Identification of novel functional TBP-binding sites and general factor repertoires

Denissov, S., Van Driel, M., Voit, R., Hekkelman, M., Hulsen, T., Hernandez, N., Grummt, I., Wehrens, R., Stunnenberg, H. (2007) Identification of novel functional TBP-binding sites and general factor repertoires. Embo Journal, 26 (4). pp. 944-954. ISSN 0261-4189

URL: http://www.nature.com/emboj/journal/v26/n4/full/76...
DOI: 10.1038/sj.emboj.7601550

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.

Item Type: Paper
Uncontrolled Keywords: ChIP-on-chip promoter TBP transcription factor profiling HISTONE ACETYLASE COMPLEX RNA-POLYMERASE-I HUMAN GENOME TRANSCRIPTION RECRUITMENT PROMOTERS CHROMOSOME-22 ENHANCERS SUBUNIT
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > RNA polymerase
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Chromatin dynamics
organism description > animal > mammal
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > pre-mRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > promoter
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Depositing User: CSHL Librarian
Date Deposited: 30 Nov 2011 20:15
Last Modified: 30 Nov 2011 20:15
PMCID: PMC1852848
URI: http://repository.cshl.edu/id/eprint/22997

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