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About the Authors:
Le Zhan
Affiliations Department of Pharmacology and Toxicology, School of Pharmacy, Rutgers University, Piscataway, New Jersey, United States of America, Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, United States of America
Hui-Xin Liu
Affiliation: Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California, United States of America
Yaping Fang
Affiliation: College of Science, Institute for Computer Applications, Huazhong Agricultural University, Wuhan, Hubei, China
Bo Kong
Affiliation: Department of Pharmacology and Toxicology, School of Pharmacy, Rutgers University, Piscataway, New Jersey, United States of America
Yuqi He
Affiliation: Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California, United States of America
Xiao-bo Zhong
Affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
Jianwen Fang
Affiliation: Biometric Research Branch, National Cancer Institute, Rockville, Maryland, United States of America
Yu-Jui Yvonne Wan
Affiliation: Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California, United States of America
Grace L. Guo
* E-mail: [email protected]
Affiliations Department of Pharmacology and Toxicology, School of Pharmacy, Rutgers University, Piscataway, New Jersey, United States of America, Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, United States of America
Introduction
Farnesoid X receptor (FXR, NR1H4) is a ligand activated transcription factor belonging to the nuclear receptor (NR) superfamily [1], and is highly expressed in the liver, intestine, and kidney, both in humans and rodents [2]. Bile acids (BAs) are the endogenous ligands of FXR [3]. FXR mainly functions as the BA sensor by regulating genes that are critically involved in BA homeostasis, including BA biosynthesis, conjugation, and enterohepatic circulation [4]. In addition, it has been shown that FXR is also involved in lipid and glucose homeostasis, inflammation, and tumorigenesis [4]–[7]. FXR normally forms a heterodimer with retinoid X receptor alpha (RXRα) and binds to DNA elements as FXR response elements (FXRREs) [1]. The most common DNA motif bound by FXR is an inverted repeat separated by one nucleotide (IR1). Upon ligand activation, the heterodimer normally activates the expression of its target genes.
Chromatin immunoprecipitation - deep sequencing (ChIP-seq) analysis has been widely used...