Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

Andrew J. Oler, Ravi K. Alla, Douglas N. Roberts, Alexander Wong, Peter C. Hollenhorst, Katherine J. Chandler, Patrick A. Cassiday, Cassie A. Nelson, Curt H. Hagedorn, Barbara J. Graves, Bradley R. Cairns

Research output: Contribution to journalArticle

160 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)620-628
Number of pages9
JournalNature Structural and Molecular Biology
Volume17
Issue number5
DOIs
StatePublished - May 1 2010
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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    Oler, A. J., Alla, R. K., Roberts, D. N., Wong, A., Hollenhorst, P. C., Chandler, K. J., Cassiday, P. A., Nelson, C. A., Hagedorn, C. H., Graves, B. J., & Cairns, B. R. (2010). Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nature Structural and Molecular Biology, 17(5), 620-628. https://doi.org/10.1038/nsmb.1801