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 Hollenhorst, Katherine J. Chandler, Patrick A. Cassiday, Cassie A. Nelson, Curt H. Hagedorn, Barbara J. Graves, Bradley R. Cairns

Research output: Contribution to journalArticle

156 Citations (Scopus)

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 2010
Externally publishedYes

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RNA Polymerase III
Transcriptome
Chromatin
Transcription Factor TFIIIB
Genes
Untranslated RNA
Transformed Cell Line
Transfer RNA
MicroRNAs
HeLa Cells
Computer Simulation
Carrier Proteins
Genome
transcription factor TFIIIC

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. / Oler, Andrew J.; Alla, Ravi K.; Roberts, Douglas N.; Wong, Alexander; Hollenhorst, Peter; Chandler, Katherine J.; Cassiday, Patrick A.; Nelson, Cassie A.; Hagedorn, Curt H.; Graves, Barbara J.; Cairns, Bradley R.

In: Nature Structural and Molecular Biology, Vol. 17, No. 5, 05.2010, p. 620-628.

Research output: Contribution to journalArticle

Oler, AJ, Alla, RK, Roberts, DN, Wong, A, Hollenhorst, P, Chandler, KJ, Cassiday, PA, Nelson, CA, Hagedorn, CH, Graves, BJ & Cairns, BR 2010, 'Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors', Nature Structural and Molecular Biology, vol. 17, no. 5, pp. 620-628. https://doi.org/10.1038/nsmb.1801
Oler, Andrew J. ; Alla, Ravi K. ; Roberts, Douglas N. ; Wong, Alexander ; Hollenhorst, Peter ; Chandler, Katherine J. ; Cassiday, Patrick A. ; Nelson, Cassie A. ; Hagedorn, Curt H. ; Graves, Barbara J. ; Cairns, Bradley R. / Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. In: Nature Structural and Molecular Biology. 2010 ; Vol. 17, No. 5. pp. 620-628.
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