Skip to main content

Thank you for visiting 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.

RNA polymerase is poised for activation across the genome


Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter1, followed by initiation of RNA synthesis and the transition to productive elongation2,3,4. In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-oncogenes, whose expression is attenuated by regulated stalling of polymerase elongation within the promoter-proximal region5,6,7,8,9,10,11,12,13. To determine the importance of polymerase stalling for transcription regulation, we carried out a genome-wide search for Drosophila melanogaster genes with Pol II stalled within the promoter-proximal region. Our data show that stalling is widespread, occurring at hundreds of genes that respond to stimuli and developmental signals. This finding indicates a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



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

Figure 1: Whole-genome mapping of Pol II binding in Drosophila S2 cells.
Figure 2: Pol II is enriched near the promoters of a subset of genes.
Figure 3: A subset of genes possess much more Pol II near their promoters than in the downstream region.
Figure 4: Permanganate mapping of open transcription bubbles reveals engaged Pol II within the promoter-proximal region of genes with PPEP.
Figure 5: Depletion of NELF relieves promoter-proximal stalling, globally reducing PPEP.
Figure 6: Gene ontology analysis shows that genes with PPEP are enriched in genes involved in development, reproduction and the response to stimulus.

Accession codes


Gene Expression Omnibus


  1. Roeder, R.G. Transcriptional regulation and the role of diverse coactivators in animal cells. FEBS Lett. 579, 909–915 (2005).

    Article  CAS  Google Scholar 

  2. Luse, D.S. & Samkurashvili, I. The transition from initiation to elongation by RNA polymerase II. Cold Spring Harb. Symp. Quant. Biol. 63, 289–300 (1998).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Sims, R.J. III, Belotserkovskaya, R. & Reinberg, D. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437–2468 (2004).

    Article  CAS  Google Scholar 

  5. Aida, M. et al. Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene. Mol. Cell. Biol. 26, 6094–6104 (2006).

    Article  CAS  Google Scholar 

  6. Gilmour, D.S. & Lis, J.T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 6, 3984–3989 (1986).

    Article  CAS  Google Scholar 

  7. Krumm, A., Hickey, L.B. & Groudine, M. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 9, 559–572 (1995).

    Article  CAS  Google Scholar 

  8. Krumm, A., Meulia, T., Brunvand, M. & Groudine, M. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 6, 2201–2213 (1992).

    Article  CAS  Google Scholar 

  9. Law, A., Hirayoshi, K., O'Brien, T. & Lis, J.T. Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila. Nucleic Acids Res. 26, 919–924 (1998).

    Article  CAS  Google Scholar 

  10. 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 

  11. Rougvie, A.E. & Lis, J.T. Postinitiation transcriptional control in Drosophila melanogaster. Mol. Cell. Biol. 10, 6041–6045 (1990).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. Strobl, L.J. & Eick, D. Hold back of RNA polymerase II at the transcription start site mediates down-regulation of c-myc in vivo. EMBO J. 11, 3307–3314 (1992).

    Article  CAS  Google Scholar 

  14. Rasmussen, E.B. & Lis, J.T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc. Natl. Acad. Sci. USA 90, 7923–7927 (1993).

    Article  CAS  Google Scholar 

  15. Rasmussen, E.B. & Lis, J.T. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J. Mol. Biol. 252, 522–535 (1995).

    Article  CAS  Google Scholar 

  16. Rougvie, A.E. & Lis, J.T. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54, 795–804 (1988).

    Article  CAS  Google Scholar 

  17. Aiyar, S.E. et al. Attenuation of estrogen receptor alpha-mediated transcription through estrogen-stimulated recruitment of a negative elongation factor. Genes Dev. 18, 2134–2146 (2004).

    Article  CAS  Google Scholar 

  18. Fujinaga, K. et al. The ability of positive transcription elongation factor B to transactivate human immunodeficiency virus transcription depends on a functional kinase domain, cyclin T1, and Tat. J. Virol. 72, 7154–7159 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Raschke, E.E., Albert, T. & Eick, D. Transcriptional regulation of the Ig kappa gene by promoter-proximal pausing of RNA polymerase II. J. Immunol. 163, 4375–4382 (1999).

    CAS  PubMed  Google Scholar 

  20. 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 

  21. 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 

  22. Pokholok, D.K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005).

    Article  CAS  Google Scholar 

  23. Qi, Y. et al. High-resolution computational models of genome binding events. Nat. Biotechnol. 24, 963–970 (2006).

    Article  CAS  Google Scholar 

  24. Kim, T.H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005).

    Article  CAS  Google Scholar 

  25. Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).

    Article  CAS  Google Scholar 

  26. 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 

  27. Narita, T. et al. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol. Cell. Biol. 23, 1863–1873 (2003).

    Article  CAS  Google Scholar 

  28. Yamaguchi, Y., Inukai, N., Narita, T., Wada, T. & Handa, H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol. Cell. Biol. 22, 2918–2927 (2002).

    Article  CAS  Google Scholar 

  29. Wang, X., Lee, C., Gilmour, D.S. & Gergen, J.P. Transcription elongation controls cell fate specification in the Drosophila embryo. Genes Dev. 21, 1031–1036 (2007).

    Article  CAS  Google Scholar 

  30. Lee, C.Y. et al. Genome-wide analyses of steroid- and radiation-triggered programmed cell death in Drosophila. Curr. Biol. 13, 350–357 (2003).

    Article  CAS  Google Scholar 

Download references


The authors acknowledge T. Kunkel, M. Resnick, G. dos Santos and P. Wade for critical reading of this manuscript. We also thank R. Young for providing support in the microarray analysis of ChIP-chip data and for helpful suggestions on this work. We thank D. Gilmour for the gift of the NELF-E antibody and for advice on permanganate mapping. This research was supported by the Intramural Research Program of the US National Institutes of Health, National Institute of Environmental Health Sciences.

Author information

Authors and Affiliations



K.A. and G.W.M. designed the experiments and prepared the manuscript. G.W.M., D.A.G. and S.N. carried out the experiments. S.F.G. conducted the hybridization of DNA and expression arrays. J.Z. designed the DNA arrays and analyzed the bound regions in ChIP-chip data. R.S., J.S.P. and K.A. carried out further data analysis.

Corresponding author

Correspondence to Karen Adelman.

Supplementary information

Supplementary Text and Figures

Supplementary Methods, Supplementary Figures 1–8 (PDF 2298 kb)

Supplementary Table 1

Supplementary Table 1 (XLS 1214 kb)

Supplementary Table 2

Supplementary Table 2 (XLS 108 kb)

Supplementary Table 3

Supplementary Table 3 (XLS 36 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Muse, G., Gilchrist, D., Nechaev, S. et al. RNA polymerase is poised for activation across the genome. Nat Genet 39, 1507–1511 (2007).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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