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.

  • Perspective
  • Published:

The hunt for RNA polymerase II elongation factors: a historical perspective

Abstract

The discovery of the three eukaryotic nuclear RNA polymerases paved the way for serious biochemical investigations of eukaryotic transcription and the identification of eukaryotic transcription factors. Here we describe this adventure from our vantage point, with a focus on the hunt for factors that regulate elongation by RNA polymerase II.

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

Access options

Buy this article

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

Fig. 1: SII-dependent reactivation of arrested Pol II.
Fig. 2: Elongin and the Elongin ubiquitin ligase.
Fig. 3: ELL−EAF-containing complexes and their targets.

Similar content being viewed by others

References

  1. Thummel, C. S., Burtis, K. C. & Hogness, D. S. Spatial and temporal patterns of E74 transcription during Drosophila development. Cell 61, 101–111 (1990).

    Article  CAS  PubMed  Google Scholar 

  2. Jonkers, I., Kwak, H. & Lis, J. T. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. eLife 3, e02407 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Saponaro, M. et al. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell 157, 1037–1049 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  5. Tamm, I., Kikuchi, T., Darnell, J. E. Jr. & Salditt-Georgieff, M. Short capped hnRNA precursor chains in HeLa cells: continued synthesis in the presence of 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole. Biochemistry 19, 2743–2748 (1980).

    Article  CAS  PubMed  Google Scholar 

  6. Jonkers, I. & Lis, J. T. Getting up to speed with transcription elongation by RNA polymerase II. Nat. Rev. Mol. Cell Biol. 16, 167–177 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sekimizu, K., Kobayashi, N., Mizuno, D. & Natori, S. Purification of a factor from Ehrlich ascites tumor cells specifically stimulating RNA polymerase II. Biochemistry 15, 5064–5070 (1976).

    Article  CAS  PubMed  Google Scholar 

  8. Fish, R. N. & Kane, C. M. Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta 1577, 287–307 (2002).

    Article  CAS  PubMed  Google Scholar 

  9. Reines, D., Ghanouni, P., Li, Q. Q. & Mote, J. Jr. The RNA polymerase II elongation complex. Factor-dependent transcription elongation involves nascent RNA cleavage. J. Biol. Chem. 267, 15516–15522 (1992).

    Article  CAS  PubMed  Google Scholar 

  10. Reines, D. Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. J. Biol. Chem. 267, 3795–3800 (1992).

    Article  CAS  PubMed  Google Scholar 

  11. Izban, M. G. & Luse, D. S. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′→5′ direction in the presence of elongation factor SII. Genes Dev. 6, 1342–1356 (1992).

    Article  CAS  PubMed  Google Scholar 

  12. Churchman, L. S. & Weissman, J. S. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469, 368–373 (2011).

    Article  CAS  PubMed  Google Scholar 

  13. Sheridan, R. M., Fong, N., D’Alessandro, A. & Bentley, D. L. widespread backtracking by RNA Pol II is a major effector of gene activation, 5′ pause release, termination, and transcription elongation rate. Mol. Cell 73, 107–118.e4 (2019).

    Article  CAS  PubMed  Google Scholar 

  14. Lemay, J. F. et al. The RNA exosome promotes transcription termination of backtracked RNA polymerase II. Nat. Struct. Mol. Biol. 21, 919–926 (2014).

    Article  CAS  PubMed  Google Scholar 

  15. Nechaev, S. et al. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327, 335–338 (2010).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  17. Sigurdsson, S., Dirac-Svejstrup, A. B. & Svejstrup, J. Q. Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability. Mol. Cell 38, 202–210 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Gamba, P. & Zenkin, N. Transcription fidelity and its roles in the cell. Curr. Opin. Microbiol. 42, 13–18 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Irvin, J. D. et al. A genetic assay for transcription errors reveals multilayer control of RNA polymerase II fidelity. PLoS Genet. 10, e1004532 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Gout, J. F. et al. The landscape of transcription errors in eukaryotic cells. Sci. Adv. 3, e1701484 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Sawadogo, M. & Sentenac, A. RNA polymerase B (II) and general transcription factors. Annu. Rev. Biochem. 59, 711–754 (1990).

