The long-term goal of our work is to understand the molecular mechanisms that control eukaryotic mRNA stability, which is a critical step in gene regulation. One major pathway of mRNA turnover in eukaryotes initiates with poly(A) tail shortening, which triggers decapping, leading to 5'to 3'exonucleolysis. Decapping is a key step in this pathway because it induces degradation of the mRNA, and is the site of numerous control inputs including the poly(A) tail and specific sequences that modulate mRNA decapping rate. Given this importance, we focused on understanding the mechanisms of mRNA decapping. In the past funding period, we clarified the nature of the decapping enzyme, identified the mechanisms by which some proteins affect the rate of decapping, and provided strong evidence that a key step in decapping is exiting the translating pool of mRNAs coupled with a specific mRNP re-arrangement. In addition, we also identified novel cytoplasmic structures (referred to as P-bodies) where the mRNA decapping machinery is concentrated and where mRNA degradation can occur. P-bodies are significant because: 1) they imply unanticipated compartmentalization of mRNA decay, which becomes a possible point of mRNA regulation, 2) are conserved in other eukaryotes and 3) are likely to be sites of additional events in mRNA biology, possibly including storage of translationally repressed mRNAs. In this grant, we will continue our analysis of mRNA decapping with a focus on understanding the composition, properties, and function of P-bodies.
The specific aims are as follows: I) Determine the composition and ultrastructure of P-bodies II) Analyze P-body assembly III) Analyze the function of the Dhhl and Pat1 proteins IV) Determine if P-bodies function in other aspects of cytoplasmic mRNA physiology.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Special Emphasis Panel (NSS)
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Bender, Michael T
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University of Colorado at Boulder
Schools of Arts and Sciences
United States
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Walters, Robert W; Shumilin, Igor A; Yoon, Je-Hyun et al. (2014) Edc3 function in yeast and mammals is modulated by interaction with NAD-related compounds. G3 (Bethesda) 4:613-22
Mitchell, Sarah F; Parker, Roy (2014) Principles and properties of eukaryotic mRNPs. Mol Cell 54:547-58
Shukla, Siddharth; Parker, Roy (2014) Quality control of assembly-defective U1 snRNAs by decapping and 5'-to-3' exonucleolytic digestion. Proc Natl Acad Sci U S A 111:E3277-86
Jain, Saumya; Parker, Roy (2013) The discovery and analysis of P Bodies. Adv Exp Med Biol 768:23-43
Mitchell, Sarah F; Jain, Saumya; She, Meipei et al. (2013) Global analysis of yeast mRNPs. Nat Struct Mol Biol 20:127-33
Ramaswami, Mani; Taylor, J Paul; Parker, Roy (2013) Altered ribostasis: RNA-protein granules in degenerative disorders. Cell 154:727-36
Rajyaguru, Purusharth; She, Meipei; Parker, Roy (2012) Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol Cell 45:244-54
Balagopal, Vidya; Parker, Roy (2011) Stm1 modulates translation after 80S formation in Saccharomyces cerevisiae. RNA 17:835-42
Buchan, J Ross; Yoon, Je-Hyun; Parker, Roy (2011) Stress-specific composition, assembly and kinetics of stress granules in Saccharomyces cerevisiae. J Cell Sci 124:228-39
Hilliker, Angela; Gao, Zhaofeng; Jankowsky, Eckhard et al. (2011) The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex. Mol Cell 43:962-72

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