David Bentley Professor Ph.D., Cambridge University, 1982 Phone: (303) 724-3238 david.bentley@uchsc.edu

MESSENGER RNA PRODUCTION by RNA polymerase II (pol II) is central to the life of cells. The amount of messenger transcribed from each gene determines the amount of each corresponding protein that is made. For this reason the process of mRNA synthesis, or transcription, is extremely carefully regulated by the cell. Corrupted regulation of mRNA synthesis is a major cause of cancer. Indeed many of the oncogenes responsible for causing cancer, code for sequence specific transcription factors whose function is to control mRNA production. Our lab has found that certain transcription factors can stimulate the elongation of RNA transcripts by pol II. One aspect of our research is aimed at understanding the molecular basis for how elongation is controlled by transcription factors.

To make functional a mRNA requires synthesis of a primary transcript and processing of the transcript into its mature form. The processing is carried out by a complex set of proteins which add a cap at the 5' end, splice out introns and add a polyA tail at the 3' end. Transcripts made by RNA polymerases other than pol II are not processed correctly into mature mRNA in vivo. A mechanism clearly exists to couple transcription by pol II with the specific RNA processing events responsible for maturation of mRNA and we are trying to work out its molecular details. Our lab uses genetic and biochemical approaches to ask how the transcriptional machinery interacts with the processing machinery to achieve co-ordinated synthesis and maturation of transcripts made by pol II. We have identified a protein domain at the C-terminus of the pol II large subunit called the CTD which is involved in targetting RNA processing factors to pol II transcripts. Our working hypothesis is that synthesis and processing of mRNA precursors is carried out in the nucleus by a 'mRNA factory' complex which comprises pol II and processing factors held together by contacts with the CTD.

Specific Projects:

1. How does the pol II CTD influence elongation of transcripts in response to sequence specific activators and repressors?
2. What genes are involved in control of transcriptional elongation by pol II in budding yeast?
3. Do RNA processing facotrs really travel with pol II as it moves down a gene?
4. What is the role of the pol II CTD in processing of mRNAs in budding yeast?
5. How does the CTD influence the RNA splicing reaction?
6. Do sequence specific factors which regulate transcription also influence RNA processing ?

Schroeder, S. Schwer, B. Shuman, S. and Bentley D. (2000) Dynamic Association of Capping Enzymes with Transcribing RNA polymerase II, Genes and Dev. 14:2435-2440.

Fong, N. and Bentley D. (2001) Capping, Splicing and 3' Processing are Independently Stimulated by RNA Polymerase II: Different Functions for Different Segments of the CTD, Genes and Dev. 15: 1783-1795.

Bentley, D (2002) The mRNA Assembly Line: Transcription and Processing Machines in the same Factory.Curr. Opin. Cell. Biol. 14:336-342.

Licatalosi, D. Geiger, G. Minet, M. Schroeder, S., Cilli K. McNeil, J. and Bentley D.(2002) Functional Interaction of Yeast Pre-mRNA 3'-End Processing Factors with RNA Polymerase II. Mol. Cell. 9:1101-1111.

Fong, N., Bird, G., Vigneron, M., and Bentley, D. L. (2003). A 10 residue motif at the C-terminus of the RNA pol II CTD is required for transcription, splicing and 3' end processing. Embo J 22, 4274-82.

Schroeder, S., Zorio, D., Schwer, B., Shuman, S., and Bentley, D. (2004). A Function of Yeast mRNA Cap Methyltransferase, Abd1, in transcription by RNA Polymerase II. Mol. Cell 13, 377-387.

Bird, G. Zorio, D. and Bentley, D. (2004) RNA Polymerase II CTD phosphorylation is required for co-transcriptional pre-mRNA splicing and 3' end formation, Mol. Cell. Biol. 24: 8963-9.

Luo, W. and Bentley (2004) A Ribonucleolytic Rat Torpedoes RNA Polymerase II, Cell, 119:911-914.

Bentley, D.(2005) Rules of engagement:co-transcriptional recruitment of pre-mRNA prcessing factors Curr. Opin. Cell. Biol. 17:251-256.

Zhang, L., Schroeder, S., Fong, N., and Bentley, D. L. (2005). Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'. EMBO J.24: 2379-90.

Bird, G. Fong, N., Gatlin J. Farabaugh, S., and Bentley (2005) Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing Mol. Cell. 20:747-758.

Luo, W. Johnson, A. and Bentley D. (2006) The role of Rat1 in coupling mRNA 3' end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev. 20:954-965.

Seward, D. Cubberley, G. Kim, S. Schonewald, M. Zhang, L. Tripet, B. and Bentley, D (2007) Demethylation of trimethylated histtone H3 Lys4 in vivo by JARID1 JmjC proteins. Nature Structural and Mol. Biol.14:240-242,2007.

Glover-Cutter, K., Kim, S, Espinosa, J. and Bentley, D. (2008) RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nature Struct. and Mol. Biol. 15:71-75.