Quantitative evaluation of all hexamers as exonic splicing elements.
Identifieur interne : 001E70 ( PubMed/Curation ); précédent : 001E69; suivant : 001E71Quantitative evaluation of all hexamers as exonic splicing elements.
Auteurs : Shengdong Ke [États-Unis] ; Shulian Shang ; Sergey M. Kalachikov ; Irina Morozova ; Lin Yu ; James J. Russo ; Jingyue Ju ; Lawrence A. ChasinSource :
- Genome research [ 1549-5469 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Chromatin, RNA.
- genetics : Exons, RNA Splicing.
- Humans, Nucleic Acid Conformation, RNA Splice Sites, Regulatory Sequences, Ribonucleic Acid.
Abstract
We describe a comprehensive quantitative measure of the splicing impact of a complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. The results allowed the assignment of a relative splicing strength score to each mutant molecule. The effect of 6-mers on splicing often depended on their location; much of this context effect could be ascribed to the creation of different overlapping sequences at each site. Taking these overlaps into account, the splicing effect of each 6-mer could be quantified, and 6-mers could be designated as enhancers (ESEseqs) and silencers (ESSseqs), with an ESRseq score indicating their strength. Some 6-mers exhibited positional bias relative to the two splice sites. The distribution and conservation of these ESRseqs in and around human exons supported their classification. Predicted RNA secondary structure effects were also seen: Effective enhancers, silencers and 3' splice sites tend to be single stranded, and effective 5' splice sites tend to be double stranded. 6-mers that may form positive or negative synergy with another were also identified. Chromatin structure may also influence the splicing enhancement observed, as a good correspondence was found between splicing performance and the predicted nucleosome occupancy scores of 6-mers. This approach may prove of general use in defining nucleic acid regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing mechanisms.
DOI: 10.1101/gr.119628.110
PubMed: 21659425
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Kalachikov</name></author><author><name sortKey="Morozova, Irina" sort="Morozova, Irina" uniqKey="Morozova I" first="Irina" last="Morozova">Irina Morozova</name></author><author><name sortKey="Yu, Lin" sort="Yu, Lin" uniqKey="Yu L" first="Lin" last="Yu">Lin Yu</name></author><author><name sortKey="Russo, James J" sort="Russo, James J" uniqKey="Russo J" first="James J" last="Russo">James J. Russo</name></author><author><name sortKey="Ju, Jingyue" sort="Ju, Jingyue" uniqKey="Ju J" first="Jingyue" last="Ju">Jingyue Ju</name></author><author><name sortKey="Chasin, Lawrence A" sort="Chasin, Lawrence A" uniqKey="Chasin L" first="Lawrence A" last="Chasin">Lawrence A. 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Kalachikov</name></author><author><name sortKey="Morozova, Irina" sort="Morozova, Irina" uniqKey="Morozova I" first="Irina" last="Morozova">Irina Morozova</name></author><author><name sortKey="Yu, Lin" sort="Yu, Lin" uniqKey="Yu L" first="Lin" last="Yu">Lin Yu</name></author><author><name sortKey="Russo, James J" sort="Russo, James J" uniqKey="Russo J" first="James J" last="Russo">James J. Russo</name></author><author><name sortKey="Ju, Jingyue" sort="Ju, Jingyue" uniqKey="Ju J" first="Jingyue" last="Ju">Jingyue Ju</name></author><author><name sortKey="Chasin, Lawrence A" sort="Chasin, Lawrence A" uniqKey="Chasin L" first="Lawrence A" last="Chasin">Lawrence A. Chasin</name></author></analytic><series><title level="j">Genome research</title><idno type="eISSN">1549-5469</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromatin (genetics)</term><term>Exons (genetics)</term><term>Humans</term><term>Nucleic Acid Conformation</term><term>RNA (genetics)</term><term>RNA Splice Sites</term><term>RNA Splicing (genetics)</term><term>Regulatory Sequences, Ribonucleic Acid</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN (génétique)</term><term>Chromatine (génétique)</term><term>Conformation d'acide nucléique</term><term>Exons (génétique)</term><term>Humains</term><term>Sites d'épissage d'ARN</term><term>Séquences régulatrices de l'acide ribonucléique</term><term>Épissage des ARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Chromatin</term><term>RNA</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Exons</term><term>RNA Splicing</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN</term><term>Chromatine</term><term>Exons</term><term>Épissage des ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Nucleic Acid Conformation</term><term>RNA Splice Sites</term><term>Regulatory Sequences, Ribonucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Conformation d'acide nucléique</term><term>Humains</term><term>Sites d'épissage d'ARN</term><term>Séquences régulatrices de l'acide ribonucléique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We describe a comprehensive quantitative measure of the splicing impact