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

Gruber, Andreas J.; Gypas, Foivos; Riba, Andrea; Schmidt, Ralf; Zavolan, Mihaela

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

Files

Gruber_2-fmqnp8yycdif8.pdf(1.36 MB)

Date

2018

Authors

Gruber, Andreas J.

Gypas, Foivos

Riba, Andrea

Schmidt, Ralf

Zavolan, Mihaela

Publication type

Journal article

Publication status

Published

Published in

Nature Methods ; 15 (2018), 10. - pp. 832-836. - Nature Publishing Group. - ISSN 1548-7091. - eISSN 1548-7105

Abstract

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.

Subject (DDC)

570 Biosciences, Biology

Cite This

ISO 690

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

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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Refereed

Yes