlap and Hnf4 alpha bound to shared target sites upstream and in close proximity to Fxr. Moreover, genes co-bound by Fxr and Hnf4 alpha are enriched in complement and coagulation cascades and drug metabolism. A direct Fxr-Hnf4 alpha protein interaction dependent on Fxr activity was detected and transcriptional assays suggest that Hnf4 alpha can increase Fxr transcriptional activity. Conversely, binding assays showed Hnf4 alpha can be either Fxr-dependent or -independent at different shared binding sites. Our results showed that Fxr cooperates with Hnf4 alpha in the liver to modulate gene transcription. This study provides the first evidence on a genome-wide scale of both cooperative and independent interactions between Fxr and Hnf4 alpha in regulating gene transcription in the liver.