Regulation of mRNA fate

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Abstract The process of alternative splicing (AS) is a powerful mechanism for generating mRNA diversity from protein coding genes. Alternative mRNA isoforms from the same gene can differ subtly from each other or have radical alterations in their sequence composition. Remarkably, very little is known about whether or not this diverse pool of mRNA is converted to protein. One intriguing clue for solving this problem comes from our recent studies suggesting that the process of alternative splicing influences the translational efficiency of the resultant mRNA isoforms. In this proposal, we use both biochemical and molecular approaches to untangle the intricate mechanisms coupling post-transcriptional gene expression. By determining how AS-TC elements reg- ulate mRNA translation we will be able to refute or support the central hypothesis of this proposal, that alterna- tively spliced transcripts are packaged into functionally distinct messenger ribonucleoprotein particles (mRNPs). If sequences associated with differential polyribosome association do not directly control translation initiation or elongation, then we will consider our alternative hypothesis: that a significant fraction of mRNA iso- form diversity arises from noisy splicing which are then excluded from polyribosomes by some unknown mRNA surveillance pathway. Solving this important problem will not only reveal how cis-elements influence transla- tional yield, but will also define mechanistic links between the processes of alternative splicing and mRNA translation. In the long-term, our research program will facilitate new opportunities for RNA-based diagnostics and therapies that will be applicable to a wide array of human diseases.