of a complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. The results allowed the assignment of a relative splicing strength score to each mutant molecule. The effect of 6-mers on splicing often depended on their location; much of this context effect could be ascribed to the creation of different overlapping sequences at each site. Taking these overlaps into account, the splicing effect of each 6-mer could be quantified, and 6-mers could be designated as enhancers (ESEseqs) and silencers (ESSseqs), with an ESRseq score indicating their strength. Some 6-mers exhibited positional bias relative to the two splice sites. The distribution and conservation of these ESRseqs in and around human exons supported their classification. Predicted RNA secondary structure effects were also seen: Effective enhancers, silencers and 3' splice sites tend to be single stranded, and effective 5' splice sites tend to be double stranded. 6-mers that may form positive or negative synergy with another were also identified. Chromatin structure may also influence the splicing enhancement observed, as a good correspondence was found between splicing performance and the predicted nucleosome occupancy scores of 6-mers. This approach may prove of general use in defining nucleic acid regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing mechanisms.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21659425</PMID><DateCompleted><Year>2012</Year><Month>02</Month><Day>03</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1549-5469</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>8</Issue><PubDate><Year>2011</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res.</ISOAbbreviation></Journal><ArticleTitle>Quantitative evaluation of all hexamers as exonic splicing elements.</ArticleTitle><Pagination><MedlinePgn>1360-74</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/gr.119628.110</ELocationID><Abstract><AbstractText>We describe a comprehensive quantitative measure of the splicing impact of a complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. The results allowed the assignment of a relative splicing strength score to each mutant molecule. The effect of 6-mers on splicing often depended on their location; much of this context effect could be ascribed to the creation of different overlapping sequences at each site. Taking these overlaps into account, the splicing effect of each 6-mer could be quantified, and 6-mers could be designated as enhancers (ESEseqs) and silencers (ESSseqs), with an ESRseq score indicating their strength. Some 6-mers exhibited positional bias relative to the two splice sites. The distribution and conservation of these ESRseqs in and around human exons supported their classification. Predicted RNA secondary structure effects were also seen: Effective enhancers, silencers and 3' splice sites tend to be single stranded, and effective 5' splice sites tend to be double stranded. 6-mers that may form positive or negative synergy with another were also identified. Chromatin structure may also influence the splicing enhancement observed, as a good correspondence was found between splicing performance and the predicted nucleosome occupancy scores of 6-mers. This approach may prove of general use in defining nucleic acid regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing mechanisms.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ke</LastName><ForeName>Shengdong</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Columbia University, New York, New York 10027, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shang</LastName><ForeName>Shulian</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Kalachikov</LastName><ForeName>Sergey M</ForeName><Initials>SM</Initials></Author><Author ValidYN="Y"><LastName>Morozova</LastName><ForeName>Irina</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Lin</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Russo</LastName><ForeName>James J</ForeName><Initials>JJ</Initials></Author><Author ValidYN="Y"><LastName>Ju</LastName><ForeName>Jingyue</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Chasin</LastName><ForeName>Lawrence A</ForeName><Initials>LA</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM072740</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R56 GM072740</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM072740</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>06</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome Res</MedlineTA><NlmUniqueID>9518021</NlmUniqueID><ISSNLinking>1088-9051</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002843">Chromatin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D022821">RNA Splice Sites</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D038621">Regulatory Sequences, Ribonucleic Acid</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002843" MajorTopicYN="N">Chromatin</DescriptorName><QualifierName UI="Q000235" 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