title: Transcription Factor Hepatocyte Nuclear Factor-1β (HNF-1β) Regulates MicroRNA-200 Expression through a Long Noncoding RNA.
abstract: The transcription factor hepatocyte nuclear factor-1β (HNF-1β) regulates tissue-specific gene expression in the kidney and other epithelial organs. Mutations of HNF-1β produce kidney cysts, and previous studies have shown that HNF-1β regulates the transcription of cystic disease genes, including Pkd2 and Pkhd1. Here, we combined chromatin immunoprecipitation and next-generation sequencing (ChIP-Seq) with microarray analysis to identify microRNAs (miRNAs) that are directly regulated by HNF-1β in renal epithelial cells. These studies identified members of the epithelial-specific miR-200 family (miR-200b/200a/429) as novel transcriptional targets of HNF-1β. HNF-1β binds to two evolutionarily conserved sites located 28 kb upstream to miR-200b. Luciferase reporter assays showed that the HNF-1β binding sites were located within a promoter that was active in renal epithelial cells. Mutations of the HNF-1β binding sites abolished promoter activity. RT-PCR analysis revealed that a long noncoding RNA (lncRNA) is transcribed from the promoter and encodes the miR-200 cluster. Inhibition of the lncRNA with siRNAs decreased the levels of miR-200 but did not affect expression of the Ttll10 host gene. The expression of the lncRNA and miR-200 was decreased in kidneys from HNF-1β knock-out mice and renal epithelial cells expressing dominant-negative mutant HNF-1β. The expression of miR-200 targets, Zeb2 and Pkd1, was increased in HNF-1β knock-out kidneys and in cells expressing mutant HNF-1β. Overexpression of miR-200 decreased the expression of Zeb2 and Pkd1 in HNF-1β mutant cells. These studies reveal a novel pathway whereby HNF-1β directly contributes to the control of miRNAs that are involved in epithelial-mesenchymal transition and cystic kidney disease.
authors: From the Departments of Internal Medicine and.
authors: Sachin S
authors: SS
authors: Hajarnis
authors: From the Departments of Internal Medicine and.
authors: Vishal
authors: V
authors: Patel
authors: From the Departments of Internal Medicine and.
authors: Karam
authors: K
authors: Aboudehen
authors: From the Departments of Internal Medicine and.
authors: Massimo
authors: M
authors: Attanasio
authors: From the Departments of Internal Medicine and.
authors: Patricia
authors: P
authors: Cobo-Stark
authors: Départment de Génétique et Développement, INSERM U1016, CNRS UMR 8104, Université Paris-Descartes. Institut Cochin, 75014 Paris, France.
authors: Marco
authors: M
authors: Pontoglio
authors: From the Departments of Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and igarashi@umn.edu.
authors: Peter
authors: P
authors: Igarashi
mesh_terms: D000818:Animals; D001483:Base Sequence; D004847:Epithelial Cells / Q000378:metabolism; D005786:Gene Expression Regulation; D055786:Gene Knockout Techniques; D023281:Genomics; D006367:HeLa Cells; D051539:Hepatocyte Nuclear Factor 1-beta / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007668:Kidney / Q000166:cytology; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D009154:Mutation; D062085:RNA, Long Noncoding / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics; D050396:TRPP Cation Channels / Q000235:genetics; D000074165:Zinc Finger E-box Binding Homeobox 2
chemical_list: D051539:Hepatocyte Nuclear Factor 1-beta; D018398:Homeodomain Proteins; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012097:Repressor Proteins; D050396:TRPP Cation Channels; D000074165:Zinc Finger E-box Binding Homeobox 2; C496496:Hnf1b protein, mouse; C543719:Mirn200 microRNA, mouse; C492363:ZEB2 protein, human
keywords: ChIP-sequencing (ChIP-seq); epithelial-mesenchymal transition (EMT); hepatocyte nuclear factor 1 (HNF-1); kidney; long noncoding RNA (long ncRNA, lncRNA); microRNA (miRNA); transcription regulation