A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence
Identifieur interne : 000377 ( Istex/Corpus ); précédent : 000376; suivant : 000378A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence
Auteurs : Nuno Miguel Nunes ; Wencheng Li ; Bin Tian ; André FurgerSource :
- The EMBO Journal [ 0261-4189 ] ; 2010-05-05.
English descriptors
- Teeft :
- Aauaaa, Additional plasmids, Adenosine, Alternative cleavage, Alternative sites, Anking, Anking regions, Anking sequences, Antisense riboprobe, Auuaaa, Auuaaa hexamer, Auxiliary sequence elements, Auxiliary sequences, Bioinformatics, Bioinformatics analysis, Biol, Biology organization, Biology organization sequences, Canonical, Canonical hexamer, Canonical hexamers, Canonical sites, Cell biol, Cells transfected, Cells transiently transfected, Cleavage, Cleavage site, Cleavage stimulation factor, Clone, Composite probe, Core sequences, Cpsf, Cstf, Deletion, Direct cleavage, Ds, Embo, Embo journal, Exact test, Gene, Hexamer, Hexamer mutations, Hexamers, Higher frequency, Human genes, Human sites, Intronless, Intronless genes, Junb, Junb site, Little effect, Many noncanonical sites, Mc4r, Mc4r site, Mrna, Mrna polyadenylation sites, Mutant plasmids, Mutation, Noncanonical, Noncanonical site, Noncanonical sites, Nucleic, Nucleic acids, Nucleotide, Nunes, Plasmid, Point mutations, Polyadenylation, Polyadenylation factor, Polymerase, Primer, Proc natl acad, Processing machinery, Processing signals, Processing site, Processing sites, Proudfoot, Readthrough, Receptor, Sequence element, Sequence elements, Site types, Supplementary figure, Terminal intron removal, Tian, Transcript, Transfected, Uguan, Uguan elements, Uguan motifs, Uguan sequences, Wilusz.
Abstract
We have analysed the sequences required for cleavage and polyadenylation in the intronless melanocortin 4 receptor (MC4R) pre‐mRNA. Unlike other intronless genes, 3′end processing of the MC4R primary transcript is independent of any auxiliary sequence elements and only requires the core poly(A) sequences. Mutation of the AUUAAA hexamer had little effect on MC4R 3′end processing but small changes in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site requires only the DSE and an A‐rich upstream sequence to direct efficient cleavage and polyadenylation. Our observation may be highly relevant for the understanding of how human noncanonical poly(A) sites are recognised. This is supported by a genome‐wide analysis of over 10 000 poly(A) sites where we show that many human noncanonical poly(A) signals contain A‐rich upstream sequences and tend to have a higher frequency of U and GU nucleotides in their DSE compared with canonical poly(A) signals. The importance of A‐rich elements for noncanonical poly(A) site recognition was confirmed by mutational analysis of the human JUNB gene, which contains an A‐rich noncanonical poly(A) signal.
Url:
DOI: 10.1038/emboj.2010.42
Links to Exploration step
ISTEX:DBF591446A2F08291203E17A804367EACDC66E15Le document en format XML
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Unlike other intronless genes, 3′end processing of the MC4R primary transcript is independent of any auxiliary sequence elements and only requires the core poly(A) sequences. Mutation of the AUUAAA hexamer had little effect on MC4R 3′end processing but small changes in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site requires only the DSE and an A‐rich upstream sequence to direct efficient cleavage and polyadenylation. Our observation may be highly relevant for the understanding of how human noncanonical poly(A) sites are recognised. This is supported by a genome‐wide analysis of over 10 000 poly(A) sites where we show that many human noncanonical poly(A) signals contain A‐rich upstream sequences and tend to have a higher frequency of U and GU nucleotides in their DSE compared with canonical poly(A) signals. The importance of A‐rich elements for noncanonical poly(A) site recognition was confirmed by mutational analysis of the human JUNB gene, which contains an A‐rich noncanonical poly(A) signal.</abstract><qualityIndicators><score>9.1</score><pdfWordCount>10024</pdfWordCount><pdfCharCount>61456</pdfCharCount><pdfVersion>1.6</pdfVersion><pdfPageCount>14</pdfPageCount><pdfPageSize>595.276 x 793.701 pts</pdfPageSize><pdfWordsPerPage>716</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>true</refBibsNative><abstractWordCount>175</abstractWordCount><abstractCharCount>1167</abstractCharCount><keywordCount>4</keywordCount></qualityIndicators><title>A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence</title><pmid><json:string>20339349</json:string></pmid><genre><json:string>article</json:string></genre><host><title>The EMBO 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processing</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>John Wiley & Sons, Ltd</publisher><pubPlace>Chichester, UK</pubPlace><availability><licence>Copyright © 2010 European Molecular Biology Organization</licence></availability><date type="published" when="2010-05-05"></date></publicationStmt><notesStmt><note