The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships.
RNA polymerase III (Pol III) transcribes small untranslated RNAs, such as tRNAs. To define the Pol III transcriptome in Saccharomyces cerevisiae, we performed genome-wide chromatin immunoprecipitation using subunits of Pol III, TFIIIB and TFIIIC. Virtually all of the predicted targets of Pol III, as well as several novel candidates, were occupied by Pol III machinery. Interestingly, TATA box-binding protein occupancy was greater at Pol III targets than virtually all Pol II targets, and the highly occupied Pol II targets are generally strongly transcribed. The temporal relationships between factor occupancy and gene activity were then investigated at selected targets. Nutrient deprivation rapidly reduced both Pol III transcription and Pol III occupancy of both a tRNA gene and RPR1. In contrast, TFIIIB remained bound, suggesting that TFIIIB release is not a critical aspect of the onset of repression. Remarkably, TFIIIC occupancy increased dramatically during repression. Nutrient addition generally reestablished transcription and initial occupancy levels. Our results are consistent with active Pol III displacing TFIIIC, and with inactivation/release of Pol III enabling TFIIIC to bind, marking targets for later activation. These studies reveal new aspects of the kinetics, dynamics, and targets of the Pol III system.
Roberts
Douglas N
DN
Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
Stewart
Allen J
AJ
Huff
Jason T
JT
Cairns
Bradley R
BR
D002843:Chromatin / Q000378:metabolism; D016678:Genome; D007700:Kinetics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D016133:Polymerase Chain Reaction; D011233:Precipitin Tests; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D012320:RNA Polymerase III / Q000737:chemistry*; D012333:RNA, Messenger / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D012365:RNA, Transfer, Tyr / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D013997:Time Factors; D035581:Transcription Factor TFIIB / Q000737:chemistry; D019474:Transcription Factors, TFIII / Q000737:chemistry; D014158:Transcription, Genetic; D000098832:Transcription Factor TFIIIC
D002843:Chromatin; D011506:Proteins; D012333:RNA, Messenger; D012365:RNA, Transfer, Tyr; D035581:Transcription Factor TFIIB; D019474:Transcription Factors, TFIII; D000098832:Transcription Factor TFIIIC; D012343:RNA, Transfer; D012320:RNA Polymerase III