Nucleic Acids Research, Vol 25, Issue 22 4619-4625, Copyright © 1997 by Oxford University Press
WM Olivas, D Muhlrad and R Parker
The genome sequences from increasing numbers of organisms allow for rapid
and organized examination of gene expression. Yet current
computational-based paradigms for gene recognition are limited and likely
to miss genes expressing non-coding RNAs or mRNAs with small open reading
frames (ORFs). We have utilized two strategies to determine if there are
additional transcripts in the yeast Saccharomyces cerevisiae that were not
identified in previous analyses of the genome. In one approach, we
identified strong consensus polymerase III promoters based on sequence, and
determined experimentally if these promoters drive the expression of an RNA
polymerase III transcript. This approach led to the identification of a
new, non-essential 170 nt non-coding RNA. An alternative 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 one is clearly non- coding and
appears to be a small nucleolar RNA. These results suggest that there are
likely to be additional previously unidentified non- coding RNAs in yeast,
and that new paradigms for gene recognition will be required to identify
all expressed genes from an organism.
ARTICLES
Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA.
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