The synthesis of messenger RNA is the primary event in gene expression and is central to the life of cells. mRNA production requires transcription by pol II and processing of the primary transcript by a set of proteins which carry out capping, splicing and cleavage/polyadenylation. Transcripts made in by polymerases other than pol II are not processed correctly into mature mRNA. A network of protein:protein contacts in the cell nucleus exists to couple transcription by pol II with the specific RNA processing events responsible for maturation of mRNA. The objective of this proposal is to elucidate how proteins communicate to achieve coupling of pol II transcription with RNA packaging and processing using biochemical and genetic approaches in mammalian cells, frog oocytes and budding yeast. Our research is testing the idea that mRNA is made by a """"""""factory"""""""" complex containing RNA pol II and RNA processing factors which contact it through a repetitive protein domain called the CTD. This model has changed the way we think about proteins which were once thought to operate independently but are now thought to be co-ordinated with one another in the nucleus. One important functional consequence of the integration between transcription and processing that we are beginning to uncover is that transcription factors can regulate the efficiency of RNA processing and conversely processing factors can potentially regulate transcription. This work may help elucidate how the transcription and processing of mRNAs are regulated under normal conditions and how they become mis-regulated in the disease state. Defects in splicing resulting of pre-mRNA's are responsible for a large fraction of all inherited diseases.
The specific aims of this work are: 1. To determine how mammalian capping, splicing and cleavage polyadenylation factors associate with pol II elongation complexes on genes in vivo. 2. To determine the extent to which introns are excised co-transcriptionally and what factors affect the efficiency of co-transcriptional splicing. 3. To test the CTD code hypothesis by determining the structural features of the CTD that contribute to co- transcriptional pre-mRNA processing, mRNA export and hnRNP packaging.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular Genetics B Study Section (MGB)
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Rhoades, Marcus M
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University of Colorado Denver
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Ebmeier, Christopher C; Erickson, Benjamin; Allen, Benjamin L et al. (2017) Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications. Cell Rep 20:1173-1186
Fong, Nova; Saldi, Tassa; Sheridan, Ryan M et al. (2017) RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction. Mol Cell 66:546-557.e3
Fusby, Becky; Kim, Soojin; Erickson, Benjamin et al. (2016) Coordination of RNA Polymerase II Pausing and 3' End Processing Factor Recruitment with Alternative Polyadenylation. Mol Cell Biol 36:295-303
Sheridan, Ryan M; Bentley, David L (2016) Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins. Biotechniques 60:69-74
Saldi, Tassa; Cortazar, Michael A; Sheridan, Ryan M et al. (2016) Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol 428:2623-2635
Bentley, David L (2015) The union of transcription and mRNA processing: 20 years of coupling. RNA 21:569-70
Bentley, David L (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15:163-75
Fong, Nova; Kim, Hyunmin; Zhou, Yu et al. (2014) Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev 28:2663-76
Johnson, Sara A; Kim, Hyunmin; Erickson, Benjamin et al. (2011) The export factor Yra1 modulates mRNA 3' end processing. Nat Struct Mol Biol 18:1164-71
Kim, Soojin; Kim, Hyunmin; Fong, Nova et al. (2011) Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A 108:13564-9

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