Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Defining mechanisms that regulate RNA polymerase II transcription in vivo

Nature volume 461, pages 186–192 (2009)Cite this article

Abstract

In the eukaryotic genome, the thousands of genes that encode messenger RNA are transcribed by a molecular machine called RNA polymerase II. Analysing the distribution and status of RNA polymerase II across a genome has provided crucial insights into the long-standing mysteries of transcription and its regulation. These studies identify points in the transcription cycle where RNA polymerase II accumulates after encountering a rate-limiting step. When coupled with genome-wide mapping of transcription factors, these approaches identify key regulatory steps and factors and, importantly, provide an understanding of the mechanistic generalities, as well as the rich diversities, of gene regulation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Transcription regulatory interactions.
Figure 2: The transcription cycle is a multistep process.

Similar content being viewed by others

References

  1. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

    Article  CAS  Google Scholar 

  2. Juven-Gershon, T., Hsu, J. Y., Theisen, J. W. & Kadonaga, J. T. The RNA polymerase II core promoter — the gateway to transcription. Curr. Opin. Cell Biol. 20, 253–259 (2008).

    Article  CAS  Google Scholar 

  3. Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae . Science 298, 799–804 (2002).

    Article  CAS  Google Scholar 

  4. Saunders, A., Core, L. J. & Lis, J. T. Breaking barriers to transcription elongation. Nature Rev. Mol. Cell Biol. 7, 557–567 (2006).

    Article  CAS  Google Scholar 

  5. Venters, B. J. & Pugh, B. F. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res. 19, 360–371 (2009). This paper examines the genome-wide distribution of Pol II in yeast and suggests that yeast have Pol II enrichment on the 59 ends of many genes.

    Article  CAS  Google Scholar 

  6. Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507–1511 (2007). This paper examines the genome-wide distribution of Pol II in Drosophila S2 cells and demonstrates that there is Pol II enrichment on many promoters in a stalled or paused state.

    Article  CAS  Google Scholar 

  7. Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512–1516 (2007). This paper examines the genome-wide distribution of Pol II in Drosophila embryos and suggests that promoter-proximal stalling/pausing occurs at many developmental genes.

    Article  CAS  Google Scholar 

  8. Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007). This paper examines the promoter architecture in human cells and suggests that there is Pol II enrichment on promoters and that Pol II seems to have initiated transcription at most genes.

    Article  CAS  Google Scholar 

  9. Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569–577 (1997). This paper reviews the evidence for regulation by Pol II recruitment in bacteria and yeast.

    Article  CAS  Google Scholar 

  10. Mirkovitch, J. & Darnell, J. Jr. Mapping of RNA polymerase on mammalian genes in cells and nuclei. Mol. Biol. Cell 3, 1085–1094 (1992).

    Article  CAS  Google Scholar 

  11. Rougvie, A. E. & Lis, J. T. The RNA polymerase II molecule at the 59 end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54, 795–804 (1988).

    Article  CAS  Google Scholar 

  12. Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008). This paper examines the transcriptionally engaged polymerase across the genome in human cells, and demonstrates a 59-end enrichment in engaged Pol II at many genes.

    Article  CAS  Google Scholar 

  13. Boehm, A. K., Saunders, A., Werner, J. & Lis, J. T. Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23, 7628–7637 (2003).

    Article  CAS  Google Scholar 

  14. Peterson, C. L. & Workman, J. L. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10, 187–192 (2000).

    Article  CAS  Google Scholar 

  15. Larschan, E. & Winston, F. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev. 15, 1946–1956 (2001).

    Article  CAS  Google Scholar 

  16. Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 39 end processing. Mol. Cell 13, 67–76 (2004).

    Article  CAS  Google Scholar 

  17. Stargell, L. A. & Struhl, K. Mechanisms of transcriptional activation in vivo: two steps forward. Trends Genet. 12, 311–315 (1996).

    Article  CAS  Google Scholar 

  18. Esnault, C. et al. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol. Cell 31, 337–346 (2008).

    Article  CAS  Google Scholar 

  19. Kim, Y. J., Bjorklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77, 599–608 (1994).

    Article  CAS  Google Scholar 

  20. Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58–69 (2007).

    Article  CAS  Google Scholar 

  21. Jacobson, R. H., Ladurner, A. G., King, D. S. & Tjian, R. Structure and function of a human TAFII250 double bromodomain module. Science 288, 1422–1425 (2000).

    Article  CAS  Google Scholar 

  22. Sakurai, H. & Fukasawa, T. Functional connections between mediator components and general transcription factors of Saccharomyces cerevisiae . J. Biol. Chem. 275, 37251–37256 (2000).

    Article  CAS  Google Scholar 

  23. Liu, Y. et al. Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol. Cell. Biol. 24, 1721–1735 (2004).

    Article  CAS  Google Scholar 

  24. Spilianakis, C. et al. CIITA regulates transcription onset via Ser5-phosphorylation of RNA Pol II. EMBO J. 22, 5125–5136 (2003).

