Uncovering the mechanisms of splice site choice

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This project is aimed at understanding how the genetic information stored in DNA is accurately processed to code for protein assembly. In order for information in DNA to be used in the cell, the DNA is first copied into an intermediate sister molecule called RNA which is then decoded into protein sequence. However, in order to be useful, internal parts of the RNA must first be removed and the surrounding sequences precisely pasted together by a process called RNA splicing. Splicing is a carried out by one of the largest and most complicated machines in the cell, the spliceosome, which consists of over 100 proteins and 5 RNA molecules that assemble onto the RNA at the region to be spliced out. Because of the complexity of assembling such a large machine onto the RNA, there is still much to learn about the mechanisms by which the spliceosome accurately chooses the sites in the RNA that will be spliced together. Genetic experiments to search for mutations that affect splice site choice are an important and cutting-edge component of this research, and these experiments will be carried out by minority undergraduate participants in an established summer undergraduate training program at the University of California-Santa Cruz (UCSC). This training will be important in preparing these students for positions in UCSC faculty research labs, and for future admission into PhD programs.This project employs the microscopic worm Caenorhabditis elegans as a model to explore pre-mRNA splicing through integrated genetic, genomic and biochemical approaches. Unique approaches have been developed in the preliminary studies that uncovered new regulatory phenomena for splice site selection at both ends of the region of RNA to be removed, called the 5' and 3' splice sites. Genetic screens have been used to uncover new roles for factors important for the regulation of 5' splice site choice. Fundamental differences have been uncovered in alternative adjacent 3' splice site selection between somatic and germ cells. The research will expand on these observations by addressing the following two questions: how do protein factors regulate the choice of 5' splice sites, and what are the mechanistic differences in 3' splice site selection between soma and germ cells? The results are expected to provide novel insights into how the splicing machinery accurately chooses the 5' and 3' splice sites.