Article: article from journal or magazin.
Identification of novel functional TBP-binding sites and general factor repertoires.
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.
Binding Sites/genetics, Chromatin Immunoprecipitation/methods, CpG Islands/genetics, Gene Expression Regulation/genetics, Genome, Human/genetics, Humans, Microarray Analysis, Principal Component Analysis, RNA Polymerase I/metabolism, RNA Polymerase II/metabolism, Reverse Transcriptase Polymerase Chain Reaction, TATA-Binding Protein Associated Factors/genetics, TATA-Binding Protein Associated Factors/metabolism, TATA-Box Binding Protein/metabolism, Transcription Factors/genetics
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