Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae

Introns have typically been discovered in an ad hoc fashion: introns are fo und as a gene is characterized for other reasons. As complete eukaryotic ge nome sequences became available, better methods for predicting RNA processi ng signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. I ntrons annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in viv o, and known introns absent from the SGD annotation were added. A novel bra nchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UA CUAAC. Analysis of the database corroborates many conclusions about pre-mRN A substrate requirements for splicing derived from experimental studies, bu t indicates that splicing in yeast may not be as rigidly determined by spli ce-site conservation as had previously been thought. Using this database an d a molecular technique that directly displays the lariat intron products o f spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing ge nes remain to be discovered in yeast. The database can be accessed at http: //www.cse.ucsc.edu/research/compbio/yeastintrons.html.