type="content-type" subtype="article" source="article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</note><note type="publication-type" subtype="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="article"><analytic><title level="a" type="main">A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence</title><title level="a" type="short">A‐rich sequences and 3′end processing</title><author xml:id="author-0000"><persName><forename type="first">Nuno Miguel</forename><surname>Nunes</surname></persName><affiliation><orgName type="institution">Laboratory of Genes and Development, Department of Biochemistry, University of Oxford</orgName><address><settlement>Oxford</settlement><country key="" xml:lang="en"></country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">Wencheng</forename><surname>Li</surname></persName><affiliation><orgName type="institution">Department of Biochemistry and Molecular Biology, UMDNJ‐New Jersey Medical School</orgName><address><settlement>Newark</settlement><region>NJ</region><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Bin</forename><surname>Tian</surname></persName><affiliation><orgName type="institution">Department of Biochemistry and Molecular Biology, UMDNJ‐New Jersey Medical 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<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract style="main"><p>We have analysed the sequences required for cleavage and polyadenylation in the intronless melanocortin 4 receptor (MC4R) pre‐mRNA. Unlike other intronless genes, 3′end processing of the MC4R primary transcript is independent of any auxiliary sequence elements and only requires the core poly(A) sequences. Mutation of the AUUAAA hexamer had little effect on MC4R 3′end processing but small changes in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site requires only the DSE and an A‐rich upstream sequence to direct efficient cleavage and polyadenylation. Our observation may be highly relevant for the understanding of how human noncanonical poly(A) sites are recognised. This is supported by a genome‐wide analysis of over 10 000 poly(A) sites where we show that many human noncanonical poly(A) signals contain A‐rich upstream sequences and tend to have a higher frequency of U and GU nucleotides in their DSE compared with canonical poly(A) signals. The importance of A‐rich elements for noncanonical poly(A) site recognition was confirmed by mutational analysis of the human <hi rend="italic">JUNB</hi> gene, which contains an A‐rich noncanonical poly(A) signal.</p></abstract><textClass><keywords><term xml:id="embj201042-kwd-0001">3′end processing</term><term xml:id="embj201042-kwd-0002">intronless genes</term><term xml:id="embj201042-kwd-0003">melanocortin 4 receptor</term><term xml:id="embj201042-kwd-0004">noncanonical poly(A) sites</term></keywords><keywords rend="articleCategory"><term>Article</term></keywords><keywords rend="tocHeading1"><term>Article</term></keywords></textClass><textClass><keywords ana="subject"><term ref="http://psi.embo.org/14602075/EMBO36">RNA Biology</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-VCCHXMK4-N/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component type="serialArticle" version="2.0" xml:lang="en" xml:id="embj201042"><header><publicationMeta level="product"><publisherInfo><publisherName>John Wiley & Sons, Ltd</publisherName><publisherLoc>Chichester, UK</publisherLoc></publisherInfo><doi>10.1002/(ISSN)1460-2075</doi><issn type="print">0261-4189</issn><issn type="electronic">1460-2075</issn><idGroup><id type="product" value="EMBJ"></id></idGroup><titleGroup><title type="main" sort="THE EMBO JOURNAL">The EMBO Journal</title></titleGroup></publicationMeta><publicationMeta level="part" position="90"><doi>10.1002/emboj.v29.9</doi><copyright ownership="publisher">Copyright © 2013 Wiley Periodicals, Inc</copyright><numberingGroup><numbering type="journalVolume" number="29">29</numbering><numbering type="journalIssue">9</numbering></numberingGroup><coverDate startDate="2010-05-05">May 5, 2010</coverDate></publicationMeta><publicationMeta level="unit" position="70" accessType="open" type="article" status="forIssue"><doi>10.1038/emboj.2010.42</doi><idGroup><id type="unit" value="EMBJ201042"></id></idGroup><countGroup><count type="pageTotal" number="14"></count></countGroup><titleGroup>
