ArticleNucleic acids research2000
Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 47 citations in OpenAlex.
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- Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements.Nucleic acids research · 2006Article
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- Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.PLoS biology · 2004Article
- In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis.Plant physiology · 2003Article
- Fending off decay: a combinatorial approach in intact cells for identifying mRNA stability elements.RNA (New York, N.Y.) · 2001Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Understanding the regulation of gene expression requires the identification of cis -acting control elements that modulate gene function. The recent availability of complete genome sequences and profiles of mRNA expression has facilitated the development and utilization of computational methods to identify discrete regulatory elements. We have developed an oligomer counting method that identifies sequences that occur significantly more often in a group of interest relative to other genes in the genome. The use of a second parameter, which measures the frequency of oligomers within the group of interest, allows the detection of false positive signals caused by very infrequent oligomers that would otherwise appear as significant. Applying this method to gene groups that have a common expression pattern or shared function should identify oligomers that comprise cis -acting control elements. As a test of this method, we applied this approach to a set of intron-containing yeast genes, where we easily identified the known splicing signals as control elements. We have used this training set to examine how this method is affected by the length of the oligomer examined, as well as the size and composition of the gene group. These simulations allowed us to identify rules for selecting groups of genes to analyze. Finally, application of this method to nuclear genes encoding proteins targeted to the mitochondria identified a new putative cis -acting sequence in the 3'-untranslated region of this family of genes, which may play a role in mRNA localization or the regulation of mRNA stability or translation.
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