Pathways regulating cytoplasmic mRNA stability and translation are major determinants of protein abundance in mammalian cells. We are interested in processes by which proteins are assembled into ribonucleoprotein complexes in response to translational repression and, in turn, regulate mRNA stability and re-initiation of translation. Recently, there has been a great deal of research into the role of cellular granules containing silenced mRNAs in regulating translation and RNA turnover, and these structures have been implicated in the progression of neurodegenerative and other diseases. However, little is known about the pathways determining assembly of mRNAs into granules and the roles of specific proteins within these structures. To address these questions, we are isolating ribonucleoprotein complexes assembled on endogenously expressed hairpin-tagged RNAs. Using a system we have previously developed to provide an unbiased catalog of proteins assembled on particular RNAs, we are now identifying proteins associated with mRNAs in a manner dependent on translational repression. Our characterization of these proteins will focus on understanding the biochemical basis for specific assembly of RNA-binding proteins into translationally repressed mRNPs in addition to uncovering their cellular functions. To this end, we are using high-throughput RNAseq approaches to determine the transcriptome-wide occupancy of these proteins under distinct cellular conditions and to characterize changes in RNA translation and abundance in response to protein overexpression and/or depletion. This approach has led to the identification of candidate factors with prominent roles in controlling the stability of mRNAs encoding important gene expression regulators.
|Haque, Nazmul; Hogg, J Robert (2016) Easier, Better, Faster, Stronger: Improved Methods for RNA-Protein Interaction Studies. Mol Cell 62:650-1|