Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.
RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type-specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico-predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome.
Oler
Andrew J
AJ
Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
Alla
Ravi K
RK
Roberts
Douglas N
DN
Wong
Alexander
A
Hollenhorst
Peter C
PC
Chandler
Katherine J
KJ
Cassiday
Patrick A
PA
Nelson
Cassie A
CA
Hagedorn
Curt H
CH
Graves
Barbara J
BJ
Cairns
Bradley R
BR
D002460:Cell Line; D002843:Chromatin / Q000378:metabolism; D004257:DNA Polymerase II / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling; D005796:Genes; D056426:Genetic Loci; D023281:Genomics; D006367:HeLa Cells; D006801:Humans; D019169:Jurkat Cells; D011401:Promoter Regions, Genetic; D050784:Proto-Oncogene Protein c-ets-1 / Q000378:metabolism; D012320:RNA Polymerase III / Q000032:analysis / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics; D050794:STAT1 Transcription Factor / Q000378:metabolism
D002843:Chromatin; C494041:ETS1 protein, human; D050784:Proto-Oncogene Protein c-ets-1; D050794:STAT1 Transcription Factor; D012343:RNA, Transfer; D012320:RNA Polymerase III; D004257:DNA Polymerase II