HNF-1β is a tissue-specific transcription factor that is expressed in the kidney and other epithelial organs. Humans with mutations in HNF-1β develop kidney cysts, and HNF-1β regulates the transcription of several cystic disease genes. However, the complete spectrum of HNF-1β-regulated genes and pathways is not known. Here, using chromatin immunoprecipitation/next generation sequencing and gene expression profiling, we identified 1545 protein-coding genes that are directly regulated by HNF-1β in murine kidney epithelial cells. Pathway analysis predicted that HNF-1β regulates cholesterol metabolism. Expression of dominant negative mutant HNF-1β or kidney-specific inactivation of HNF-1β decreased the expression of genes that are essential for cholesterol synthesis, including sterol regulatory element binding factor 2 (Srebf2) and 3-hydroxy-3-methylglutaryl-CoA reductase (Hmgcr). HNF-1β mutant cells also expressed lower levels of cholesterol biosynthetic intermediates and had a lower rate of cholesterol synthesis than control cells. Additionally, depletion of cholesterol in the culturemediummitigated the inhibitory effects ofmutant HNF-1β on the proteins encoded by Srebf2 andHmgcr, andHNF-1β directly controlled the renal epithelial expression of proprotein convertase subtilisin-like kexin type 9, a key regulator of cholesterol uptake. These findings reveal a novel role of HNF-1β in a transcriptional network that regulates intrarenal cholesterol metabolism.
Bibliographical noteFunding Information:
We thankPatriciaCobo-Stark and SachinHajarnis for expert technical assistance, Zhendong Ma for assistance with chromatin immunoprecipitation sequencing, and Jeffery McDonald for assistance with liquid chromatography-Tandemmass spectrometry.We also thank Jay Horton and David Russell for helpful discussions. This work was supported by National Institutes of Health (NIH) Grant R37DK042921 (to P.I.) and University of Texas Southwestern O'Brien Kidney Research Core Center NIH Grant P30DK079328. K.A. and L.N. were supported by NIH Training Grant T32DK007257. M.P. was supported by Fondation pour la recherche m?dicale (FRM), European Community's Seventh Framework Programmme FP7/2009 Agreement 241955 (SYSCILIA), and Agence Nationale pour le Recherche. R.D.-B. is an Early Career Scientist of the Howard Hughes Medical Institute and was supported by NIH Grant HL20948.