MersV1, PubMed, Checkpoint, bibRecord, 000909

Functional classification of long non-coding RNAs by k-mer content.

Identifieur interne : 000909 ( PubMed/Checkpoint ); précédent : 000908; suivant : 000910

Functional classification of long non-coding RNAs by k-mer content.

Auteurs : Jessime M. Kirk [États-Unis] ; Susan O. Kim [États-Unis] ; Kaoru Inoue [États-Unis] ; Matthew J. Smola [États-Unis] ; David M. Lee [États-Unis] ; Megan D. Schertzer [États-Unis] ; Joshua S. Wooten [États-Unis] ; Allison R. Baker [États-Unis] ; Daniel Sprague [États-Unis] ; David W. Collins [États-Unis] ; Christopher R. Horning [États-Unis] ; Shuo Wang [États-Unis] ; Qidi Chen [États-Unis] ; Kevin M. Weeks [États-Unis] ; Peter J. Mucha [États-Unis] ; J Mauro Calabrese [États-Unis]

Source :

Nature genetics [ 1546-1718 ] ; 2018.

RBID : pubmed:30224646

Descripteurs français

English descriptors

KwdEn :
- Algorithms, Animals, Base Sequence, Cluster Analysis, Conserved Sequence, Databases, Genetic, Hep G2 Cells, Humans, K562 Cells, Mice, Molecular Sequence Annotation, Nucleic Acid Conformation, Nucleotide Motifs (genetics), Potassium Channels, Voltage-Gated (genetics), RNA, Long Noncoding (chemistry), RNA, Long Noncoding (classification), RNA, Long Noncoding (genetics), Sequence Alignment, Sequence Analysis, RNA (methods).
MESH :
- chemical , chemistry : RNA, Long Noncoding.
- chemical , classification : RNA, Long Noncoding.
- chemical , genetics : Potassium Channels, Voltage-Gated, RNA, Long Noncoding.
- genetics : Nucleotide Motifs.
- methods : Sequence Analysis, RNA.
- Algorithms, Animals, Base Sequence, Cluster Analysis, Conserved Sequence, Databases, Genetic, Hep G2 Cells, Humans, K562 Cells, Mice, Molecular Sequence Annotation, Nucleic Acid Conformation, Sequence Alignment.

Abstract

The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.

DOI: 10.1038/s41588-018-0207-8
PubMed: 30224646

Affiliations:

