The coding regions of most eukaryotic genes are interrupted by non-coding introns which must be removed from the pre-mRNA prior to translation. We are taking a genome-wide approach to (1) identify the different conditions under which this process is used as a control point for regulating gene expression, and (2) determine the mechanisms by which this control is manifested.

While the presence of introns in eukaryotic genes has been known for over 30 years now, the completion of the human genome sequencing project made clear the significance of this process. It seems likely that the relatively small number of genes identified in the genome is largely offset by the fact that alternative splicing of these genes can be used to generate a significant amount of proteomic diversity. While alternatively spliced isoforms of different genes can be observed under many conditions (different tissue types, developmental states, etc.), and indeed the misregulation of these processes are associated with a large number of human diseases, it remains largely unknown how the splicing of these different isoforms is controlled.

During my post-doctoral work, prior to my arrival at Cornell, I developed microarrays that allowed me to examine pre-mRNA splicing from a genome-wide perspective in the budding yeast, Saccharomyces cerevisiae. The yeast genome is relatively devoid of introns, containing only ~300 introns in its ~6000 genes (the human genome, by comparison, has over 250,000 introns). Furthermore, yeast appeared to lack many of features associated with alternative splicing in higher systems. As such, it had previously been widely believed that yeast lacked the capacity to regulate pre-mRNA splicing in a transcript specific fashion. However, by systematically examining the global changes in pre-mRNA splicing in response to changing environmental conditions, I was able to demonstrate that this process could be utilized as an important regulatory control point. This important finding demonstrates that mechanisms exist by which changes in external environment can be sensed by the organism and can lead to rapid and specific changes in the activity of this process. We are now aggressively examining how widely this regulatory paradigm is used, as well as its mechanistic underpinnings. In addition to our work in budding yeast, we are expanding this work into organisms with more complex intron architecture, including the fission yeast Schizosaccharomyces pombe.

The demonstration that pre-mRNA processing can be used as a regulatory control point has had a major impact in the field. Indeed, while the two manuscripts describing my work have been in press for less than a year, they have been covered by no fewer than 6 different review articles to date. A more complete understanding of how splicing is regulated is an essential component of understanding the more general question of how organisms regulate their genetic information. Importantly, many disease states involve the misregulation of pre-mRNA splicing ... we are now perfectly positioned to begin to investigate the underpinnings of this process.

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