UNDERSTANDING THE TRANSCRIPT SPECIFICITY OF PRE-MRNA SPLICING BY EXAMINING IN VIVO KINETIC MEASUREMENTS
The coding regions of most eukaryotic genes are interrupted by non-coding regions which must be removed from nascent pre-mRNAs prior to their translation. The spliceosome is a large macromolecular complex which is responsible for removing these non-coding regions, called introns, and ligating the flanking regions, called exons, to one another. The spliceosome must identify and assemble anew upon each of its intron substrates, prior to catalyzing intron removal and exon ligation through two sequential transesterification reactions. While the spliceosome itself is highly evolutionarily conserved, eukaryotic genomes show considerable variety in the number of introns encoded within their genomes, and indeed introns within a given genome can display huge variety in their sequence and structure. The spliceosome must interact with the full complement of introns despite extensive variability. The mechanisms by which splicing is regulated remains largely unknown. To better understand how the spliceosome is able to efficiently and precisely interact with its full complement of substrates, I leveraged a powerful method recently developed by our lab which allows us to measure the rates of the two chemical steps of splicing to understand which introns the spliceosome processes most efficiently. Previous work from our lab using this method in the budding yeast, S. cerevisiae, demonstrated astonishing variability in observed splicing rates across the genome and that different classes of transcripts were regulated in distinct ways. To build upon this earlier work, I have extended our studies into the fission yeast, S. pombe, an organism whose splicing architecture more closely resembles the complexity seen in human splicing. I developed and implemented changes to the protocol that drastically improved its performance in S. pombe, and leveraging these improvements allowed me to measure splicing efficiency for a representative subset of introns S. pombe. This work revealed that the first step of splicing, which includes spliceosome assembly, is significantly slower than the second step for nearly all splicing events. It also showed that the splicing of pre-mRNAs which contain just a single intron is slower than the splicing of transcripts from genes which contain multiple introns, regardless of the position of the introns in those transcripts, suggesting that there may be synergistic effects of multiple spliceosomes assembled upon a single transcript. These studies provide important insights into the different mechanisms by which the spliceosome is able to act upon its diverse group of substrates.