title: Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription.
abstract: 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 approximately 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.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Yoh
authors.initials: Y
authors.lastname: Isogai
authors.forename: Shinako
authors.initials: S
authors.lastname: Takada
authors.forename: Robert
authors.initials: R
authors.lastname: Tjian
authors.forename: Sündüz
authors.initials: S
authors.lastname: Keleş
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004258:DNA Polymerase III / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D004331:Drosophila melanogaster; D016678:Genome; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes / Q000737:chemistry; D011485:Protein Binding; D020537:RNA, Small Nucleolar / Q000378:metabolism; D035321:Telomeric Repeat Binding Protein 1 / Q000378:metabolism / Q000502:physiology*; D035361:Transcription Factor TFIIIB / Q000378:metabolism / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D015345:Oligonucleotide Probes; D020537:RNA, Small Nucleolar; D035321:Telomeric Repeat Binding Protein 1; D035361:Transcription Factor TFIIIB; D004258:DNA Polymerase III; D003850:Deoxyribonuclease I