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| Subject Categories: Chromatin & Transcription | Genomic & Computational Biology |
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| The EMBO Journal
(2007) 26, 79–89, doi:10.1038/sj.emboj.7601448 Published online 14 December 2006 |
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| Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription |
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Yoh Isogai1, Shinako Takada2, Robert Tjian1, 3 and Sündüz Kele 4
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1 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA 2 Department of Biochemistry and Molecular Biology, Gene and Development, Program of Graduate School of Biomedical Science, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA 3 Howard Hughes Medical Institute, UC Berkeley, Department of Molecular and Cell Biology, Berkeley, CA, USA 4 Departments of Statistics and Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA To whom correspondence should be addressed Robert Tjian, Department of Molecular and Cell Biology, University of California, Berkeley/HHMI, 16 Barker Hall, Berkeley, CA 94720-3204, USA. Tel.: +1 510 642 0884; Fax: +1 510 643 9547; E-mail: jmlim@berkeley.edu Received 29 August 2006; Accepted 23 October 2006; Published online 14 December 2006. |
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| Abstract |
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Metazoans have evolved multiple paralogues of the TATA binding protein (TBP), adding another tunable level of gene control at core promoters. While TBP-related factor 1 (TRF1) shares extensive homology with TBP and can direct both Pol II and Pol III transcription in vitro, TRF1 target sites in vivo have remained elusive. Here, we report the genome-wide identification of TRF1-binding sites using high-resolution genome tiling microarrays. We found 354 TRF1-binding sites genome-wide with  78% of these sites displaying colocalization with BRF. Strikingly, the majority of TRF1 target genes are Pol III-dependent small noncoding RNAs such as tRNAs and small nonmessenger RNAs. We provide direct evidence that the TRF1/BRF complex is functionally required for the activity of two novel TRF1 targets (7SL RNA and small nucleolar RNAs). Our studies suggest that unlike most other eukaryotic organisms that rely on TBP for Pol III transcription, in Drosophila and possibly other insects the alternative TRF1/BRF complex appears responsible for the initiation of all known classes of Pol III transcription. |
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| Keywords: ChIP-on-chip analysis, RNA polymerase III transcription, small nonmessenger RNA, TBP-related factor |
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Top of page MORE ARTICLES LIKE THISThese links to content published by NPG are automatically generated RESEARCHNovel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription The EMBO Journal Article Genome-wide location of yeast RNA polymerase III transcription machinery The EMBO Journal Article (15 Sep 2003) Genome-wide location of yeast RNA polymerase III transcription machinery The EMBO Journal Article (15 Sep 2003) |
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