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Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms
Nature Methods ( IF 48.0 ) Pub Date : 2018-09-10 , DOI: 10.1038/s41592-018-0114-z
Andreas J Gruber 1 , Foivos Gypas 2 , Andrea Riba 3 , Ralf Schmidt 2 , Mihaela Zavolan 2
Affiliation  

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.



中文翻译:

使用 TECtool 进行末端外显子表征揭示了丰富的细胞特异性亚型

RNA 3' 末端的测序发现了许多与已知转录物的终止位点不对应的位点。通过其 3' 非翻译区,蛋白质编码 RNA 与 RNA 结合蛋白和 microRNA 相互作用,从而调节许多特性,包括 RNA 稳定性和亚细胞定位。我们开发了末端外显子表征 (TEC) 工具 (http://tectool.unibas.ch),该工具可用于任何物种的 RNA 测序数据,只要该物种的基因组注释(包括 RNA 切割和聚腺苷酸化位点)可用。我们在人类细胞中发现了数百种以前未知的亚型和细胞类型特异性末端外显子。核糖体分析数据显示,许多同工型都被翻译了。通过将 TECtool 应用到单细胞测序数据,我们发现新鉴定的亚型在细胞亚群中表达。因此,TECtool 能够识别经过充分研究的细胞系统和稀有细胞类型中以前未知的亚型。

更新日期:2018-09-11
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