<title type="articleCategory">Article</title><title type="tocHeading1">Article</title></titleGroup><copyright ownership="thirdParty">Copyright © 2010 European Molecular Biology Organization</copyright><legalStatement type="creativeCommonsBy-nc-sa" role="origin:nonWiley"><p>This is an open‐access article distributed under the terms of the <url href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution License</url>, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.</p></legalStatement><eventGroup><event type="manuscriptReceived" date="2009-10-05"></event><event type="manuscriptAccepted" date="2010-03-03"></event><event type="publishedOnlineEarlyUnpaginated" date="2010-03-25"></event><event type="publishedOnlineFinalForm" date="2010-05-05"></event><event type="xmlConverted" agent="SPi Global Converter_TO_WileyML3Gv2.0 version:1.0; WileyML 3G Packaging Tool v1.0" date="2013-10-22"></event><event type="xmlCorrected" agent="Wiley-VCH" date="2013-11-19"></event><event type="firstOnline" date="2010-03-25"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-11-04"></event></eventGroup><numberingGroup><numbering type="pageFirst">1523</numbering><numbering type="pageLast">1536</numbering></numberingGroup><correspondenceTo>Corresponding author. Laboratory of Genes and Development, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. Tel.: +44 0 1865 613 261; Fax: +44 0 1865 613 276; E-mail: <email>andre.furger@bioch.ox.ac.uk</email></correspondenceTo><subjectInfo><subject href="http://psi.embo.org/14602075/EMBO36">RNA Biology</subject></subjectInfo><linkGroup><link type="toTypesetVersion" href="file:EMBJ.EMBJ201042.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main">A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence</title><title type="short">A‐rich sequences and 3′end processing</title></titleGroup><creators><creator creatorRole="author" xml:id="embj201042-cr-0001" affiliationRef="#embj201042-aff-0001"><personName><givenNames>Nuno Miguel</givenNames><familyName>Nunes</familyName></personName></creator><creator creatorRole="author" xml:id="embj201042-cr-0002" affiliationRef="#embj201042-aff-0002"><personName><givenNames>Wencheng</givenNames><familyName>Li</familyName></personName></creator><creator creatorRole="author" xml:id="embj201042-cr-0003" affiliationRef="#embj201042-aff-0002"><personName><givenNames>Bin</givenNames><familyName>Tian</familyName></personName></creator><creator creatorRole="author" xml:id="embj201042-cr-0004" affiliationRef="#embj201042-aff-0001" corresponding="yes"><personName><givenNames>André</givenNames><familyName>Furger</familyName></personName></creator></creators><affiliationGroup><affiliation countryCode="" type="organization" xml:id="embj201042-aff-0001"><orgName>Laboratory of Genes and Development, Department of Biochemistry, University of Oxford</orgName><address><city>Oxford</city><country>UK</country></address></affiliation><affiliation countryCode="US" type="organization" xml:id="embj201042-aff-0002"><orgName>Department of Biochemistry and Molecular Biology, UMDNJ‐New Jersey Medical School</orgName><address><city>Newark</city><countryPart>NJ</countryPart><country>USA</country></address></affiliation></affiliationGroup><keywordGroup type="author"><keyword xml:id="embj201042-kwd-0001">3′end processing</keyword><keyword xml:id="embj201042-kwd-0002">intronless genes</keyword><keyword xml:id="embj201042-kwd-0003">melanocortin 4 receptor</keyword><keyword xml:id="embj201042-kwd-0004">noncanonical poly(A) sites</keyword></keywordGroup><supportingInformation><supportingInfoItem xml:id="embj201042-sup-0001"><mediaResource alt="supplementary data" mimeType="application/pdf" href="urn-x:wiley:02614189:media:embj201042:embj201042-sup-0001"></mediaResource><caption>Supplementary Information</caption></supportingInfoItem><supportingInfoItem xml:id="embj201042-sup-0002"><mediaResource alt="supplementary data" mimeType="application/xls" href="urn-x:wiley:02614189:media:embj201042:embj201042-sup-0002"></mediaResource><caption>Supplementary data 2</caption></supportingInfoItem><supportingInfoItem xml:id="embj201042-sup-0003"><mediaResource alt="supplementary data" mimeType="application/pdf" href="urn-x:wiley:02614189:media:embj201042:embj201042"></mediaResource><caption>Review Process File</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main"><p>We have analysed the sequences required for cleavage and polyadenylation in the intronless melanocortin 4 receptor (MC4R) pre‐mRNA. Unlike other intronless genes, 3′end processing of the MC4R primary transcript is independent of any auxiliary sequence elements and only requires the core poly(A) sequences. Mutation of the AUUAAA hexamer had little effect on MC4R 3′end processing but small changes in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site requires only the DSE and an A‐rich upstream sequence to direct efficient cleavage and polyadenylation. Our observation may be highly relevant for the understanding of how human noncanonical poly(A) sites are recognised. This is supported by a genome‐wide analysis of over 10 000 poly(A) sites where we show that many human noncanonical poly(A) signals contain A‐rich upstream sequences and tend to have a higher frequency of U and GU nucleotides in their DSE compared with canonical poly(A) signals. The importance of A‐rich elements for noncanonical poly(A) site recognition was confirmed by mutational analysis of the human <i>JUNB</i> gene, which contains an A‐rich noncanonical poly(A) signal.</p></abstract></abstractGroup></contentMeta><noteGroup><note type="associatedArticle" xml:id="embj201042-note-0001">There is a <accessionId ref="info:doi/10.1038/emboj.2010.67">Have you seen ...?</accessionId> (May 2010) associated with this Article.