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<author><name sortKey="Wang, Shuo" sort="Wang, Shuo" uniqKey="Wang S" first="Shuo" last="Wang">Shuo Wang</name>
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<author><name sortKey="Mucha, Peter J" sort="Mucha, Peter J" uniqKey="Mucha P" first="Peter J" last="Mucha">Peter J. Mucha</name>
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<author><name sortKey="Calabrese, J Mauro" sort="Calabrese, J Mauro" uniqKey="Calabrese J" first="J Mauro" last="Calabrese">J Mauro Calabrese</name>
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<orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName>
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<author><name sortKey="Wang, Shuo" sort="Wang, Shuo" uniqKey="Wang S" first="Shuo" last="Wang">Shuo Wang</name>
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<author><name sortKey="Chen, Qidi" sort="Chen, Qidi" uniqKey="Chen Q" first="Qidi" last="Chen">Qidi Chen</name>
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<author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M" last="Weeks">Kevin M. Weeks</name>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC</wicri:regionArea>
<placeName><region type="state">Caroline du Nord</region>
<settlement type="city">Chapel Hill (Caroline du Nord)</settlement>
</placeName>
<orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName>
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<author><name sortKey="Mucha, Peter J" sort="Mucha, Peter J" uniqKey="Mucha P" first="Peter J" last="Mucha">Peter J. Mucha</name>
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</placeName>
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<author><name sortKey="Calabrese, J Mauro" sort="Calabrese, J Mauro" uniqKey="Calabrese J" first="J Mauro" last="Calabrese">J Mauro Calabrese</name>
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<series><title level="j">Nature genetics</title>
<idno type="eISSN">1546-1718</idno>
<imprint><date when="2018" type="published">2018</date>
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<term>Animals</term>
<term>Base Sequence</term>
<term>Cluster Analysis</term>
<term>Conserved Sequence</term>
<term>Databases, Genetic</term>
<term>Hep G2 Cells</term>
<term>Humans</term>
<term>K562 Cells</term>
<term>Mice</term>
<term>Molecular Sequence Annotation</term>
<term>Nucleic Acid Conformation</term>
<term>Nucleotide Motifs (genetics)</term>
<term>Potassium Channels, Voltage-Gated (genetics)</term>
<term>RNA, Long Noncoding (chemistry)</term>
<term>RNA, Long Noncoding (classification)</term>
<term>RNA, Long Noncoding (genetics)</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, RNA (methods)</term>
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<term>ARN long non codant (génétique)</term>
<term>Algorithmes</term>
<term>Alignement de séquences</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ARN ()</term>
<term>Animaux</term>
<term>Annotation de séquence moléculaire</term>
<term>Bases de données génétiques</term>
<term>Canaux potassiques voltage-dépendants (génétique)</term>
<term>Cellules HepG2</term>
<term>Cellules K562</term>
<term>Conformation d'acide nucléique</term>
<term>Humains</term>
<term>Motifs nucléotidiques (génétique)</term>
<term>Souris</term>
<term>Séquence conservée</term>
<term>Séquence nucléotidique</term>
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</keywords>
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<term>Base Sequence</term>
<term>Cluster Analysis</term>
<term>Conserved Sequence</term>
<term>Databases, Genetic</term>
<term>Hep G2 Cells</term>
<term>Humans</term>
<term>K562 Cells</term>
<term>Mice</term>
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<term>Nucleic Acid Conformation</term>
<term>Sequence Alignment</term>
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<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ARN</term>
<term>Animaux</term>
<term>Annotation de séquence moléculaire</term>
<term>Bases de données génétiques</term>
<term>Cellules HepG2</term>
<term>Cellules K562</term>
<term>Conformation d'acide nucléique</term>
<term>Humains</term>
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<front><div type="abstract" xml:lang="en">The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.</div>
</front>
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<DateCompleted><Year>2019</Year>
<Month>04</Month>
<Day>26</Day>
</DateCompleted>
<DateRevised><Year>2019</Year>
<Month>09</Month>
<Day>03</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1546-1718</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>50</Volume>
<Issue>10</Issue>
<PubDate><Year>2018</Year>
<Month>10</Month>
</PubDate>
</JournalIssue>
<Title>Nature genetics</Title>
<ISOAbbreviation>Nat. Genet.</ISOAbbreviation>
</Journal>
<ArticleTitle>Functional classification of long non-coding RNAs by k-mer content.</ArticleTitle>
<Pagination><MedlinePgn>1474-1482</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1038/s41588-018-0207-8</ELocationID>
<Abstract><AbstractText>The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kirk</LastName>
<ForeName>Jessime M</ForeName>
<Initials>JM</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
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<ForeName>Susan O</ForeName>
<Initials>SO</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.</Affiliation>
</AffiliationInfo>
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<ForeName>Kaoru</ForeName>
<Initials>K</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Smola</LastName>
<ForeName>Matthew J</ForeName>
<Initials>MJ</Initials>
<AffiliationInfo><Affiliation>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Ribometrix, Durham, NC, USA.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Lee</LastName>
<ForeName>David M</ForeName>
<Initials>DM</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
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<ForeName>Megan D</ForeName>
<Initials>MD</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
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<ForeName>Joshua S</ForeName>
<Initials>JS</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
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<ForeName>Allison R</ForeName>
<Initials>AR</Initials>
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<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Harvard Medical School, Ph.D. Program in Biological and Biomedical Sciences, Boston, MA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Sprague</LastName>
<ForeName>Daniel</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Collins</LastName>
<ForeName>David W</ForeName>
<Initials>DW</Initials>
<AffiliationInfo><Affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Horning</LastName>
<ForeName>Christopher R</ForeName>
<Initials>CR</Initials>
<AffiliationInfo><Affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Shuo</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Qidi</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Weeks</LastName>
<ForeName>Kevin M</ForeName>
<Initials>KM</Initials>
<Identifier Source="ORCID">http://orcid.org/0000-0002-6748-9985</Identifier>
<AffiliationInfo><Affiliation>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Mucha</LastName>
<ForeName>Peter J</ForeName>
<Initials>PJ</Initials>
<AffiliationInfo><Affiliation>Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Calabrese</LastName>
<ForeName>J Mauro</ForeName>
<Initials>JM</Initials>
<Identifier Source="ORCID">http://orcid.org/0000-0002-1213-2540</Identifier>
<AffiliationInfo><Affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. jmcalabr@med.unc.edu.</Affiliation>
</AffiliationInfo>
</Author>
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<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant><GrantID>T32 GM008570</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant><GrantID>T32 GM067553</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
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<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
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<Grant><GrantID>T32 GM007092</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant><GrantID>R01 GM121806</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020014" MajorTopicYN="N">K562 Cells</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName>
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Functional classification of long non-coding RNAs by k-mer content.

Functional classification of long non-coding RNAs by k-mer content.

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