    Article  CAS  Google Scholar 

  25. Core, L. J. & Lis, J. T. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791–1792 (2008).

    Article  CAS  Google Scholar 

  26. Ni, Z. et al. P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo . Mol. Cell. Biol. 28, 1161–1170 (2008).

    Article  CAS  Google Scholar 

  27. Chao, S. H. & Price, D. H. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo . J. Biol. Chem. 276, 31793–31799 (2001).

    Article  CAS  Google Scholar 

  28. Eberhardy, S. R. & Farnham, P. J. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J. Biol. Chem. 277, 40156–40162 (2002).

    Article  CAS  Google Scholar 

  29. Wittmann, B. M., Fujinaga, K., Deng, H., Ogba, N. & Montano, M. M. The breast cell growth inhibitor, estrogen down regulated gene 1, modulates a novel functional interaction between estrogen receptor α and transcriptional elongation factor cyclin T1. Oncogene 24, 5576–5588 (2005).

    Article  CAS  Google Scholar 

  30. Nowak, D. E. et al. RelA Ser276 phosphorylation is required for activation of a subset of NF-κB-dependent genes by recruiting cyclin-dependent kinase 9/cyclin T1 complexes. Mol. Cell. Biol. 28, 3623–3638 (2008).

    Article  CAS  Google Scholar 

  31. Peterlin, B. M. & Price, D. H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 23, 297–305 (2006).

    Article  CAS  Google Scholar 

  32. Mavrich, T. N. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358–362 (2008).

    Article  CAS  Google Scholar 

  33. Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009).

    Article  CAS  Google Scholar 

  34. Yudkovsky, N., Ranish, J. A. & Hahn, S. A transcription reinitiation intermediate that is stabilized by activator. Nature 408, 225–229 (2000).

    Article  CAS  Google Scholar 

  35. Blau, J. et al. Three functional classes of transcriptional activation domain. Mol. Cell. Biol. 16, 2044–2055 (1996).

    Article  CAS  Google Scholar 

  36. Petesch, S. J. & Lis, J. T. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 134, 74–84 (2008).

    Article  CAS  Google Scholar 

  37. Herschlag, D. & Johnson, F. B. Synergism in transcriptional activation: a kinetic view. Genes Dev. 7, 173–179 (1993). The paper proposes a role for kinetic synergism in the mechanism of transcriptional activation.

    Article  CAS  Google Scholar 

  38. Boettiger A. N. & Levine, M. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 325, 471–473 (2009).

    Article  CAS  Google Scholar 

  39. Mason, P. B. & Struhl, K. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo . Mol. Cell 17, 831–840 (2005).

    Article  CAS  Google Scholar 

  40. Dejardin, J. & Kingston, R. E. Purification of proteins associated with specific genomic loci. Cell 136, 175–186 (2009).

    Article  CAS  Google Scholar 

  41. Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008).

    Article  CAS  Google Scholar 

  42. Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851–1854 (2008).

    Article  CAS  Google Scholar 

  43. Wuarin, J. & Schibler, U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol. Cell. Biol. 14, 7219–7225 (1994).

    Article  CAS  Google Scholar 

  44. Bhaumik, S. R., Raha, T., Aiello, D. P. & Green, M. R. In vivo target of a transcriptional activator revealed by fluorescence resonance energy transfer. Genes Dev. 18, 333–343 (2004).

    Article  CAS  Google Scholar 

  45. Patterson, G. H. & Lippincott-Schwartz, J. Selective photolabeling of proteins using photoactivatable GFP. Methods 32, 445–450 (2004).

    Article  CAS  Google Scholar 

  46. Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008).

    Article  CAS  Google Scholar 

  47. Yao, J., Munson, K. M., Webb, W. W. & Lis, J. T. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442, 1050–1053 (2006).

    Article  CAS  Google Scholar 

  48. Janicki, S. M. et al. From silencing to gene expression: real-time analysis in single cells. Cell 116, 683–698 (2004).

    Article  CAS  Google Scholar 

  49. Chen, H.-T., Warfield, L. & Hahn, S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nature Struct. Mol. Biol. 14, 696–703 (2007).

    Article  CAS  Google Scholar 

  50. Shi, H., Hoffman, B. E. & Lis, J. T. RNA aptamers as effective protein antagonists in a multicellular organism. Proc. Natl Acad. Sci. USA 96, 10033–10038 (1999).

    Article  CAS  Google Scholar 

  51. Boeger, H., Griesenbeck, J., Strattan, J. S. & Kornberg, R. D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587–1598 (2003).

    Article  CAS  Google Scholar 

  52. Svaren, J. & Hörz, W. Transcription factors vs nucleosomes: regulation of the PH05 promoter in yeast. Trends Biochem. Sci. 22, 93–97 (1997).

    Article  CAS  Google Scholar 

  53. O'Neill, E. M., Kaffman, A., Jolly, E. R. & O'Shea, E. K. Regulation of PHO4 nuclear localization by the PHO80−PHO85 cyclin–CDK complex. Science 271, 209–212 (1996).

