UC Santa Cruz

Alternative splicing is a form of pre-mRNA processing that modifies gene expression through selective and differential inclusion of genetic material in the mature messenger RNA. This process is dependent upon accurate selection of splice sites in the primary transcript. Site selection has been shown to be differentially regulated between organisms as well as throughout development of tissues within a single organism. In C. elegans, we have uncovered over 200 examples of tissue-specific regulation of a class of alternative 3’ splice sites, those found within 18 nucleotides of each other. While germline cells prefer to splice at the 3’ splice site closest to the 5’ end of the intron, somatic cells tend to splice at the site further from the 5’ end. These splicing patterns are conserved in the related nematode species C. briggsae. Normal cis-regulatory features of alternative splice sites are either overlapping in these adjacent sites or are undetermined. Branchpoint selection does not correlate with 3’ splice sites chosen in these cases, but total intron length is correlated with upstream 3’ splice site usage in the germline, likely due to spatial restrictions on the spliceosome. We also provide evidence that use of the upstream site in somatic cells is correlated with enrichment for pyrimidines at the upstream site and decreased enrichment at the downstream site, a change we do not see for 3’ splice sites that are preferred in the germline. We propose several models to explain this regulation: 1) Differential expression of spliceosome-associated factors in the germline; 2) The spliceosome scans downstream sequences for the first appropriate 3’ splice site environment it can detect; 3) Fidelity of splice site choice is relaxed allowing for deviation of site choice from the strictly-regulated somatic splicing pattern.