Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast

Abstract

Correct identification of all introns is necessary to discern the protein-coding potential of a eukaryotic genome. The existence of most of the spliceosomal introns predicted in the genome of Saccharomyces cerevisiae remains unsupported by molecular evidence. We tested the intron predictions for 87 introns predicted to be present in non-ribosomal protein genes, more than a third of all known or suspected introns in the yeast genome. Evidence supporting 61 of these predictions was obtained, 20 predicted intron sequences were not spliced and six predictions identified an intron-containing region but failed to specify the correct splice sites, yielding a successful prediction rate of <80%. Alternative splicing has not been previously described for this organism, and we identified two genes (YKL186C/ MTR2 and YML034W) which encode alternatively spliced mRNAs; YKL186C/ MTR2 produces at least five different spliced mRNAs. One gene (YGR225W/ SPO70 ) has an intron whose removal is activated during meiosis under control of the MER1 gene. We found eight new introns, suggesting that numerous introns still remain to be discovered. The results show that correct prediction of introns remains a significant barrier to understanding the structure, function and coding capacity of eukaryotic genomes, even in a supposedly simple system like yeast.

Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae

“…However, splicing might still be mediated by splice acceptor sites contained within N18 sequences if the appropriate splice donor and branch point sequences were present upstream. This possibility appears to be unlikely, as 5Ј splice site͞branch point sequences are highly conserved in S. cerevisiae (29,30) and sequence analysis of the Renilla͞HIS3 dicistronic mRNA failed to identify any potential combinations (31) upstream of the intercistronic region. Experimental evidence was also inconsistent with the possibility of splicing in these constructs.…”

Alternative Splicing of PTC7 inSaccharomyces cerevisiaeDetermines Protein Localization

“…been predicted, but could not be validated in yeast grown under standard conditions in YPD (Davis et al 2000). It could be that splicing is condition specific, as was found for introns in meiotic genes (Engebrecht et al 1991;Nakagawa and Ogawa 1999;Juneau et al 2007); this suggests that mapping introns under a variety of growth conditions could be worthwhile.…”

A computational analysis of sequence features involved in recognition of short introns

“…In yeast, the 5Јss, 3Јss, and branch signal motifs contain sufficient information to detect the locations of introns in transcripts with very high accuracy (98%; see also ref. 22), but the low information content of the yeast 3Јss motif is sufficient to determine the precise 3Ј splice junction for only about 86% of yeast introns (Table 1). Some additional transcript feature(s) not included in our models must play a role in specifying the 3Ј splice junction of at least some yeast introns.…”