title: Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1.
abstract: We used mouse hepatic chromatin enriched with an FXR antibody and chromatin immunoprecipitation-sequencing (ChIP-seq) to evaluate FXR binding on a genome-wide scale. This identified 1656 FXR-binding sites and 10% were located within 2 kb of a transcription start site which is much higher than predicted by random occurrence. A motif search uncovered a canonical nuclear receptor IR-1 site, consistent with in vitro DNA-binding studies reported previously. A separate nuclear receptor half-site for monomeric receptors such as LRH-1 was co-enriched and FXR activation of four newly identified promoters was significantly augmented by an LRH-1 expression vector in a co-transfection assay. There were 1038 genes located within 20 kb of a peak and a gene set enrichment analysis showed that genes identified by our ChIP-seq analysis are highly correlated with genes activated by an FXR-VP16 adenovirus in primary mouse hepatocytes providing functional relevance to the genome-wide binding study. Gene Ontology analysis showed FXR-binding sites close to many genes in lipid, fatty acid and steroid metabolism. Other broad gene clusters related to metabolism, transport, signaling and glycolysis were also significantly enriched. Thus, FXR may have a much wider role in cellular metabolism than previously appreciated.
authors.affiliation: Department of Molecular Biology and Biochemistry, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA.
authors.forename: Hansook Kim
authors.initials: HK
authors.lastname: Chong
authors.forename: Aniello M
authors.initials: AM
authors.lastname: Infante
authors.forename: Young-Kyo
authors.initials: YK
authors.lastname: Seo
authors.forename: Tae-Il
authors.initials: TI
authors.lastname: Jeon
authors.forename: Yanqiao
authors.initials: Y
authors.lastname: Zhang
authors.forename: Peter A
authors.initials: PA
authors.lastname: Edwards
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Xie
authors.forename: Timothy F
authors.initials: TF
authors.lastname: Osborne
mesh_terms: D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D005786:Gene Expression Regulation; D016678:Genome; D008099:Liver / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D011401:Promoter Regions, Genetic; D018160:Receptors, Cytoplasmic and Nuclear / Q000378:metabolism*; D020218:Response Elements; D017422:Sequence Analysis, DNA; D000099150:Receptor, Farnesoid X-Activated
chemical_list: D018160:Receptors, Cytoplasmic and Nuclear; D000099150:Receptor, Farnesoid X-Activated; C431936:Nr5a2 protein, mouse