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RNA polymerase is poised for activation across the genome

Nature Genetics volume 39, pages 1507–1511 (2007)Cite this article

Abstract

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.

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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.

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Acknowledgements

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.

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Authors and Affiliations

  1. Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, 27709, North Carolina, USA

    Ginger W Muse, Daniel A Gilchrist, Sergei Nechaev & Karen Adelman

  2. Constella Group, 2605 Meridian Parkway, Suite 200, Durham, 27713, North Carolina, USA

    Ruchir Shah & Joel S Parker

  3. Microarray Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, 27709, North Carolina, USA

    Sherry F Grissom

  4. Expression Analysis, 4312 South Alston Ave., Durham, 27713, North Carolina, USA

    Joel S Parker

  5. Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, 02142, Massachusetts, USA

    Julia Zeitlinger

  6. Stowers Institute for Medical Research, 1000 East 50th St., Kansas City, 64110, Missouri, USA

    Julia Zeitlinger

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Contributions

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.

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Correspondence to Karen Adelman.

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Muse, G., Gilchrist, D., Nechaev, S. et al. RNA polymerase is poised for activation across the genome. Nat Genet 39, 1507–1511 (2007). https://doi.org/10.1038/ng.2007.21

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