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Open Access Highly Accessed Research article

Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR

Hansook Kim Chong125, Jacob Biesinger23, Young-Kyo Seo1, Xiaohui Xie23 and Timothy F Osborne14*

Author Affiliations

1 Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 USA

2 Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697 USA

3 Department of Computer Science, University of California, Irvine, CA 92697 USA

4 Metabolic Signaling and Disease Program, Burnham Institute for Medical Research, Lake Nona FL 32827 USA

5 Ambry Genetics, 100 Columbia #200 Aliso Viejo, California 92656 USA

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BMC Genomics 2012, 13:51  doi:10.1186/1471-2164-13-51

Published: 1 February 2012

Abstract

Background

In a previous genome-wide analysis of FXR binding to hepatic chromatin, we noticed that an extra nuclear receptor (NR) half-site was co-enriched close to the FXR binding IR-1 elements and we provided limited support that the monomeric LRH-1 receptor that binds to NR half-sites might function together with FXR to activate gene expression.

Results

To analyze the global pattern for LRH-1 binding and to determine whether it might associate with FXR on a whole genome-wide scale, we analyzed LRH-1 binding to the entire hepatic genome using a non-biased genome-wide ChIP-seq approach. We identified over 10,600 LRH-1 binding sites in hepatic chromatin and over 20% were located within 2 kb of the 5' end of a known mouse gene. Additionally, the results demonstrate that a significant fraction of the genome sites occupied by LRH-1 are located close to FXR binding sites revealed in our earlier study. A Gene ontology analysis revealed that genes preferentially enriched in the LRH-1/FXR overlapping gene set are related to lipid metabolism. These results demonstrate that LRH-1 recruits FXR to lipid metabolic genes. A significant fraction of FXR binding peaks also contain a nuclear receptor half-site that does not bind LRH-1 suggesting that additional monomeric nuclear receptors such as RORs and NR4As family members may also target FXR to other pathway selective genes related to other areas of metabolism such as glucose metabolism where FXR has also been shown to play an important role.

Conclusion

These results document an important role for LRH-1 in hepatic metabolism through acting predominantly at proximal promoter sites and working in concert with additional nuclear receptors that bind to neighboring sites

Keywords:
LRH-1; FXR; ChIP-seq; lipid metabolism