The experiments described in this proposal are designed to provide insight into the mechanism and regulation of pre-mRNA polyadenylation. The following Specific Aims are proposed. 1. Structural studies on 3'processing. Studies with Liang Tong to determine the x-ray structures of a CPSF-73/CPSF-100 complex and of the scaffolding protein symplekin will be pursued. Studies on the former will be complemented with endonuclease assays employing the purified complex as well as structure-based mutant derivatives of CPSF- 73. Recent structural studies of the symplekin N terminus will be pursued, and efforts to crystallize the evolutionarily conserved central domain continued. Using previously developed methods to purify the assembled 3'processing complex, a collaboration with Joachim Frank will be continued, with the goal of obtaining a 3D reconstruction of the entire complex by cryo EM. 2. 3'processing and links to transcription. Experiments examining the function of the multisubunit PAF complex in linking transcription and processing using an in vitro coupled reaction will be pursued. Our recent finding that a model transcription factor, GAL4- VP16, can directly activate 3'processing, will be further investigated. Genetic studies employing DT40 cells expressing a conditional RNA polymerase II largest subunit (LS) will be pursued to investigate the role of the LS C-terminal domain (CTD) in 3'processing. Studies on transcription termination will include structure-based analysis of the yeast 5'3'exonuclease Rat1. The possible role of the human protein Senataxin, the apparent homologue of the yeast RNA-DNA helicase Sen1, in transcription-termination will be investigated. 3. 3'processing factors and their regulation. Two proteins discovered in our recent proteomic analysis of the 3'processing complex, Rbbp6 (Rb binding protein 6) and PARP1 (poly(ADP) ribosylase 1), will be investigated. Experiments suggesting that Rbbp6 is necessary for 3'cleavage will be pursued. The role of a RING domain and domains binding the tumor suppressors p53 and Rb will be analyzed. Data indicating that PARP1 regulates polyadenylation, perhaps by PARylating poly(A) polymerase (PAP), will be extended, and the effects of agents that induce PARP1 on polyadenylation determined. PAP is extensively modified by sumoylation in a tissue-specific manner. Experiments that identified an E3 SUMO ligase, PIAS3, that enhances PAP sumoylation will be extended, and the possibility that PIAS3 and/or the SUMO protease SENP1 are involved in tissue specificity explored. The function of the evolutionarily conserved sumoylation of CPSF-73 will be investigated by analysis of the yeast homologue, Ysh1. Finally, recent studies of others have indicated that global changes in alternative polyadenylation occur during cell differentiation. The mechanistic basis for this will be investigated with a model in vitro system using C2C12 myoblasts, which will allow identification of the factor(s) involved. 3'processing will be reconstituted with purified factors, which will allow analysis of how variations in concentrations of specific components influence poly(A) site choice.

Public Health Relevance

The experiments described in this proposal are designed to increase our understanding of the mechanism and regulation of the essential reaction that creates the polyadenylated 3'ends of mRNA. Recent studies have revealed that changes in polyadenylation occur during development and disease, and our studies will provide a mechanistic understanding for these changes.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Program Officer
Bender, Michael T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Columbia University (N.Y.)
Other Domestic Higher Education
New York
United States
Zip Code
Ogami, Koichi; Richard, Patricia; Chen, Yaqiong et al. (2017) An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev 31:1257-1271
Tian, Bin; Manley, James L (2017) Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol 18:18-30
Morales, Julio C; Richard, Patricia; Patidar, Praveen L et al. (2016) XRN2 Links Transcription Termination to DNA Damage and Replication Stress. PLoS Genet 12:e1006107
Shi, Yongsheng; Manley, James L (2015) The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev 29:889-97
Drisaldi, Bettina; Colnaghi, Luca; Fioriti, Luana et al. (2015) SUMOylation Is an Inhibitory Constraint that Regulates the Prion-like Aggregation and Activity of CPEB3. Cell Rep 11:1694-702
Nagaike, Takashi; Manley, James L (2014) In vitro analysis of transcriptional activators and polyadenylation. Methods Mol Biol 1125:65-74
Xiang, Kehui; Tong, Liang; Manley, James L (2014) Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery. Mol Cell Biol 34:1894-910
Di Giammartino, Dafne Campigli; Li, Wencheng; Ogami, Koichi et al. (2014) RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs. Genes Dev 28:2248-60
Morales, Julio C; Richard, Patricia; Rommel, Amy et al. (2014) Kub5-Hera, the human Rtt103 homolog, plays dual functional roles in transcription termination and DNA repair. Nucleic Acids Res 42:4996-5006
Di Giammartino, Dafne Campigli; Manley, James L (2014) New links between mRNA polyadenylation and diverse nuclear pathways. Mol Cells 37:644-9

Showing the most recent 10 out of 76 publications