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dc.contributor.authorWarden, Charles Daviden_US
dc.contributor.authorKim, Seong-Hoen_US
dc.contributor.authorYi, Soojin V.en_US
dc.date.accessioned2009-12-11T20:20:32Z
dc.date.available2009-12-11T20:20:32Z
dc.date.issued2008-02-13
dc.identifier.citationWarden CD, Kim S-H, Yi SV (2008) Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins. PLoS ONE 3(2): e1559. doi:10.1371/journal.pone.0001559en
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/1853/31379
dc.description© 2008 Warden et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.descriptionDOI: 10.1371/journal.pone.0001559
dc.description.abstractFunctional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.en
dc.language.isoen_USen
dc.publisherGeorgia Institute of Technologyen
dc.subjectFunctional RNAen
dc.subjectConserved fRNA secondary structuresen
dc.subjectEvolutionary rate of protein-coding genesen
dc.subjectEukaryotesen
dc.titlePredicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteinsen
dc.typeArticleen
dc.contributor.corporatenameGeorgia Institute of Technology. School of Biologyen_US
dc.contributor.corporatenameIndiana University School of Medicine. Division of Biostatisticsen_US
dc.publisher.originalPublic Library of Science
dc.identifier.doi10.1371/journal.pone.0001559


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