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Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

Nature Structural & Molecular Biology volume 17, pages 635–640 (2010)Cite this article

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Abstract

Genome-wide occupancy profiles of five components of the RNA polymerase III (Pol III) machinery in human cells identified the expected tRNA and noncoding RNA targets and revealed many additional Pol III–associated loci, mostly near short interspersed elements (SINEs). Several genes are targets of an alternative transcription factor IIIB (TFIIIB) containing Brf2 instead of Brf1 and have extremely low levels of TFIIIC. Strikingly, expressed Pol III genes, unlike nonexpressed Pol III genes, are situated in regions with a pattern of histone modifications associated with functional Pol II promoters. TFIIIC alone associates with numerous ETC loci, via the B box or a novel motif. ETCs are often near CTCF binding sites, suggesting a potential role in chromosome organization. Our results suggest that human Pol III complexes associate preferentially with regions near functional Pol II promoters and that TFIIIC-mediated recruitment of TFIIIB is regulated in a locus-specific manner.

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Figure 1: Pairwise comparison of occupancy by proteins at Pol III loci.
Figure 2: Properties of Pol III targets.
Figure 3: Distinctions between TFIIIB isoforms.
Figure 4: Relationship of TFIIIC occupancy to Pol III occupancy and identification of ETC loci.
Figure 5: ETC motifs.
Figure 6: Cell specificity of ETC loci.

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Acknowledgements

We thank T. Liu and X. Liu for initial comments about the sequencing data, J. Mellor for helpful advice on programming in Python, N. Lamarre-Vincent, X. Fan, H. Hirsch and M. Lindahl Allen for discussion, G. Euskirchen, H. Monahan, M. Shi and P. Lacroute for help with DNA sequencing and M. Wilson for help with database submission. Funding for this work was provided by US National Institutes of Health grants GM 30186 (K.S.), HG 4558 (M.S. and K.S.) and HG 4695 (Z.W.).

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Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA

    Zarmik Moqtaderi & Kevin Struhl

  2. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Jie Wang & Zhiping Weng

  3. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA

    Debasish Raha

  4. Beatson Institute for Cancer Research, Glasgow, UK

    Robert J White

  5. Department of Genetics, Stanford University School of Medicine, Stanford, California, USA

    Michael Snyder

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Contributions

Z.M. designed the experiments, performed and analyzed the ChIP and validation experiments, performed bioinformatics analysis, constructed figures and wrote the paper; J.W. performed bioinformatics analysis, discussed the results and constructed figures; D.R. supervised the library construction and Illumina sequencing of the immunoprecipitated DNA; R.J.W. provided the antibodies used in the ChIPs, discussed the results and suggested modifications to the text; M.S. supervised the library construction and Illumina sequencing of the immunoprecipitated DNA; Z.W. supervised the bioinformatics analysis and participated in substantial discussion of the bioinformatics and figures; K.S. participated in substantial discussion of all experiments, results and figures and contributed to the text.

Corresponding author

Correspondence to Kevin Struhl.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1 (PDF 193 kb)

Supplementary Data 1

Peak lists obtained by MACS analysis of each ChIP sequencing data set (XLS 1033 kb)

Supplementary Data 2

Rpc155 targets with gene annotations. (XLS 557 kb)

Supplementary Data 3

List of ETC loci as defined by a TFIIIC-110/Rpc155 ratio greater than three standard deviations above the median ratio at tRNA genes. (XLS 973 kb)

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Moqtaderi, Z., Wang, J., Raha, D. et al. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 17, 635–640 (2010). https://doi.org/10.1038/nsmb.1794

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