Type of Publication: | Journal article |
Publication status: | Published |
Author: | Gruber, Andreas J.; Gypas, Foivos; Riba, Andrea; Schmidt, Ralf; Zavolan, Mihaela |
Year of publication: | 2018 |
Published in: | Nature Methods ; 15 (2018), 10. - pp. 832-836. - Nature Publishing Group. - ISSN 1548-7091. - eISSN 1548-7105 |
Pubmed ID: | 30202060 |
DOI (citable link): | https://dx.doi.org/10.1038/s41592-018-0114-z |
Summary: |
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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Subject (DDC): | 570 Biosciences, Biology |
Refereed: | Yes |
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GRUBER, 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. 15(10), pp. 832-836. ISSN 1548-7091. eISSN 1548-7105. Available under: doi: 10.1038/s41592-018-0114-z
@article{Gruber2018Termi-50943, title={Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms}, year={2018}, doi={10.1038/s41592-018-0114-z}, 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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