Olivas W M, Muhlrad D, Parker R
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA.
Nucleic Acids Res. 1997 Nov 15;25(22):4619-25. doi: 10.1093/nar/25.22.4619.
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.
越来越多生物体的基因组序列使得对基因表达进行快速且有组织的检查成为可能。然而，当前基于计算的基因识别范式存在局限性，很可能会遗漏表达非编码RNA或具有小开放阅读框（ORF）的mRNA的基因。我们采用了两种策略来确定在酿酒酵母中是否存在先前基因组分析未识别出的其他转录本。在一种方法中，我们基于序列鉴定出了强一致性聚合酶III启动子，并通过实验确定这些启动子是否驱动RNA聚合酶III转录本的表达。这种方法导致鉴定出一种新的、非必需的170 nt非编码RNA。另一种策略分析了预测ORF之间大于2 kb的大序列间隙中的RNA表达。从总共59个序列间隙中鉴定出了15种大小从161到1200 nt不等的独特RNA转录本。其中几种RNA含有异常小的潜在ORF，而有一种显然是非编码的，似乎是一种小核仁RNA。这些结果表明，酵母中可能存在其他先前未鉴定出的非编码RNA，并且需要新的基因识别范式来识别生物体中所有表达的基因。
