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

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2018
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Gypas, Foivos
Riba, Andrea
Schmidt, Ralf
Zavolan, Mihaela
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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.

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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}
}
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