    Article  CAS  PubMed  Google Scholar 

  22. Conaway, R. C., Garrett, K. P., Hanley, J. P. & Conaway, J. W. Mechanism of promoter selection by RNA polymerase II: mammalian transcription factors α and β γ promote entry of polymerase into the preinitiation complex. Proc. Natl Acad. Sci. USA 88, 6205–6209 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bradsher, J. N., Jackson, K. W., Conaway, R. C. & Conaway, J. W. RNA polymerase II transcription factor SIII. I. Identification, purification, and properties. J. Biol. Chem. 268, 25587–25593 (1993).

    Article  CAS  PubMed  Google Scholar 

  24. Bradsher, J. N., Tan, S., McLaury, H.-J., Conaway, J. W. & Conaway, R. C. RNA polymerase II transcription factor SIII. II. Functional properties and role in RNA chain elongation. J. Biol. Chem. 268, 25594–25603 (1993).

    Article  CAS  PubMed  Google Scholar 

  25. Shilatifard, A., Lane, W. S., Jackson, K. W., Conaway, R. C. & Conaway, J. W. An RNA polymerase II elongation factor encoded by the human ELL gene. Science 271, 1873–1876 (1996).

    Article  CAS  PubMed  Google Scholar 

  26. Simone, F. et al. EAF1, a novel ELL-associated factor that is delocalized by expression of the MLL-ELL fusion protein. Blood 98, 201–209 (2001).

    Article  CAS  PubMed  Google Scholar 

  27. Simone, F., Luo, R. T., Polak, P. E., Kaberlein, J. J. & Thirman, M. J. ELL-associated factor 2 (EAF2), a functional homolog of EAF1 with alternative ELL binding properties. Blood 101, 2355–2362 (2003).

    Article  CAS  PubMed  Google Scholar 

  28. Kong, S. E., Banks, C. A. S., Shilatifard, A., Conaway, J. W. & Conaway, R. C. ELL-associated factors 1 and 2 are positive regulators of RNA polymerase II elongation factor ELL. Proc. Natl Acad. Sci. USA 102, 10094–10098 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Price, D. H., Sluder, A. E. & Greenleaf, A. L. Dynamic interaction between a Drosophila transcription factor and RNA polymerase II. Mol. Cell. Biol. 9, 1465–1475 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Bengal, E., Flores, O., Krauskopf, A., Reinberg, D. & Aloni, Y. Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II. Mol. Cell. Biol. 11, 1195–1206 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Shilatifard, A., Conaway, R. C. & Conaway, J. W. The RNA polymerase II elongation complex. Annu. Rev. Biochem. 72, 693–715 (2003).

    Article  CAS  PubMed  Google Scholar 

  32. Yan, Q., Moreland, R. J., Conaway, J. W. & Conaway, R. C. Dual roles for transcription factor IIF in promoter escape by RNA polymerase II. J. Biol. Chem. 274, 35668–35675 (1999).

    Article  CAS  PubMed  Google Scholar 

  33. Joo, Y. J., Ficarro, S. B., Chun, Y., Marto, J. A. & Buratowski, S. In vitro analysis of RNA polymerase II elongation complex dynamics. Genes Dev. 33, 578–589 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Gerber, M. et al. In vivo requirement of the RNA polymerase II elongation factor elongin A for proper gene expression and development. Mol. Cell. Biol. 24, 9911–9919 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Eissenberg, J. C. et al. dELL is an essential RNA polymerase II elongation factor with a general role in development. Proc. Natl Acad. Sci. USA 99, 9894–9899 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Mitani, K. et al. Nonredundant roles of the elongation factor MEN in postimplantation development. Biochem. Biophys. Res. Commun. 279, 563–567 (2000).

