title: Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.
abstract: 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.
authors.affiliation: Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Oler
authors.forename: Ravi K
authors.initials: RK
authors.lastname: Alla
authors.forename: Douglas N
authors.initials: DN
authors.lastname: Roberts
authors.forename: Alexander
authors.initials: A
authors.lastname: Wong
authors.forename: Peter C
authors.initials: PC
authors.lastname: Hollenhorst
authors.forename: Katherine J
authors.initials: KJ
authors.lastname: Chandler
authors.forename: Patrick A
authors.initials: PA
authors.lastname: Cassiday
authors.forename: Cassie A
authors.initials: CA
authors.lastname: Nelson
authors.forename: Curt H
authors.initials: CH
authors.lastname: Hagedorn
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Graves
authors.forename: Bradley R
authors.initials: BR
authors.lastname: Cairns
mesh_terms: 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
chemical_list: 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