Functional classification of long non-coding RNAs by k-mer content.
Identifieur interne : 000964 ( Main/Exploration ); précédent : 000963; suivant : 000965Functional 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.
Descripteurs français
- KwdFr :
- ARN long non codant (), ARN long non codant (génétique), Algorithmes, Alignement de séquences, Analyse de regroupements, Analyse de séquence d'ARN (), Animaux, Annotation de séquence moléculaire, Bases de données génétiques, Canaux potassiques voltage-dépendants (génétique), Cellules HepG2, Cellules K562, Conformation d'acide nucléique, Humains, Motifs nucléotidiques (génétique), Souris, Séquence conservée, Séquence nucléotidique.
- MESH :
- génétique : ARN long non codant, Canaux potassiques voltage-dépendants, Motifs nucléotidiques.
- ARN long non codant, Algorithmes, Alignement de séquences, Analyse de regroupements, Analyse de séquence d'ARN, Animaux, Annotation de séquence moléculaire, Bases de données génétiques, Cellules HepG2, Cellules K562, Conformation d'acide nucléique, Humains, Souris, Séquence conservée, Séquence nucléotidique.
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:
- États-Unis
- Caroline du Nord
- Chapel Hill (Caroline du Nord)
- Université de Caroline du Nord à Chapel Hill
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000779
- to stream PubMed, to step Curation: 000779
- to stream PubMed, to step Checkpoint: 000909
- to stream Ncbi, to step Merge: 001F66
- to stream Ncbi, to step Curation: 001F66
- to stream Ncbi, to step Checkpoint: 001F66
- to stream Main, to step Merge: 000967
- to stream Main, to step Curation: 000964
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Functional classification of long non-coding RNAs by k-mer content.</title><author><name sortKey="Kirk, Jessime M" sort="Kirk, Jessime M" uniqKey="Kirk J" first="Jessime M" last="Kirk">Jessime M. Kirk</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Kim, Susan O" sort="Kim, Susan O" uniqKey="Kim S" first="Susan O" last="Kim">Susan O. Kim</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Inoue, Kaoru" sort="Inoue, Kaoru" uniqKey="Inoue K" first="Kaoru" last="Inoue">Kaoru Inoue</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Smola, Matthew J" sort="Smola, Matthew J" uniqKey="Smola M" first="Matthew J" last="Smola">Matthew J. Smola</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><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></affiliation></author><author><name sortKey="Lee, David M" sort="Lee, David M" uniqKey="Lee D" first="David M" last="Lee">David M. Lee</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Schertzer, Megan D" sort="Schertzer, Megan D" uniqKey="Schertzer M" first="Megan D" last="Schertzer">Megan D. Schertzer</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Wooten, Joshua S" sort="Wooten, Joshua S" uniqKey="Wooten J" first="Joshua S" last="Wooten">Joshua S. Wooten</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Baker, Allison R" sort="Baker, Allison R" uniqKey="Baker A" first="Allison R" last="Baker">Allison R. Baker</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Sprague, Daniel" sort="Sprague, Daniel" uniqKey="Sprague D" first="Daniel" last="Sprague">Daniel Sprague</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Collins, David W" sort="Collins, David W" uniqKey="Collins D" first="David W" last="Collins">David W. Collins</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Horning, Christopher R" sort="Horning, Christopher R" uniqKey="Horning C" first="Christopher R" last="Horning">Christopher R. Horning</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Wang, Shuo" sort="Wang, Shuo" uniqKey="Wang S" first="Shuo" last="Wang">Shuo Wang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Chen, Qidi" sort="Chen, Qidi" uniqKey="Chen Q" first="Qidi" last="Chen">Qidi Chen</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M" last="Weeks">Kevin M. Weeks</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><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></affiliation></author><author><name sortKey="Mucha, Peter J" sort="Mucha, Peter J" uniqKey="Mucha P" first="Peter J" last="Mucha">Peter J. Mucha</name><affiliation wicri:level="4"><nlm:affiliation>Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, 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></affiliation></author><author><name sortKey="Calabrese, J Mauro" sort="Calabrese, J Mauro" uniqKey="Calabrese J" first="J Mauro" last="Calabrese">J Mauro Calabrese</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. jmcalabr@med.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:30224646</idno><idno type="pmid">30224646</idno><idno type="doi">10.1038/s41588-018-0207-8</idno><idno type="wicri:Area/PubMed/Corpus">000779</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000779</idno><idno type="wicri:Area/PubMed/Curation">000779</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000779</idno><idno type="wicri:Area/PubMed/Checkpoint">000909</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000909</idno><idno type="wicri:Area/Ncbi/Merge">001F66</idno><idno type="wicri:Area/Ncbi/Curation">001F66</idno><idno type="wicri:Area/Ncbi/Checkpoint">001F66</idno><idno type="wicri:Area/Main/Merge">000967</idno><idno type="wicri:Area/Main/Curation">000964</idno><idno type="wicri:Area/Main/Exploration">000964</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Functional classification of long non-coding RNAs by k-mer content.