Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

Lade...
Vorschaubild
Dateien
Gruber_2-fmqnp8yycdif8.pdf
Gruber_2-fmqnp8yycdif8.pdfGröße: 1.36 MBDownloads: 9
Datum
2018
Autor:innen
Gypas, Foivos
Riba, Andrea
Schmidt, Ralf
Zavolan, Mihaela
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
ArXiv-ID
Internationale Patentnummer
EU-Projektnummer
DFG-Projektnummer
Projekt
Open Access-Veröffentlichung
Sammlungen
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Nature Methods. Nature Publishing Group. 2018, 15(10), pp. 832-836. ISSN 1548-7091. eISSN 1548-7105. Available under: doi: 10.1038/s41592-018-0114-z
Zusammenfassung

Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization. We developed the terminal exon characterization (TEC) tool ( http://tectool.unibas.ch ), which can be used with RNA-sequencing data from any species for which a genome annotation that includes sites of RNA cleavage and polyadenylation is available. We discovered hundreds of previously unknown isoforms and cell-type-specific terminal exons in human cells. Ribosome profiling data revealed that many of these isoforms were translated. By applying TECtool to single-cell sequencing data, we found that the newly identified isoforms were expressed in subpopulations of cells. Thus, TECtool enables the identification of previously unknown isoforms in well-studied cell systems and in rare cell types.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
570 Biowissenschaften, Biologie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690GRUBER, Andreas J., Foivos GYPAS, Andrea RIBA, Ralf SCHMIDT, Mihaela ZAVOLAN, 2018. Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. In: Nature Methods. Nature Publishing Group. 2018, 15(10), pp. 832-836. ISSN 1548-7091. eISSN 1548-7105. Available under: doi: 10.1038/s41592-018-0114-z
BibTex
@article{Gruber2018Termi-50943,
  year={2018},
  doi={10.1038/s41592-018-0114-z},
  title={Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms},
  number={10},
  volume={15},
  issn={1548-7091},
  journal={Nature Methods},
  pages={832--836},
  author={Gruber, Andreas J. and Gypas, Foivos and Riba, Andrea and Schmidt, Ralf and Zavolan, Mihaela}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/50943">
    <dc:creator>Zavolan, Mihaela</dc:creator>
    <dc:language>eng</dc:language>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-22T08:10:27Z</dc:date>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/50943"/>
    <dc:contributor>Gruber, Andreas J.</dc:contributor>
    <dc:contributor>Schmidt, Ralf</dc:contributor>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/50943/1/Gruber_2-fmqnp8yycdif8.pdf"/>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-22T08:10:27Z</dcterms:available>
    <dc:creator>Schmidt, Ralf</dc:creator>
    <dc:contributor>Riba, Andrea</dc:contributor>
    <dcterms:abstract xml:lang="eng">Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization. We developed the terminal exon characterization (TEC) tool ( http://tectool.unibas.ch ), which can be used with RNA-sequencing data from any species for which a genome annotation that includes sites of RNA cleavage and polyadenylation is available. We discovered hundreds of previously unknown isoforms and cell-type-specific terminal exons in human cells. Ribosome profiling data revealed that many of these isoforms were translated. By applying TECtool to single-cell sequencing data, we found that the newly identified isoforms were expressed in subpopulations of cells. Thus, TECtool enables the identification of previously unknown isoforms in well-studied cell systems and in rare cell types.</dcterms:abstract>
    <dc:creator>Riba, Andrea</dc:creator>
    <dc:contributor>Zavolan, Mihaela</dc:contributor>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Gruber, Andreas J.</dc:creator>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:contributor>Gypas, Foivos</dc:contributor>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/50943/1/Gruber_2-fmqnp8yycdif8.pdf"/>
    <dc:rights>terms-of-use</dc:rights>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dcterms:title>Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms</dcterms:title>
    <dcterms:issued>2018</dcterms:issued>
    <dc:creator>Gypas, Foivos</dc:creator>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
URL der Originalveröffentl.
Prüfdatum der URL
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Begutachtet
Ja