    Article  CAS  PubMed  Google Scholar 

  37. Yasukawa, T. et al. Transcriptional elongation factor elongin A regulates retinoic acid-induced gene expression during neuronal differentiation. Cell Rep. 2, 1129–1136 (2012).

    Article  CAS  PubMed  Google Scholar 

  38. Gerber, M. et al. Regulation of heat shock gene expression by RNA polymerase II elongation factor, Elongin A. J. Biol. Chem. 280, 4017–4020 (2005).

    Article  CAS  PubMed  Google Scholar 

  39. Kawauchi, J. et al. Transcriptional properties of mammalian elongin A and its role in stress response. J. Biol. Chem. 288, 24302–24315 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Chopra, V. S., Hong, J. W. & Levine, M. Regulation of Hox gene activity by transcriptional elongation in Drosophila. Curr. Biol. 19, 688–693 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ardehali, M. B. et al. Polycomb repressive complex 2 methylates Elongin A to regulate transcription. Mol. Cell 68, 872–884.e6 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Kamura, T. et al. Muf1, a novel Elongin BC-interacting leucine-rich repeat protein that can assemble with Cul5 and Rbx1 to reconstitute a ubiquitin ligase. J. Biol. Chem. 276, 29748–29753 (2001).

    Article  CAS  PubMed  Google Scholar 

  43. Selth, L. A., Sigurdsson, S. & Svejstrup, J. Q. Transcript elongation by RNA polymerase II. Annu. Rev. Biochem. 79, 271–293 (2010).

    Article  CAS  PubMed  Google Scholar 

  44. Kamura, T. et al. The Elongin BC complex interacts with the conserved SOCS-box motif present in members of the SOCS, ras, WD-40 repeat, and ankyrin repeat families. Genes Dev. 12, 3872–3881 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Kamura, T. et al. Rbx1, a component of the VHL tumor suppressor complex and SCF ubiquitin ligase. Science 284, 657–661 (1999).

    Article  CAS  PubMed  Google Scholar 

  46. Okumura, F., Matsuzaki, M., Nakatsukasa, K. & Kamura, T. The role of Elongin BC-containing ubiquitin ligases. Front. Oncol. 2, 10 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Ribar, B., Prakash, L. & Prakash, S. ELA1 and CUL3 are required along with ELC1 for RNA polymerase II polyubiquitylation and degradation in DNA-damaged yeast cells. Mol. Cell. Biol. 27, 3211–3216 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Yasukawa, T. et al. Mammalian Elongin A complex mediates DNA-damage-induced ubiquitylation and degradation of Rpb1. EMBO J. 27, 3256–3266 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Harreman, M. et al. Distinct ubiquitin ligases act sequentially for RNA polymerase II polyubiquitylation. Proc. Natl Acad. Sci. USA 106, 20705–20710 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Weems, J. C. et al. Assembly of the Elongin A ubiquitin ligase is regulated by genotoxic and other stresses. J. Biol. Chem. 290, 15030–15041 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Weems, J. C. et al. Cockayne syndrome B protein regulates recruitment of the Elongin A ubiquitin ligase to sites of DNA damage. J. Biol. Chem. 292, 6431–6437 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Boetefuer, E. L., Lake, R. J. & Fan, H. Y. Mechanistic insights into the regulation of transcription and transcription-coupled DNA repair by Cockayne syndrome protein B. Nucleic Acids Res. 46, 7471–7479 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Wang, W., Xu, J., Chong, J. & Wang, D. Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair (Amst.) 71, 43–55 (2018).

    Article  CAS  Google Scholar 

  54. Dahmus, M. E. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271, 19009–19012 (1996).

    Article  CAS  PubMed  Google Scholar 

  55. Marshall, N. F. & Price, D. H. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J. Biol. Chem. 270, 12335–12338 (1995).

