Tracking transcriptome diversity in real-time

Univ Of Massachusetts Med Sch Worcester, Worcester MA

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Abstract

SUMMARY Recent studies have provided unprecedented insights into how individual molecular mechanisms are correlated to changes in gene expression levels. It is now recognized that substantial transcriptome complexity arises from decisions involved in the processing of nascent mRNAs. However, by and large, the many studies of gene expression have focused on characterizing steady-state mRNA levels, even though living systems are inherently dynamic. Thus, a key open question in functional genomics is: how to the dynamics of individual molecular mechanisms combine to influence the cellular transcriptome? Our overarching hypothesis is that the fate of an mRNA is governed by kinetic interactions underlying molecular efficiency across disparate steps in the mRNA lifecycle – at the core, transcription elongation, mRNA splicing, and 3’ end cleavage. Current knowledge of spatiotemporal coordination across these processes likely represents the tip of the iceberg. Our work combines genetic, molecular, and cellular genomic techniques with high-dimensional computational analyses to address fundamental themes in mechanistic efficiency. First, we aim to dissect the kinetic basis for efficient mRNA biogenesis and maturation. Work from our research and others has suggested that there is substantial variability in kinetic actions and rate-limiting steps for mature mRNA production across genes. Determining the molecular logic underlying this variability will inform our understanding of the molecular basis for transcriptome complexity in both homeostatic and diseased cells. Second, we will investigate how coordinated RNA processing decisions underlie mRNA isoform expression. Despite decades of research on individual mechanistic steps, we are still unable to predict the expression of specific mRNA isoforms in either homeostatic or dynamic cellular conditions. Building on our recent work, we will characterize how coupled kinetic and spatial mechanisms regulate alternative mRNA isoforms. Finally, we will determine how RNA processing kinetics underlie the regulation of cellular transitions. The kinetics of gene regulatory processes likely play a crucial role in cellular responses or transitions, by altering the order of molecular events or speed of processes to rapidly regulate gene expression dynamics. Our research will result in insights crucial to uncovering the cascade of molecular events that cumulatively establish steady-state gene expression levels, with implications for improved therapeutic designs or strategies that target the early progression of cellular shifts rather than only the final outcome.