Post-transcriptional control of gene expression by the mTORC1 signaling pathway

Project summary The translation of mRNAs into protein is a fundamental step in gene expression that is regulated by diverse cellular signals. How these regulatory mechanisms are used to orchestrate changes in gene expression and cellular function remains poorly understood. We have been studying this question through examination of the mTOR Complex 1 (mTORC1) signaling pathway, a master regulator of growth throughout eukaryotes. This pathway senses nutrient signals and responds by activating the cellular biosynthesis machinery to drive growth. Deregulation is linked to human diseases ranging from cancers to neurological disorders. A central function of mTORC1 is to activate “cap-dependent” translation through the eIF4F translation factor. Over the past five years, my laboratory has shown how this mechanism is used to control the translation and stability of hundreds of mRNAs with essential growth functions, including nearly all ribosomal proteins. More recently, we identified hundreds of mRNAs that are hyper-dependent on cap- dependent translation for unknown reasons and thousands that access “cap-independent” initiation mechanisms that remain unclear. Going forward, our research program seeks to answer several basic questions that emerge from these observations. First, what mRNA features define dependence on cap-dependent and cap-independent translation mechanisms and how are they detected? Second, how does regulation of cap-dependent translation trigger global and specific changes in mRNA stability? Third, how does variation in the structure of the transcriptome (e.g. alternative promoters) specialize the post-transcriptional regulation of mRNAs across tissues in vivo? We propose to tackle these questions using a combination of transcriptomic strategies, massively parallel reporter assays, and bioinformatic analyses in cells and in vivo that we have established over the last five years. Our ultimate goal is to fully understand the molecular systems that control growth-regulated gene expression, establish their function in the cellular growth process, and link their function to growth-related physiology. We expect these efforts to yield insights into basic principles of gene regulation that are used to adapt cells and organisms to changing nutrient availability.