    Article  CAS  PubMed  Google Scholar 

  56. Zhu, Y. et al. Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev. 11, 2622–2632 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Peng, J., Marshall, N. F. & Price, D. H. Identification of a cyclin subunit required for the function of Drosophila P-TEFb. J. Biol. Chem. 273, 13855–13860 (1998).

    Article  CAS  PubMed  Google Scholar 

  58. Wada, T. et al. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12, 343–356 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Yamaguchi, Y. et al. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97, 41–51 (1999).

    Article  CAS  PubMed  Google Scholar 

  60. Swanson, M. S. & Winston, F. SPT4, SPT5 and SPT6 interactions: effects on transcription and viability in Saccharomyces cerevisiae. Genetics 132, 325–336 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Fujinaga, K. et al. Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol. Cell. Biol. 24, 787–795 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Yamada, T. et al. P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. Mol. Cell 21, 227–237 (2006).

    Article  CAS  PubMed  Google Scholar 

  63. Lin, C. et al. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol. Cell 37, 429–437 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. He, N. et al. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol. Cell 38, 428–438 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Sobhian, B. et al. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol. Cell 38, 439–451 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Takahashi, H. et al. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell 146, 92–104 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Lin, C. et al. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes Dev. 25, 1486–1498 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Galbraith, M. D. et al. HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia. Cell 153, 1327–1339 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Wan, L. et al. ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia. Nature 543, 265–269 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Liang, K. et al. Targeting processive transcription elongation via SEC disruption for MYC-induced cancer therapy. Cell 175, 766–779.e17 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Marschalek, R. Mixed lineage leukemia: roles in human malignancies and potential therapy. FEBS J. 277, 1822–1831 (2010).

    Article  CAS  PubMed  Google Scholar 

  72. Yokoyama, A., Lin, M., Naresh, A., Kitabayashi, I. & Cleary, M. L. A higher-order complex containing AF4 and ENL family proteins with P-TEFb facilitates oncogenic and physiologic MLL-dependent transcription. Cancer Cell 17, 198–212 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Lin, C., Garruss, A. S., Luo, Z., Guo, F. & Shilatifard, A. The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. Cell 152, 144–156 (2013).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  75. Lens, Z. et al. Solution structure of the N-terminal domain of Mediator subunit MED26 and molecular characterization of its interaction with EAF1 and TAF7. J. Mol. Biol. 429, 3043–3055 (2017).

    Article  CAS  PubMed  Google Scholar 

  76. He, N. et al. Human polymerase-associated factor complex (PAFc) connects the super elongation complex (SEC) to RNA polymerase II on chromatin. Proc. Natl Acad. Sci. USA 108, E636–E645 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Yadav, D., Ghosh, K., Basu, S., Roeder, R. G. & Biswas, D. Multivalent role of human TFIID in recruiting elongation components at the promoter-proximal region for transcriptional control. Cell Rep. 26, 1303–1317.e7 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Li, Y. et al. Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol. Cell 62, 181–193 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Smith, E. R. et al. The little elongation complex regulates small nuclear RNA transcription. Mol. Cell 44, 954–965 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Hu, D. et al. The little elongation complex functions at initiation and elongation phases of snRNA gene transcription. Mol. Cell 51, 493–505 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Egloff, S. et al. The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression. EMBO J. 36, 934–948 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Takahashi, H. et al. MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex. Nat. Commun. 6, 5941 (2015).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank J. Weems for help with figures and all of the many colleagues who have contributed to our laboratory’s research on Pol II elongation over the years. Because of length limitations, we have not provided exhaustive references and in some cases have cited reviews rather than primary papers. We apologize to those whose contributions to the primary literature were not cited.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Joan W. Conaway.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information: Beth Moorefield was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Conaway, R.C., Conaway, J.W. The hunt for RNA polymerase II elongation factors: a historical perspective. Nat Struct Mol Biol 26, 771–776 (2019). https://doi.org/10.1038/s41594-019-0283-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41594-019-0283-1

This article is cited by

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