</title><author><name sortKey="Kirk, Jessime M" sort="Kirk, Jessime M" uniqKey="Kirk J" first="Jessime M" last="Kirk">Jessime M. Kirk</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Kim, Susan O" sort="Kim, Susan O" uniqKey="Kim S" first="Susan O" last="Kim">Susan O. Kim</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Inoue, Kaoru" sort="Inoue, Kaoru" uniqKey="Inoue K" first="Kaoru" last="Inoue">Kaoru Inoue</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Smola, Matthew J" sort="Smola, Matthew J" uniqKey="Smola M" first="Matthew J" last="Smola">Matthew J. Smola</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><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></affiliation></author><author><name sortKey="Lee, David M" sort="Lee, David M" uniqKey="Lee D" first="David M" last="Lee">David M. Lee</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Schertzer, Megan D" sort="Schertzer, Megan D" uniqKey="Schertzer M" first="Megan D" last="Schertzer">Megan D. Schertzer</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Wooten, Joshua S" sort="Wooten, Joshua S" uniqKey="Wooten J" first="Joshua S" last="Wooten">Joshua S. Wooten</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Baker, Allison R" sort="Baker, Allison R" uniqKey="Baker A" first="Allison R" last="Baker">Allison R. Baker</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Sprague, Daniel" sort="Sprague, Daniel" uniqKey="Sprague D" first="Daniel" last="Sprague">Daniel Sprague</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author><author><name sortKey="Collins, David W" sort="Collins, David W" uniqKey="Collins D" first="David W" last="Collins">David W. Collins</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Horning, Christopher R" sort="Horning, Christopher R" uniqKey="Horning C" first="Christopher R" last="Horning">Christopher R. Horning</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Wang, Shuo" sort="Wang, Shuo" uniqKey="Wang S" first="Shuo" last="Wang">Shuo Wang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Chen, Qidi" sort="Chen, Qidi" uniqKey="Chen Q" first="Qidi" last="Chen">Qidi Chen</name><affiliation wicri:level="4"><nlm:affiliation>Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, 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></affiliation></author><author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M" last="Weeks">Kevin M. Weeks</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><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></affiliation></author><author><name sortKey="Mucha, Peter J" sort="Mucha, Peter J" uniqKey="Mucha P" first="Peter J" last="Mucha">Peter J. Mucha</name><affiliation wicri:level="4"><nlm:affiliation>Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, 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></affiliation></author><author><name sortKey="Calabrese, J Mauro" sort="Calabrese, J Mauro" uniqKey="Calabrese J" first="J Mauro" last="Calabrese">J Mauro Calabrese</name><affiliation wicri:level="4"><nlm:affiliation>Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. jmcalabr@med.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Lineberger Comprehensive Cancer Center, 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></affiliation></author></analytic><series><title level="j">Nature genetics</title><idno type="eISSN">1546-1718</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><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></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN long non codant ()</term><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></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Potassium Channels, Voltage-Gated</term><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nucleotide Motifs</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN long non codant</term><term>Canaux potassiques voltage-dépendants</term><term>Motifs nucléotidiques</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><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>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN long non codant</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>Cellules HepG2</term><term>Cellules K562</term><term>Conformation d'acide nucléique</term><term>Humains</term><term>Souris</term><term>Séquence conservée</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><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></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Caroline du Nord</li></region><settlement><li>Chapel Hill (Caroline du Nord)</li></settlement><orgName><li>Université de Caroline du Nord à Chapel Hill</li></orgName></list><tree><country name="États-Unis"><region name="Caroline du Nord"><name sortKey="Kirk, Jessime M" sort="Kirk, Jessime M" uniqKey="Kirk J" first="Jessime M" last="Kirk">Jessime M. Kirk</name></region><name sortKey="Baker, Allison R" sort="Baker, Allison R" uniqKey="Baker A" first="Allison R" last="Baker">Allison R. Baker</name><name sortKey="Calabrese, J Mauro" sort="Calabrese, J Mauro" uniqKey="Calabrese J" first="J Mauro" last="Calabrese">J Mauro Calabrese</name><name sortKey="Chen, Qidi" sort="Chen, Qidi" uniqKey="Chen Q" first="Qidi" last="Chen">Qidi Chen</name><name sortKey="Collins, David W" sort="Collins, David W" uniqKey="Collins D" first="David W" last="Collins">David W. Collins</name><name sortKey="Horning, Christopher R" sort="Horning, Christopher R" uniqKey="Horning C" first="Christopher R" last="Horning">Christopher R. Horning</name><name sortKey="Inoue, Kaoru" sort="Inoue, Kaoru" uniqKey="Inoue K" first="Kaoru" last="Inoue">Kaoru Inoue</name><name sortKey="Kim, Susan O" sort="Kim, Susan O" uniqKey="Kim S" first="Susan O" last="Kim">Susan O. Kim</name><name sortKey="Lee, David M" sort="Lee, David M" uniqKey="Lee D" first="David M" last="Lee">David M. Lee</name><name sortKey="Mucha, Peter J" sort="Mucha, Peter J" uniqKey="Mucha P" first="Peter J" last="Mucha">Peter J. Mucha</name><name sortKey="Schertzer, Megan D" sort="Schertzer, Megan D" uniqKey="Schertzer M" first="Megan D" last="Schertzer">Megan D. Schertzer</name><name sortKey="Smola, Matthew J" sort="Smola, Matthew J" uniqKey="Smola M" first="Matthew J" last="Smola">Matthew J. Smola</name><name sortKey="Sprague, Daniel" sort="Sprague, Daniel" uniqKey="Sprague D" first="Daniel" last="Sprague">Daniel Sprague</name><name sortKey="Wang, Shuo" sort="Wang, Shuo" uniqKey="Wang S" first="Shuo" last="Wang">Shuo Wang</name><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M" last="Weeks">Kevin M. Weeks</name><name sortKey="Wooten, Joshua S" sort="Wooten, Joshua S" uniqKey="Wooten J" first="Joshua S" last="Wooten">Joshua S. Wooten</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000964 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000964 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:30224646
|texte= Functional classification of long non-coding RNAs by k-mer content.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:30224646" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |