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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.

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Figure 1: Occupancy analysis of Pol III and associated machinery in HeLa cells.
Figure 2: Differential Pol III occupancy in various cell types.
Figure 3: Genomic features of Pol III–occupied and unoccupied tDNAs in HeLa cells.
Figure 4: Chromatin features at Pol III–bound tDNAs in HeLa cells.
Figure 5: Chromatin marks and factors associated with Pol III–bound regions in Jurkat cells.
Figure 6: Model depicting how chromatin features affect Pol III recruitment at three different regions: promoters, enhancer-like promoters and heterochromatin.

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References

  1. White, R.J. RNA Polymerase III Transcription (Springer-Verlag, New York, 1998).

  2. Dieci, G., Fiorino, G., Castelnuovo, M., Teichmann, M. & Pagano, A. The expanding RNA polymerase III transcriptome. Trends Genet. 23, 614–622 (2007).

    Article  CAS  Google Scholar 

  3. White, R.J. RNA polymerases I and III, non-coding RNAs and cancer. Trends Genet. 24, 622–629 (2008).

    Article  CAS  Google Scholar 

  4. Marshall, L. & White, R.J. Non-coding RNA production by RNA polymerase III is implicated in cancer. Nat. Rev. Cancer 8, 911–914 (2008).

    Article  CAS  Google Scholar 

  5. Willis, I.M. RNA polymerase III. Genes, factors and transcriptional specificity. Eur. J. Biochem. 212, 1–11 (1993).

    Article  CAS  Google Scholar 

  6. Geiduschek, E.P. & Kassavetis, G.A. The RNA polymerase III transcription apparatus. J. Mol. Biol. 310, 1–26 (2001).

    Article  CAS  Google Scholar 

  7. Schramm, L. & Hernandez, N. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16, 2593–2620 (2002).

    Article  CAS  Google Scholar 

  8. Noma, K., Cam, H.P., Maraia, R.J. & Grewal, S.I. A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859–872 (2006).

    Article  CAS  Google Scholar 

  9. Simms, T.A. et al. TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in Saccharomyces cerevisiae. Eukaryot. Cell 7, 2078–2086 (2008).

    Article  CAS  Google Scholar 

  10. Moqtaderi, Z. & Struhl, K. Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol. Cell. Biol. 24, 4118–4127 (2004).

    Article  CAS  Google Scholar 

  11. Valenzuela, L., Dhillon, N. & Kamakaka, R.T. Transcription independent insulation at TFIIIC-dependent insulators. Genetics 183, 131–148 (2009).

    Article  CAS  Google Scholar 

  12. Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994).

    CAS  PubMed  Google Scholar 

  13. Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27, 66–75 (2009).

    Article  CAS  Google Scholar 

  14. Robertson, A.G. et al. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 18, 1906–1917 (2008).

    Article  CAS  Google Scholar 

  15. Jin, C. et al. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet. 41, 941–945 (2009).

    Article  CAS  Google Scholar 

  16. Cuddapah, S. et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 19, 24–32 (2009).

    Article  CAS  Google Scholar 

  17. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).

    Article  CAS  Google Scholar 

  18. Koka, P. et al. Increased expression of CD4 molecules on Jurkat cells mediated by human immunodeficiency virus tat protein. J. Virol. 62, 4353–4357 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

    Article  CAS  Google Scholar 

  20. Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897–903 (2008).

    Article  CAS  Google Scholar 

  21. Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5, 829–834 (2008).

    Article  CAS  Google Scholar 

  22. Hollenhorst, P.C. et al. DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet. 5, e1000778 (2009).

    Article  Google Scholar 

  23. Barski, A. et al. Chromatin poises miRNA- and protein-coding genes for expression. Genome Res. 19, 1742–1751 (2009).

    Article  CAS  Google Scholar 

  24. Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).

    Article  CAS  Google Scholar 

  25. Felton-Edkins, Z.A. et al. Direct regulation of RNA polymerase III transcription by RB, p53 and c-Myc. Cell Cycle 2, 181–184 (2003).

    Article  CAS  Google Scholar 

  26. Gomez-Roman, N., Grandori, C., Eisenman, R.N. & White, R.J. Direct activation of RNA polymerase III transcription by c-Myc. Nature 421, 290–294 (2003).

    Article  CAS  Google Scholar 

  27. Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).

    Article  CAS  Google Scholar 

  28. Borchert, G.M., Lanier, W. & Davidson, B.L. RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13, 1097–1101 (2006).

