Dissecting RNA regulation in single cells and tissues

ABSTRACT The fate and function of individual cells and tissues is often dictated at the transcriptional level by the activity of cell- and tissue-specific transcription factors, as well as by RNA Binding Proteins (RBPs) that determine aspects of mRNA processing such as alternative splicing, stability, and localization. The physiological importance of RBPs in regulating RNA processing is illustrated by many human diseases, for example Spinal Muscular Atrophy and ALS/FTD, which can result from RBP mutation or dysregulation. A major open question for many of these diseases is: why does disruption of a widely-expressed RBP result in highly cell-specific phenotypes? For example, in SMA, why does mutation of the ubiquitously-expressed SMN1 result specifically in motor neuron degeneration? A second major question is: which target(s) of a given RBP are responsible for a specific phenotype? And a third related question: are the physiologically-relevant targets of a given RBP different in different cell or tissue types? Collectively these open questions illustrate that much remains unresolved about the relationship between RBP regulation and function in specific cells and tissues. Thus, we will ask how broadly-expressed RBPs result in highly specific functional outcomes, focusing on cell- specific regulatory mechanisms of two model RBPs, MEC-8/RBPMS and SMN-1. In addition to well-established roles for RBPs in regulating processes such as RNA stability and alternative splicing, the known universe of RNA regulation modalities continues to expand. Our lab is particularly interested in novel types of alternative splicing, aiming to dissect new and emerging types of alternative splicing at the cell-specific level, focusing on (1) formation of circular RNAs (circRNAs) due to back-splicing as opposed to canonical forward splicing, and (2) alternative splicing of exons that are not multiples of 3 nucleotides, and thus may lead to unusual outcomes including amino acid recoding, alternative C-termini lengths, and regulated RNA degradation. Together these experiments will address a significant gap in our understanding of the regulation and function of RNA processing at the cell- and tissue-specific level.