title: Identification of novel functional TBP-binding sites and general factor repertoires.
abstract: Our current knowledge of the general factor requirement in transcription by the three mammalian RNA polymerases is based on a small number of model promoters. Here, we present a comprehensive chromatin immunoprecipitation (ChIP)-on-chip analysis for 28 transcription factors on a large set of known and novel TATA-binding protein (TBP)-binding sites experimentally identified via ChIP cloning. A large fraction of identified TBP-binding sites is located in introns or lacks a gene/mRNA annotation and is found to direct transcription. Integrated analysis of the ChIP-on-chip data and functional studies revealed that TAF12 hitherto regarded as RNA polymerase II (RNAP II)-specific was found to be also involved in RNAP I transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG and non-CpG islands suggesting distinct transcription initiation pathways. Our study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TBP-binding sites in the human genome.
authors.affiliation: Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
authors.forename: Sergey
authors.initials: S
authors.lastname: Denissov
authors.forename: Marc
authors.initials: M
authors.lastname: van Driel
authors.forename: Renate
authors.initials: R
authors.lastname: Voit
authors.forename: Maarten
authors.initials: M
authors.lastname: Hekkelman
authors.forename: Tim
authors.initials: T
authors.lastname: Hulsen
authors.forename: Nouria
authors.initials: N
authors.lastname: Hernandez
authors.forename: Ingrid
authors.initials: I
authors.lastname: Grummt
authors.forename: Ron
authors.initials: R
authors.lastname: Wehrens
authors.forename: Hendrik
authors.initials: H
authors.lastname: Stunnenberg
mesh_terms: D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods; D018899:CpG Islands / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D046228:Microarray Analysis; D025341:Principal Component Analysis; D012318:RNA Polymerase I / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D035381:TATA-Binding Protein Associated Factors / Q000235:genetics / Q000378:metabolism*; D035181:TATA-Box Binding Protein / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: C470012:TAF12 protein, human; D035381:TATA-Binding Protein Associated Factors; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; D012319:RNA Polymerase II; D012318:RNA Polymerase I