Biochemistry and Molecular Biology
Penn State Science
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David Gilmour

David Gilmour

Main Content

  • Professor of Molecular and Cell Biology and
  • Graduate Education Co-Director
465A North Frear Laboratory
University Park, PA 16802
Email: dsg11@psu.edu
Phone: (814) 863-8905

Research Interests

Transcriptional regulation of the hsp70 heat shock gene in Drosophila

Graduate Programs

BMMB, MCIBS

Research Summary 

We are interested in understanding mechanisms of transcriptional control in eukaryotes and are currently focusing on the function and mechanism of promoter proximal pausing.  Much research over the past 20 years has focused on transcriptional regulatory mechanisms that control the association of RNA polymerase II (Pol II) with a gene’s promoter.  During this time, however, a small number of genes including the heat shock genes of Drosophila were found to have Pol II concentrated in the promoter region even though the genes were weakly transcribed.  The Pol II at these genes has initiated transcription and paused in the promoter proximal region approximately 30 nucleotides downstream from the transcription start site.  The behavior of Pol II in the promoter proximal region appears to be governed by the opposing actions of two negative regulators of elongation called NELF and DSIF and a positive regulator called P-TEFb.

Recent genome-wide mapping techniques now show that Pol II is concentrated in the promoter proximal region of thousands of genes in Drosophila and mammalian cells.  Many genes involved in development, cell division, and stress responses have paused Pol II.  Included among these genes are the myc and fos proto-oncogenes, and the p53 tumor suppressor gene. In addition, promoter proximal pausing represses transcription of the HIV provirus.  Thus the biological and medical implications of promoter proximal pausing have dramatically increased during the past few years.

Using primarily Drosophila as a model system, we are combining biochemical, molecular genetic, and cytological methods to achieve a uniquely comprehensive approach to the study of promoter proximal pausing.  We have reconstituted promoter proximal pausing in Drosophila nuclear extracts and are using this to investigate the mechanism by which specific proteins control promoter proximal pausing.  Recently, we have determined that GAGA factor, a sequence specific DNA binding protein, promotes pausing by recruiting NELF to the promoter.  We envision that kinetic competition between elongation and the rate at which inhibitors of elongation are able to capture the Pol II dictate the efficiency and the location of promoter proximal pausing.  Support for this model has been obtained by analyzing flies that have a mutation in Pol II that slows the rate of elongation.  We have discovered that the mutation shifts the location of the paused Pol II closer to the transcription start site.  We often use a technique called permanganate genomic footprinting to monitor the behavior of transcriptionally engage Pol II at high resolution in living cells or tissues.  To gain insight into the role of specific proteins in promoter proximal pausing, we monitor changes in the behavior of Pol II in living cells following depletion of specific proteins by RNA interference.  Most recently, we have combined an in vivo crosslinking technique known as chromatin immunoprecipitation with permanganate genomic footprinting to detect paused Pol II throughout the Drosophila genome.  This sets the stage for evaluating global changes in promoter proximal pausing caused by manipulating specific proteins or growth conditions in vivo.

 

Gilmour figure 1

 