</note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>A‐rich sequences and 3′end processing</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence</title></titleInfo><name type="personal"><namePart type="given">Nuno Miguel</namePart><namePart type="family">Nunes</namePart><affiliation>Laboratory of Genes and Development, Department of Biochemistry, University of Oxford, Oxford, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Wencheng</namePart><namePart type="family">Li</namePart><affiliation>Department of Biochemistry and Molecular Biology, UMDNJ‐New Jersey Medical School, NJ, Newark, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bin</namePart><namePart type="family">Tian</namePart><affiliation>Department of Biochemistry and Molecular Biology, UMDNJ‐New Jersey Medical School, NJ, Newark, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">André</namePart><namePart type="family">Furger</namePart><affiliation>Laboratory of Genes and Development, Department of Biochemistry, University of Oxford, Oxford, UK</affiliation><affiliation>E-mail: andre.furger@bioch.ox.ac.uk</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>John Wiley & Sons, Ltd</publisher><place><placeTerm type="text">Chichester, UK</placeTerm></place><dateIssued encoding="w3cdtf">2010-05-05</dateIssued><dateCaptured encoding="w3cdtf">2009-10-05</dateCaptured><dateValid encoding="w3cdtf">2010-03-03</dateValid><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract>We have analysed the sequences required for cleavage and polyadenylation in the intronless melanocortin 4 receptor (MC4R) pre‐mRNA. Unlike other intronless genes, 3′end processing of the MC4R primary transcript is independent of any auxiliary sequence elements and only requires the core poly(A) sequences. Mutation of the AUUAAA hexamer had little effect on MC4R 3′end processing but small changes in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site requires only the DSE and an A‐rich upstream sequence to direct efficient cleavage and polyadenylation. Our observation may be highly relevant for the understanding of how human noncanonical poly(A) sites are recognised. This is supported by a genome‐wide analysis of over 10 000 poly(A) sites where we show that many human noncanonical poly(A) signals contain A‐rich upstream sequences and tend to have a higher frequency of U and GU nucleotides in their DSE compared with canonical poly(A) signals. The importance of A‐rich elements for noncanonical poly(A) site recognition was confirmed by mutational analysis of the human JUNB gene, which contains an A‐rich noncanonical poly(A) signal.</abstract><note type="additional physical form">Supplementary InformationSupplementary data 2Review Process File</note><subject><genre>keywords</genre><topic>3′end processing</topic><topic>intronless genes</topic><topic>melanocortin 4 receptor</topic><topic>noncanonical poly(A) sites</topic></subject><relatedItem type="host"><titleInfo><title>The EMBO Journal</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>index-terms</genre><topic authorityURI="http://psi.embo.org/14602075/EMBO36">RNA Biology</topic></subject><subject><genre>article-category</genre><topic>Article</topic><topic>Article</topic></subject><identifier type="ISSN">0261-4189</identifier><identifier type="eISSN">1460-2075</identifier><identifier type="DOI">10.1002/(ISSN)1460-2075</identifier><identifier type="PublisherID">EMBJ</identifier><part><date>2010</date><detail type="volume"><caption>vol.</caption><number>29</number></detail><detail type="issue"><caption>no.</caption><number>9</number></detail><extent unit="pages"><start>1523</start><end>1536</end><total>14</total></extent></part></relatedItem><relatedItem type="references" displayLabel="embj201042-citation-0001"><titleInfo><title>Multiple transcripts of the murine immunoglobulin epsilon membrane locus are generated by alternative splicing and differential usage of two polyadenylation sites</title></titleInfo><name type="personal"><namePart type="given">S</namePart><namePart type="family">Anand</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">FD</namePart><namePart type="family">Batista</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">T</namePart><namePart type="family">Tkach</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">DG</namePart><namePart type="family">Efremov</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">OR</namePart><namePart type="family">Burrone</namePart><role><roleTerm type="text">author</roleTerm></role></name><genre>journal-article</genre><note type="citation/reference">Anand S, Batista FD, Tkach T, Efremov DG, Burrone OR (1997) Multiple transcripts of the murine immunoglobulin epsilon membrane locus are generated by alternative splicing and differential usage of two polyadenylation sites. 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|clé= ISTEX:DBF591446A2F08291203E17A804367EACDC66E15
|texte= A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence
}}
| This area was generated with Dilib version V0.6.33. |  |