title: NFI transcription factors interact with FOXA1 to regulate prostate-specific gene expression.
abstract: Androgen receptor (AR) action throughout prostate development and in maintenance of the prostatic epithelium is partly controlled by interactions between AR and forkhead box (FOX) transcription factors, particularly FOXA1. We sought to identity additional FOXA1 binding partners that may mediate prostate-specific gene expression. Here we identify the nuclear factor I (NFI) family of transcription factors as novel FOXA1 binding proteins. All four family members (NFIA, NFIB, NFIC, and NFIX) can interact with FOXA1, and knockdown studies in androgen-dependent LNCaP cells determined that modulating expression of NFI family members results in changes in AR target gene expression. This effect is probably mediated by binding of NFI family members to AR target gene promoters, because chromatin immunoprecipitation (ChIP) studies found that NFIB bound to the prostate-specific antigen enhancer. Förster resonance energy transfer studies revealed that FOXA1 is capable of bringing AR and NFIX into proximity, indicating that FOXA1 facilitates the AR and NFI interaction by bridging the complex. To determine the extent to which NFI family members regulate AR/FOXA1 target genes, motif analysis of publicly available data for ChIP followed by sequencing was undertaken. This analysis revealed that 34.4% of peaks bound by AR and FOXA1 contain NFI binding sites. Validation of 8 of these peaks by ChIP revealed that NFI family members can bind 6 of these predicted genomic elements, and 4 of the 8 associated genes undergo gene expression changes as a result of individual NFI knockdown. These observations suggest that NFI regulation of FOXA1/AR action is a frequent event, with individual family members playing distinct roles in AR target gene expression.
authors.affiliation: Department of Urologic Surgery (M.M.G., G.A. H.Y., Q.S., X.Y., R.J.M.), Department of Molecular Physiology and Biophysics (A.D.E., D.W.P.), and Vanderbilt-Ingram Cancer Center (R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Pathology (D.J.D.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Biological Sciences (P.D.A.), Salisbury University, Salisbury, Maryland 21801; Mass Spectrometry Research Center (D.B.F., D.L.H.), Department of Biochemistry, Department of Biochemistry and Center for Structural Biology (J.H.S.), and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37232; Department of Chemistry (J.-M.A.), University of Texas Dallas, Dallas, Texas 75080; Department of Urology (G.V.R.), University of Texas Southwestern, Dallas, Texas 75390; and Department of Biochemistry (R.M.G.), Developmental Genomics Group, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203.
authors.forename: Magdalena M
authors.initials: MM
authors.lastname: Grabowska
authors.forename: Amicia D
authors.initials: AD
authors.lastname: Elliott
authors.forename: David J
authors.initials: DJ
authors.lastname: DeGraff
authors.forename: Philip D
authors.initials: PD
authors.lastname: Anderson
authors.forename: Govindaraj
authors.initials: G
authors.lastname: Anumanthan
authors.forename: Hironobu
authors.initials: H
authors.lastname: Yamashita
authors.forename: Qian
authors.initials: Q
authors.lastname: Sun
authors.forename: David B
authors.initials: DB
authors.lastname: Friedman
authors.forename: David L
authors.initials: DL
authors.lastname: Hachey
authors.forename: Xiuping
authors.initials: X
authors.lastname: Yu
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Sheehan
authors.forename: Jung-Mo
authors.initials: JM
authors.lastname: Ahn
authors.forename: Ganesh V
authors.initials: GV
authors.lastname: Raj
authors.forename: David W
authors.initials: DW
authors.lastname: Piston
authors.forename: Richard M
authors.initials: RM
authors.lastname: Gronostajski
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Matusik
mesh_terms: D000727:Androgen-Binding Protein / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D006367:HeLa Cells; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000378:metabolism*; D006801:Humans; D008297:Male; D051839:NFI Transcription Factors / Q000378:metabolism*; D009928:Organ Specificity; D011401:Promoter Regions, Genetic; D011467:Prostate / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D011944:Receptors, Androgen / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D000727:Androgen-Binding Protein; C496499:FOXA1 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; D051839:NFI Transcription Factors; D011944:Receptors, Androgen; C027519:probasin