ANALYSIS OF THE YEAST GENOME - IDENTIFICATION OF NEW NONCODING AND SMALL ORF-CONTAINING RNAS

The genome sequences from increasing numbers of organisms allow for ra pid and organized examination of gene expression. Yet current computat ional-based paradigms for gene recognition are limited and likely to m iss genes expressing non-coding RNAs or mRNAs with small open reading frames (ORFs). We have utilized two strategies to determine if there a re additional transcripts in the yeast Saccharomyces cerevisiae that w ere not identified in previous analyses of the genome, In one approach , we identified strong consensus polymerase III promoters based on seq uence, and determined experimentally if these promoters drive the expr ession of an RNA polymerase III transcript. This approach led to the i dentification of a new, non-essential 170 nt non-coding RNA. An altern ative strategy analyzed RNA expression from large sequence gaps >2 kb between predicted ORFs. Fifteen unique RNA transcripts ranging in size from 161 to 1200 nt were identified from a total of 59 sequence gaps. Several of these RNAs contain unusually small potential ORFs, while o ne is clearly non-coding and appears to be a small nucleolar RNA. Thes e results suggest that there are likely to be additional previously un identified non-coding RNAs in yeast, and that new paradigms for gene r ecognition will be required to identify all expressed genes from an or ganism.