A code for transcription elongation speed.
Identifieur interne : 000A74 ( PubMed/Curation ); précédent : 000A73; suivant : 000A75A code for transcription elongation speed.
Auteurs : Eyal Cohen [Israël] ; Zohar Zafrir [Israël] ; Tamir Tuller [Israël]Source :
- RNA biology [ 1555-8584 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Codon, DNA-Directed RNA Polymerases, RNA, Messenger.
- genetics : Escherichia coli, Ribosomes.
- Genetic Fitness, Peptide Chain Elongation, Translational, Transcription, Genetic.
Abstract
The two major steps of gene expression are transcription and translation. While hundreds of studies regarding the effect of sequence features on the translation elongation process have been published, very few connect sequence features to the transcription elongation rate. We suggest, for the first time, that short transcript sub-sequences have a typical effect on RNA polymerase (RNAP) speed: we show that nucleotide 5-mers tend to have typical RNAP speed (or transcription rate), which is consistent along different parts of genes and among different groups of genes with high correlation. We also demonstrate that relative RNAP speed correlates with mRNA levels of endogenous and heterologous genes. Furthermore, we show that the estimated transcription and translation elongation rates correlate in endogenous genes. Finally, we demonstrate that our results are consistent for different high resolution experimental measurements of RNAP densities. These results suggest for the first time that transcription elongation is partly encoded in the transcript, affected by the codon-usage, and optimized by evolution with a significant effect on gene expression and organismal fitness.
DOI: 10.1080/15476286.2017.1384118
PubMed: 29165040
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</wicri:regionArea></affiliation></author><author><name sortKey="Tuller, Tamir" sort="Tuller, Tamir" uniqKey="Tuller T" first="Tamir" last="Tuller">Tamir Tuller</name><affiliation wicri:level="1"><nlm:affiliation>b Department of Biomedical Engineering , Tel Aviv University , Tel Aviv , Israel.</nlm:affiliation><country xml:lang="fr">Israël</country><wicri:regionArea>b Department of Biomedical Engineering , Tel Aviv University , Tel Aviv </wicri:regionArea></affiliation></author></analytic><series><title level="j">RNA biology</title><idno type="eISSN">1555-8584</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Codon (genetics)</term><term>DNA-Directed RNA Polymerases (genetics)</term><term>Escherichia coli (genetics)</term><term>Genetic Fitness</term><term>Peptide Chain Elongation, Translational</term><term>RNA, Messenger (genetics)</term><term>Ribosomes (genetics)</term><term>Transcription, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Aptitude génétique</term><term>Codon (génétique)</term><term>DNA-directed RNA polymerases (génétique)</term><term>Escherichia coli (génétique)</term><term>Ribosomes (génétique)</term><term>Transcription génétique</term><term>Élongation de la traduction</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Codon</term><term>DNA-Directed RNA Polymerases</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term><term>Ribosomes</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Codon</term><term>DNA-directed RNA polymerases</term><term>Escherichia coli</term><term>Ribosomes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genetic Fitness</term><term>Peptide Chain Elongation, Translational</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Aptitude génétique</term><term>Transcription génétique</term><term>Élongation de la traduction</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The two major steps of gene expression are transcription and translation. While hundreds of studies regarding the effect of sequence features on the translation elongation process have been published, very few connect sequence features to the transcription elongation rate. We suggest, for the first time, that short transcript sub-sequences have a typical effect on RNA polymerase (RNAP) speed: we show that nucleotide 5-mers tend to have typical RNAP speed (or transcription rate), which is consistent along different parts of genes and among different groups of genes with high correlation. We also demonstrate that relative RNAP speed correlates with mRNA levels of endogenous and heterologous genes. Furthermore, we show that the estimated transcription and translation elongation rates correlate in endogenous genes. Finally, we demonstrate that our results are consistent for different high resolution experimental measurements of RNAP densities. These results suggest for the first time that transcription elongation is partly encoded in the transcript, affected by the codon-usage, and optimized by evolution with a significant effect on gene expression and organismal fitness.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29165040</PMID><DateCompleted><Year>2018</Year><Month>10</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1555-8584</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>01</Month><Day>02</Day></PubDate></JournalIssue><Title>RNA biology</Title><ISOAbbreviation>RNA Biol</ISOAbbreviation></Journal><ArticleTitle>A code for transcription elongation speed.</ArticleTitle><Pagination><MedlinePgn>81-94</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/15476286.2017.1384118</ELocationID><Abstract><AbstractText>The two major steps of gene expression are transcription and translation. While hundreds of studies regarding the effect of sequence features on the translation elongation process have been published, very few connect sequence features to the transcription elongation rate. We suggest, for the first time, that short transcript sub-sequences have a typical effect on RNA polymerase (RNAP) speed: we show that nucleotide 5-mers tend to have typical RNAP speed (or transcription rate), which is consistent along different parts of genes and among different groups of genes with high correlation. We also demonstrate that relative RNAP speed correlates with mRNA levels of endogenous and heterologous genes. Furthermore, we show that the estimated transcription and translation elongation rates correlate in endogenous genes. Finally, we demonstrate that our results are consistent for different high resolution experimental measurements of RNAP densities. These results suggest for the first time that transcription elongation is partly encoded in the transcript, affected by the codon-usage, and optimized by evolution with a significant effect on gene expression and organismal fitness.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cohen</LastName><ForeName>Eyal</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>a Balavatnick School of Computer Science , Tel Aviv University , Tel Aviv , Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zafrir</LastName><ForeName>Zohar</ForeName><Initials>Z</Initials><Identifier Source="ORCID">0000-0003-1358-7202</Identifier><AffiliationInfo><Affiliation>b Department of Biomedical Engineering , Tel Aviv University , Tel Aviv , Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuller</LastName><ForeName>Tamir</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>b Department of Biomedical Engineering , Tel Aviv University , Tel Aviv , Israel.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>c Sagol School of Neuroscience , Tel Aviv University , Tel Aviv , Israel.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>RNA Biol</MedlineTA><NlmUniqueID>101235328</NlmUniqueID><ISSNLinking>1547-6286</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003062">Codon</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, 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