Gilmour figure 2

Selected Publications

  • Achary, B.G., K.M. Campbell, I.S. Co, D.S. Gilmour (2014) RNAi screen in Drosophila larvae identifies histone deacetylase 3 as a positive regulator of the hsp70 heat shock gene expression during heat shock. BBA – Gene Regulatory Mechanisms 1839:355-363.
  • Natarajan, M., G.M. Schiralli Lester, C. Lee, A. Missra, G.A. Wasserman, M. Steffen, D.S. Gilmour, A.J. Henderson (2013) Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription. Journal of Biological Chemistry 288:25995-26003.
  • Li, J, Y. Liu, H.S. Rhee, S.K. Ghosh, L. Bai, B.F. Pugh, D.S. Gilmour (2013) Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing. Molecular Cell 6:711-722.
  • Li, J., and D.S. Gilmour (2013) Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J. 32:1829-1841.
  • Lagha, M., J.P. Bothma, E. Esposito, S. Ng, L. Stefanik, C. Tsui, J. Johnston, K. Chen, D.S. Gilmour, J. Zeitlinger, M.S. Levine (2013) Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo. Cell 153:976-987.
  • Cernilogar, F.M., M.C. Onorati, G.O. Kothe, A.M. Burroughs, K.M. Parsi, A. Breiling, F.L. Sardo, A. Saxena, K. Miyoshi, H. Siomi, M.C. Siomi, P. Carninci, D.S. Gilmour, D.F. Corona, and V. Orlando (2011) Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480:391-395.
  • Fay, A., Z. Misulovin, J. Li, C.A. Schaff, M. Gause, D.S. Gilmour, D. Dorsett (2011) Cohesin selectively binds and regulates genes with paused RNA polymerase. Current Biology 21:1624-1634.
  • Ghosh, S.K., A. Missra, and D.S. Gilmour (2011) Negative elongation factor accelerates the rate at which heat shock genes are shut off by facilitating dissociation of heat shock factor. Molecular and Cellular Biology 31:4232-4243.
  • Kruk, J.A., A. Dutta, J. Fu, D.S. Gilmour, and J.C. Reese (2011) The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes and Development 26:581-593.
  • Li, J. and D.S. Gilmour (2011) Promoter proximal pausing and the control of gene expression. Current Opinion in Genetics and Development. 21:231-235.
  • Missra, A. and D.S. Gilmour (2010) Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex. Proceedings of the National Academy of Sciences, USA 107:11301-11306.
  • Gilmour, D.S. and R. Fan (2009) Detecting transcriptionally engaged RNA polymerase in eukaryotic cells with permanganate genomic footprinting. Methods 48:368-374.
  • Gilmour, D.S. (2009) Promoter proximal pausing on genes in metazoans. Chromosoma 118:1-10
  • Gilmour, D.S., and R. Fan (2008) Derailing the locomotive: transcription termination. Journal of Biological Chemistry 283:661-664.
  • Lee, C., X. Li, A. Hechmer, M. Eisen, M.D. Biggin, B.J. Venters, C. Jiang, J. Li, B.F. Pugh, D.S. Gilmour (2008) NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Molecular and Cellular Biology 28:3290-3300.
  • Gilchrist, D.A., S. Nechav, C. Lee, S.K. Ghosh, J.B. Collins, L. Li, D.S. Gilmour, K. Adelman (2008) NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes and Development 22:1921-1933.
  • Li, P., H. Yao, Z. Zhang, M. Li, Y. Luo, P.R. Thompson, D.S. Gilmour, Y. Wang (2008) Regulation of p53 target gene expression by peptidylarginine deiminase 4. Molecular and Cellular Biology 28:4745-4758
  • Mavrich, T.N., C. Jiang, I.P. Ioshikhes, X. Li, B.J. Venters, S.J. Zanton, L.P. Tomsho, J. Qi, R.L. Glaser, S.C. Schuster, D.S. Gilmour, I. Albert, B.F. Pugh (2008) Nucleosome organization in the Drosophila genome. Nature 453:358-362.
  • Zhang, Z., A. Klatt, A.J. Henderson, and D.S. Gilmour (2007) Transcription termination factor Pcf11 limits the processivity of Pol II on an HIV provirus to repress gene expression. Genes and Development 21:1609-1614.
  • Wang, X., C. Lee, D.S. Gilmour, J.P. Gergen (2007) Transcription elongation controls cell fate specification in the Drosophila embryos. Genes and Development 21:1031-1036.
  • Zhang, Z., A. Klatt, D.S. Gilmour, A.J. Henderson (2007) Negative elongation factor, NELF, represses human immunodeficiency virus transcription by pausing the RNA polymerase II complex. Journal of Biological Chemistry 282:16981-16988.