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.

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

Abstract

It is widely assumed that the key rate-limiting step in gene activation is the recruitment of RNA polymerase II (Pol II) to the core promoter1. Although there are well-documented examples in which Pol II is recruited to a gene but stalls2,3,4,5,6,7,8,9,10,11,12, a general role for Pol II stalling in development has not been established. We have carried out comprehensive Pol II chromatin immunoprecipitation microarray (ChIP-chip) assays in Drosophila embryos and identified three distinct Pol II binding behaviors: active (uniform binding across the entire transcription unit), no binding, and stalled (binding at the transcription start site). The notable feature of the 10% genes that are stalled is that they are highly enriched for developmental control genes, which are either repressed or poised for activation during later stages of embryogenesis. We propose that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Different classes of Pol II binding profiles.
Figure 2: Whole-genome analysis of Pol II binding.
Figure 3: Confirmation of the class of genes with Pol II stalling.
Figure 4: Functional analysis of the three classes of genes.
Figure 5: Pol II profile comparison of genes in the repressed versus active state.
Figure 6: Pol II stalling at genes before activation.

Accession codes

Accessions

ArrayExpress

References

  1. Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569–577 (1997).

    Article  CAS  Google Scholar 

  2. Conaway, J.W., Shilatifard, A., Dvir, A. & Conaway, R.C. Control of elongation by RNA polymerase II. Trends Biochem. Sci. 25, 375–380 (2000).

    Article  CAS  Google Scholar 

  3. 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 

  4. 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 

  5. Bender, T.P., Thompson, C.B. & Kuehl, W.M. Differential expression of c-myb mRNA in murine B lymphomas by a block to transcription elongation. Science 237, 1473–1476 (1987).

    Article  CAS  Google Scholar 

  6. 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 

  7. 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 

  8. Laspia, M.F., Wendel, P. & Mathews, M.B. HIV-1 Tat overcomes inefficient transcriptional elongation in vitro. J. Mol. Biol. 232, 732–746 (1993).

    Article  CAS  Google Scholar 

  9. Cheng, C. & Sharp, P.A. RNA polymerase II accumulation in the promoter-proximal region of the dihydrofolate reductase and gamma-actin genes. Mol. Cell. Biol. 23, 1961–1967 (2003).

    Article  CAS  Google Scholar 

  10. 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 

  11. Radonjic, M. et al. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18, 171–183 (2005).

    Article  CAS  Google Scholar 

  12. 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 

  13. Lis, J. & Wu, C. Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell 74, 1–4 (1993).

    Article  CAS  Google Scholar 

  14. Reppas, N.B., Wade, J.T., Church, G.M. & Struhl, K. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol. Cell 24, 747–757 (2006).

    Article  CAS  Google Scholar 

  15. Agalioti, T. et al. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell 103, 667–678 (2000).

    Article  CAS  Google Scholar 

  16. Soutoglou, E. & Talianidis, I. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901–1904 (2002).

    Article  CAS  Google Scholar 

  17. Schneider, D.S., Hudson, K.L., Lin, T.Y. & Anderson, K.V. Dominant and recessive mutations define functional domains of Toll, a transmembrane protein required for dorsal-ventral polarity in the Drosophila embryo. Genes Dev. 5, 797–807 (1991).

    Article  CAS  Google Scholar 

  18. Leptin, M. twist and snail as positive and negative regulators during Drosophila mesoderm development. Genes Dev. 5, 1568–1576 (1991).

    Article  CAS  Google Scholar 

  19. Kosman, D., Ip, Y.T., Levine, M. & Arora, K. Establishment of the mesoderm-neuroectoderm boundary in the Drosophila embryo. Science 254, 118–122 (1991).

    Article  CAS  Google Scholar 

  20. Furlong, E.E., Andersen, E.C., Null, B., White, K.P. & Scott, M.P. Patterns of gene expression during Drosophila mesoderm development. Science 293, 1629–1633 (2001).

    Article  CAS  Google Scholar 

  21. Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M. & Levine, M. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell 111, 687–701 (2002).

    Article  CAS  Google Scholar 

  22. Biemar, F. et al. Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc. Natl. Acad. Sci. USA 103, 12763–12768 (2006).

    Article  CAS  Google Scholar 

  23. Zeitlinger, J. et al. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev. 21, 385–390 (2007).

    Article  CAS  Google Scholar 

  24. Markstein, M., Markstein, P., Markstein, V. & Levine, M.S. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 99, 763–768 (2002).

    Article  CAS  Google Scholar 

  25. Tomancak, P. et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 3, research0088.1–research0088.14 (2002).

  26. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).

    Article  CAS  Google Scholar 

  27. Huang, A.M., Rusch, J. & Levine, M. An anteroposterior Dorsal gradient in the Drosophila embryo. Genes Dev. 11, 1963–1973 (1997).

    Article  CAS  Google Scholar 

  28. Boulay, J.L., Dennefeld, C. & Alberga, A. The Drosophila developmental gene snail encodes a protein with nucleic acid binding fingers. Nature 330, 395–398 (1987).

    Article  CAS  Google Scholar 

  29. Sandmann, T. et al. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Dev. Cell 10, 797–807 (2006).

    Article  CAS  Google Scholar 

  30. Furlong, E.E. Integrating transcriptional and signalling networks during muscle development. Curr. Opin. Genet. Dev. 14, 343–350 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank R. Zinzen for collecting the Toll10b, Tollrm9/rm10 and gd7 embryos, T. Volkert and J. Love for microarray experimental support and members of the Young laboratory for critical reading of the manuscript. This research was supported in part by the Intramural Research Program of the US National Institutes of Health, National Institute of Environmental Health Sciences (K.A.), US National Institutes of Health grants HG002668 and GM069676 to R.A.Y. and GM34431 to M.L., a grant by the Moore Foundation and a postdoctoral fellowship by the Human Frontier Science Program Organization (HFSPO, A.S.).

Author information

Authors and Affiliations

Authors

Contributions

J.Z. and M.L. designed the experiment. J.Z. designed the arrays and carried out the experiments and analysis. A.S., M.K. and J.Z. analyzed expression data and functional categories. J.-W.H., S.N. and K.A. carried out the permanganate footprint assays. J.Z., M.L. and R.A.Y. prepared the manuscript.

Corresponding authors

Correspondence to Michael Levine or Richard A Young.

Ethics declarations

Competing interests

One of the authors (R.A.Y.) consults for Agilent Technologies.

Supplementary information

Supplementary Text and Figures

Supplementary Note (PDF 713 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zeitlinger, J., Stark, A., Kellis, M. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39, 1512–1516 (2007). https://doi.org/10.1038/ng.2007.26

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.2007.26

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