Identification of a dinucleotide signature that discriminates coding from non-coding long RNAs.
Identifieur interne : 003489 ( PubMed/Corpus ); précédent : 003488; suivant : 003490Identification of a dinucleotide signature that discriminates coding from non-coding long RNAs.
Auteurs : Damien Ulveling ; Marcel E. Dinger ; Claire Francastel ; Florent HubéSource :
- Frontiers in genetics [ 1664-8021 ] ; 2014.
Abstract
To date, the main criterion by which long ncRNAs (lncRNAs) are discriminated from mRNAs is based on the capacity of the transcripts to encode a protein. However, it becomes important to identify non-ORF-based sequence characteristics that can be used to parse between ncRNAs and mRNAs. In this study, we first established an extremely selective workflow to define a highly refined database of lncRNAs which was used for comparison with mRNAs. Then using this highly selective collection of lncRNAs, we found the CG dinucleotide frequencies were clearly distinct. In addition, we showed that the bias in CG dinucleotide frequency was conserved in human and mouse genomes. We propose that this sequence feature will serve as a useful classifier in transcript classification pipelines. We also suggest that our refined database of "bona fide" lncRNAs will be valuable for the discovery of other sequence characteristics distinct to lncRNAs.
DOI: 10.3389/fgene.2014.00316
PubMed: 25250049
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Dinger</name><affiliation><nlm:affiliation>The University of Queensland Diamantina Institute, The University of Queensland Brisbane, QLD, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Francastel, Claire" sort="Francastel, Claire" uniqKey="Francastel C" first="Claire" last="Francastel">Claire Francastel</name><affiliation><nlm:affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France.</nlm:affiliation></affiliation></author><author><name sortKey="Hube, Florent" sort="Hube, Florent" uniqKey="Hube F" first="Florent" last="Hubé">Florent Hubé</name><affiliation><nlm:affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25250049</idno><idno type="pmid">25250049</idno><idno type="doi">10.3389/fgene.2014.00316</idno><idno type="wicri:Area/PubMed/Corpus">003489</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003489</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Identification of a dinucleotide signature that discriminates coding from non-coding long RNAs.</title><author><name sortKey="Ulveling, Damien" sort="Ulveling, Damien" uniqKey="Ulveling D" first="Damien" last="Ulveling">Damien Ulveling</name><affiliation><nlm:affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France.</nlm:affiliation></affiliation></author><author><name sortKey="Dinger, Marcel E" sort="Dinger, Marcel E" uniqKey="Dinger M" first="Marcel E" last="Dinger">Marcel E. Dinger</name><affiliation><nlm:affiliation>The University of Queensland Diamantina Institute, The University of Queensland Brisbane, QLD, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Francastel, Claire" sort="Francastel, Claire" uniqKey="Francastel C" first="Claire" last="Francastel">Claire Francastel</name><affiliation><nlm:affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France.</nlm:affiliation></affiliation></author><author><name sortKey="Hube, Florent" sort="Hube, Florent" uniqKey="Hube F" first="Florent" last="Hubé">Florent Hubé</name><affiliation><nlm:affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Frontiers in genetics</title><idno type="ISSN">1664-8021</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To date, the main criterion by which long ncRNAs (lncRNAs) are discriminated from mRNAs is based on the capacity of the transcripts to encode a protein. However, it becomes important to identify non-ORF-based sequence characteristics that can be used to parse between ncRNAs and mRNAs. In this study, we first established an extremely selective workflow to define a highly refined database of lncRNAs which was used for comparison with mRNAs. Then using this highly selective collection of lncRNAs, we found the CG dinucleotide frequencies were clearly distinct. In addition, we showed that the bias in CG dinucleotide frequency was conserved in human and mouse genomes. We propose that this sequence feature will serve as a useful classifier in transcript classification pipelines. We also suggest that our refined database of "bona fide" lncRNAs will be valuable for the discovery of other sequence characteristics distinct to lncRNAs.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25250049</PMID><DateCreated><Year>2014</Year><Month>09</Month><Day>24</Day></DateCreated><DateCompleted><Year>2014</Year><Month>09</Month><Day>24</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-8021</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in genetics</Title><ISOAbbreviation>Front Genet</ISOAbbreviation></Journal><ArticleTitle>Identification of a dinucleotide signature that discriminates coding from non-coding long RNAs.</ArticleTitle><Pagination><MedlinePgn>316</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fgene.2014.00316</ELocationID><Abstract><AbstractText>To date, the main criterion by which long ncRNAs (lncRNAs) are discriminated from mRNAs is based on the capacity of the transcripts to encode a protein. However, it becomes important to identify non-ORF-based sequence characteristics that can be used to parse between ncRNAs and mRNAs. In this study, we first established an extremely selective workflow to define a highly refined database of lncRNAs which was used for comparison with mRNAs. Then using this highly selective collection of lncRNAs, we found the CG dinucleotide frequencies were clearly distinct. In addition, we showed that the bias in CG dinucleotide frequency was conserved in human and mouse genomes. We propose that this sequence feature will serve as a useful classifier in transcript classification pipelines. We also suggest that our refined database of "bona fide" lncRNAs will be valuable for the discovery of other sequence characteristics distinct to lncRNAs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ulveling</LastName><ForeName>Damien</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dinger</LastName><ForeName>Marcel E</ForeName><Initials>ME</Initials><AffiliationInfo><Affiliation>The University of Queensland Diamantina Institute, The University of Queensland Brisbane, QLD, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Francastel</LastName><ForeName>Claire</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, 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