    Article  CAS  Google Scholar 

  29. Bortolin-Cavaille, M.L., Dance, M., Weber, M. & Cavaille, J. C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 37, 3464–3473 (2009).

    Article  CAS  Google Scholar 

  30. Mrazek, J., Kreutmayer, S.B., Grasser, F.A., Polacek, N. & Huttenhofer, A. Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells. Nucleic Acids Res. 35, e73 (2007).

    Article  Google Scholar 

  31. Parrott, A.M. & Mathews, M.B. Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution. Nucleic Acids Res. 35, 6249–6258 (2007).

    Article  CAS  Google Scholar 

  32. Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007).

    Article  CAS  Google Scholar 

  33. Gupta, S., Stamatoyannopoulos, J.A., Bailey, T.L. & Noble, W.S. Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).

    Article  Google Scholar 

  34. Listerman, I., Bledau, A.S., Grishina, I. & Neugebauer, K.M. Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet. 3, e212 (2007).

    Article  Google Scholar 

  35. Yuan, C.C. et al. CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription. Mol. Cell. Biol. 27, 8729–8738 (2007).

    Article  CAS  Google Scholar 

  36. Straussman, R. et al. Developmental programming of CpG island methylation profiles in the human genome. Nat. Struct. Mol. Biol. 16, 564–571 (2009).

    Article  CAS  Google Scholar 

  37. Roberts, D.N., Stewart, A.J., Huff, J.T. & Cairns, B.R. The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc. Natl. Acad. Sci. USA 100, 14695–14700 (2003).

    Article  CAS  Google Scholar 

  38. Harismendy, O. et al. Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J. 22, 4738–4747 (2003).

    Article  CAS  Google Scholar 

  39. Willis, I.M. & Moir, R.D. Integration of nutritional and stress signaling pathways by Maf1. Trends Biochem. Sci. 32, 51–53 (2007).

    Article  CAS  Google Scholar 

  40. Weiner, A.M., Deininger, P.L. & Efstratiadis, A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55, 631–661 (1986).

    Article  CAS  Google Scholar 

  41. Boyle, A.P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).

    Article  CAS  Google Scholar 

  42. Gordon, M. et al. Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol. Cell. Biol. 27, 4058–4069 (2007).

    Article  CAS  Google Scholar 

  43. Choi, Y.H. & Hagedorn, C.H. Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3′ poly(A) end phenotype. Proc. Natl. Acad. Sci. USA 100, 7033–7038 (2003).

    Article  Google Scholar 

  44. Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008).

    Article  CAS  Google Scholar 

  45. Nix, D.A., Courdy, S.J. & Boucher, K.M. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9, 523 (2008).

    Article  Google Scholar 

  46. Hammoud, S.S. et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460, 473–478 (2009).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank D. Ayer and S. Lessnick at the Huntsman Cancer Institute for cells, B. Dalley for his expertise in Illumina sequencing, D. Nix for suggestions for ChIP-seq analysis and R. Roeder (Rockefeller University) for the gift of anti-RPB90 antibody. Financial support was from the Howard Hughes Medical Institute (HHMI; supplies and genomics resources), the US National Institutes of Health (grants GM38663 to B.J.G., CA42014 to the Huntsman Cancer Institute for support of core facilities and CA63640 to C.H.H.), the Huntsman Cancer Institute and Huntsman Cancer Foundation and the Agilent Technologies Foundation (supplies). B.R.C. is an investigator with the HHMI.

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Authors

Contributions

B.R.C. and A.J.O., overall scope and design; A.J.O., overall experimental execution; D.N.R. and A.W., ChIP-array experiments; C.A.N. and C.H.H., cap-purified RNA; P.A.C., qPCR; P.C.H., K.J.C. and B.J.G., ETS1 and CBP data sets and analysis; A.J.O., R.K.A. and B.R.C., data analysis and interpretation; A.J.O. and R.K.A., figures, tables and data organization. B.R.C. and A.J.O. wrote the manuscript, with comments from all authors.

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Correspondence to Bradley R Cairns.

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Supplementary Text and Figures

Supplementary Figures 1–8 and Supplementary Table 1 (PDF 8603 kb)

Supplementary Data 1

Lists of genes and enriched regions. (XLS 2068 kb)

Supplementary Data 2 (XLS 372 kb)

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Oler, A., Alla, R., Roberts, D. et al. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol 17, 620–628 (2010). https://doi.org/10.1038/nsmb.1801

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