Context-dependent codon bias and messenger RNA longevity in the yeast transcriptome
Context-dependent codon bias and its relationship with messenger RNA (mRNA) longevity was examined in 4,648 mRNA transcripts of the Saccharomyces cerevisiae transcriptome for which mRNA half-lives have been empirically determined. Surprisingly, rare codon usage (codons used
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| Veröffentlicht in: | Molecular biology and evolution 2005-06, Vol.22 (6), p.1403-1411 |
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| container_title | Molecular biology and evolution |
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| creator | Carlini, David B |
| description | Context-dependent codon bias and its relationship with messenger RNA (mRNA) longevity was examined in 4,648 mRNA transcripts of the Saccharomyces cerevisiae transcriptome for which mRNA half-lives have been empirically determined. Surprisingly, rare codon usage (codons used |
| doi_str_mv | 10.1093/molbev/msi135 |
| format | Article |
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Surprisingly, rare codon usage (codons used <13 times per 1,000 codons in the genome) increased with mRNA half-life. However, it is shown that this pattern was not due to preference for rare codon use within codon families containing both rare and nonrare codons. Rather, the pattern was due to an increase in the frequency of amino acids encoded solely by rare codons, and a decrease in the frequency of amino acids never encoded by rare codons, with mRNA half-life. When standardized by open reading frame length, the use of consecutive rare codons was also positively correlated with mRNA half-life. There was negative correlation between the usage of synonymous A|T dinucleotides spanning codon boundaries and mRNA half-life, despite the fact that the frequency of AT dinucleotide usage overall, and AT dinucleotide usage at other codon position contexts (e.g., 1-2, 2-3, or 3|1 total), was not correlated with mRNA half-life. 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The use of A|T dinucleotides at synonymous dicodon boundaries could potentially allow for more efficient 3'-5' degradation by endonucleolytic cleavage.</description><subject>Codon</subject><subject>Computational Biology - methods</subject><subject>Databases, Genetic</subject><subject>Genome, Fungal</subject><subject>Models, Genetic</subject><subject>Models, Statistical</subject><subject>Models, Theoretical</subject><subject>Open Reading Frames</subject><subject>Proteome</subject><subject>RNA - chemistry</subject><subject>RNA - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Saccharomyces cerevisiae</subject><subject>Saccharomyces cerevisiae - genetics</subject><issn>0737-4038</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkDtPwzAYRT2AaCmMrMgTW6gd27EzVhEvqQKJxxw59hcwiu0QuxX991SizEhXOnc4usNF6IKSa0pqtvRx6GC79MlRJo7QnEgmC06YmqHTlD4JoZxX1QmaUSFlyaSao5cmhgzfubAwQrAQMjbRxoA7pxPWwWIPKUF4hwk_P67wEPd16_IOu4DzB-Ad6JRxnnRIZnJjjh7O0HGvhwTnBy7Q2-3Na3NfrJ_uHprVuhipJLmQipWaEqitrLnulQEiOKuoEYTVhlnFNZdWyY4S1fddb4jRWuieU1oDL2u2QFe_u-MUvzaQcutdMjAMOkDcpLaSqpSC8n9FKgWp2D4LdHkQN50H246T83ratX9_sR8qCWxk</recordid><startdate>200506</startdate><enddate>200506</enddate><creator>Carlini, David B</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7TM</scope><scope>M7N</scope><scope>7X8</scope></search><sort><creationdate>200506</creationdate><title>Context-dependent codon bias and messenger RNA longevity in the yeast transcriptome</title><author>Carlini, David B</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p170t-7832a10e9d794af8ce054361c5039c3d84a47d87b108ffbfc0caa5af4119e4293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Codon</topic><topic>Computational Biology - methods</topic><topic>Databases, Genetic</topic><topic>Genome, Fungal</topic><topic>Models, Genetic</topic><topic>Models, Statistical</topic><topic>Models, Theoretical</topic><topic>Open Reading Frames</topic><topic>Proteome</topic><topic>RNA - chemistry</topic><topic>RNA - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Saccharomyces cerevisiae</topic><topic>Saccharomyces cerevisiae - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Carlini, David B</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Nucleic Acids Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Carlini, David B</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Context-dependent codon bias and messenger RNA longevity in the yeast transcriptome</atitle><jtitle>Molecular biology and evolution</jtitle><addtitle>Mol Biol Evol</addtitle><date>2005-06</date><risdate>2005</risdate><volume>22</volume><issue>6</issue><spage>1403</spage><epage>1411</epage><pages>1403-1411</pages><issn>0737-4038</issn><abstract>Context-dependent codon bias and its relationship with messenger RNA (mRNA) longevity was examined in 4,648 mRNA transcripts of the Saccharomyces cerevisiae transcriptome for which mRNA half-lives have been empirically determined. Surprisingly, rare codon usage (codons used <13 times per 1,000 codons in the genome) increased with mRNA half-life. However, it is shown that this pattern was not due to preference for rare codon use within codon families containing both rare and nonrare codons. Rather, the pattern was due to an increase in the frequency of amino acids encoded solely by rare codons, and a decrease in the frequency of amino acids never encoded by rare codons, with mRNA half-life. When standardized by open reading frame length, the use of consecutive rare codons was also positively correlated with mRNA half-life. There was negative correlation between the usage of synonymous A|T dinucleotides spanning codon boundaries and mRNA half-life, despite the fact that the frequency of AT dinucleotide usage overall, and AT dinucleotide usage at other codon position contexts (e.g., 1-2, 2-3, or 3|1 total), was not correlated with mRNA half-life. 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| source | MEDLINE; Access via Oxford University Press (Open Access Collection); EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | Codon Computational Biology - methods Databases, Genetic Genome, Fungal Models, Genetic Models, Statistical Models, Theoretical Open Reading Frames Proteome RNA - chemistry RNA - genetics RNA, Messenger - metabolism Saccharomyces cerevisiae Saccharomyces cerevisiae - genetics |
| title | Context-dependent codon bias and messenger RNA longevity in the yeast transcriptome |
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