    Article  CAS  Google Scholar 

  54. Barbaric, S., Munsterkotter, M., Goding, C. & Horz, W. Cooperative Pho2–Pho4 interactions at the PHO5 promoter are critical for binding of Pho4 to UASp1 and for efficient transactivation by Pho4 at UASp2. Mol. Cell. Biol. 18, 2629–2639 (1998).

    Article  CAS  Google Scholar 

  55. Svaren, J., Schmitz, J. & Horz, W. The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter. EMBO J. 13, 4856–4862 (1994).

    Article  CAS  Google Scholar 

  56. Reinke, H. & Hörz, W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11, 1599–1607 (2003).

    Article  CAS  Google Scholar 

  57. Steger, D. J., Haswell, E. S., Miller, A. L., Wente, S. R. & O'Shea, E. K. Regulation of chromatin remodeling by inositol polyphosphates. Science 299, 114–116 (2003).

    Article  CAS  Google Scholar 

  58. Korber, P. et al. The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J. Biol. Chem. 281, 5539–5545 (2006).

    Article  CAS  Google Scholar 

  59. Adkins, M. W., Howar, S. R. & Tyler, J. K. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell 14, 657–666 (2004).

    Article  CAS  Google Scholar 

  60. Barbaric, S. et al. Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo . J. Biol. Chem. 282, 27610–27621 (2007).

    Article  CAS  Google Scholar 

  61. Lam, F. H., Steger, D. J. & O'Shea, E. K. Chromatin decouples promoter threshold from dynamic range. Nature 453, 246–250 (2008).

    Article  CAS  Google Scholar 

  62. Wu, C. The 59 ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286, 854–860 (1980).

    Article  CAS  Google Scholar 

  63. Lis, J. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. Cold Spring Harb. Symp. Quant. Biol. 63, 347–356 (1998).

    Article  CAS  Google Scholar 

  64. Lee, H., Kraus, K. W., Wolfner, M. F. & Lis, J. T. DNA sequence requirements for generating paused polymerase at the start of hsp70 . Genes Dev. 6, 284–295 (1992).

    Article  CAS  Google Scholar 

  65. Wang, Y. V., Tang, H. & Gilmour, D. S. Identification in vivo of different rate-limiting steps associated with transcriptional activators in the presence and absence of a GAGA element. Mol. Cell. Biol. 25, 3543–3552 (2005).

    Article  CAS  Google Scholar 

  66. Lee, C. et al. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila . Mol. Cell. Biol. 28, 3290–3300 (2008).

    Article  CAS  Google Scholar 

  67. Tsukiyama, T., Becker, P. B. & Wu, C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature 367, 525–532 (1994).

    Article  CAS  Google Scholar 

  68. Wu, C. H. et al. Molecular characterization of Drosophila NELF. Nucleic Acids Res. 33, 1269–1279 (2005).

    Article  CAS  Google Scholar 

  69. Wu, C.-H. et al. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila . Genes Dev. 17, 1402–1414 (2003).

    Article  CAS  Google Scholar 

  70. Schwartz, B. E., Larochelle, S., Suter, B. & Lis, J. T. Cdk7 is required for full activation of Drosophila heat shock genes and RNA polymerase II phosphorylation in vivo . Mol. Cell. Biol. 23, 6876–6886 (2003).

    Article  CAS  Google Scholar 

  71. Ardehali, M. B. et al. Spt6 enhances the elongation rate of RNA polymerase II in vivo . EMBO J. 28, 1067–1077 (2009).

    Article  CAS  Google Scholar 

  72. Lis, J. T., Mason, P., Peng, J., Price, D. H. & Werner, J. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev. 14, 792–803 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Renner, D. B., Yamaguchi, Y., Wada, T., Handa, H. & Price, D. H. A highly purified RNA polymerase II elongation control system. J. Biol. Chem. 276, 42601–42609 (2001).

    Article  CAS  Google Scholar 

  74. Ni, Z., Schwartz, B. E., Werner, J., Suarez, J. R. & Lis, J. T. Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol. Cell 13, 55–65 (2004).

    Article  CAS  Google Scholar 

  75. Adelman, K. et al. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol. Cell 17, 103–112 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank members of the Lis laboratory for discussions and critical reading of the manuscript. Work in our laboratory is supported by US National Institutes of Health grant GM25232.

Author information

Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Cornell University, Ithaca, 14853, New York, USA

    Nicholas J. Fuda, M. Behfar Ardehali & John T. Lis

Authors
  1. Nicholas J. Fuda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Behfar Ardehali
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John T. Lis
    View author publications

    You can also search for this author in PubMed Google Scholar

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reprints and permissions information is available at http://www.nature.com/reprints.

Correspondence should be addressed to J.T.L. (jtl10@cornell.edu).

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fuda, N., Ardehali, M. & Lis, J. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461, 186–192 (2009). https://doi.org/10.1038/nature08449

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08449

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing