Regulation of Messenger RNA Turnover in Mammalian Cells

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Project Description Research in my laboratory focuses on elucidating the principles and regulatory mechanisms that govern messenger RNA turnover in mammalian cells. mRNA turnover plays an essential role in regulating gene expression via control of mRNA stability and quality, both globally and at the level of individual mRNAs. In mammalian cells, all major modes of mRNA decay are triggered by deadenylation (i.e., the removal of the poly(A) tails from the 3' end of mRNAs), a rate-limiting process involving two consecutive kinetic phases. Although previous studies provided a clear picture of the mechanistic steps and participating factors of mRNA decay pathways, relatively little is known about the impact of deadenylation and its modulation on mRNA turnover at the transcriptome level. Particularly lacking is an understanding of how coordinated changes in stability for whole groups of mRNAs contribute to programming or reprogramming of the transcriptome when mammalian cells respond to intra- or extra-cellular stimuli. In the cytoplasm, mRNAs fulfill their functions in the form of mRNA-protein complexes (mRNPs). mRNPs are highly dynamic entities, being continuously remodeled by rapid exchanges of their protein constituents, dictating individual mRNAs' fates at each step of their lifespan. Any inappropriate remodeling of an mRNP complex has the potential to disrupt its proper engagement in downstream events. Currently, one exciting and underexplored area of research in RNA biology is the remodeling of mRNPs at individual, group, and global levels during the process of mRNA deadenylation and decay. Our present proposal focuses on three seemingly disparate aspects of mammalian RNA biology that are linked by their potential to shape the mammalian transcriptome through modulating global mRNA turnover and mRNP remodeling. These are: 1) Alternative 3' end processing and polyadenylation (APA), which generates mRNA isoforms with distinct 3' untranslated regions; 2) mRNA N6-methyladenosine (m6A) modification, which creates mRNA isoforms with different metabolic fate; and 3) Phosphorylation of ancillary deadenylation factors, which alters mRNA deadenylation and decay. In the past few years, we have made several key findings regarding these three areas that have helped lay the groundwork for the proposed studies in this application. We have also adapted and further developed key analytical approaches to elucidating the impacts of the targeted processes on mRNA turnover across the transcriptome and the mechanisms by which deadenylation impacts mRNA stability through mRNP remodeling. Successful completion of the proposed studies will offer a new framework for elucidating the signal-dependent regulation of mRNA stability and mRNP remodeling at the transcriptome level, and the results will significantly expand understanding of the fundamental principles governing eukaryotic mRNA turnover.