Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
Nat Methods. 2018 Oct;15(10):832-836. doi: 10.1038/s41592-018-0114-z. Epub 2018 Sep 10.
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.
对 RNA 3' 端的测序揭示了许多不对应于已知转录本终止位点的位点。通过它们的 3' 非翻译区，蛋白编码 RNA 与 RNA 结合蛋白和 microRNAs 相互作用，这些蛋白和 microRNAs 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特征（TEC）工具（http://tectool.unibas.ch），它可以与来自任何物种的 RNA-seq 数据一起使用，前提是该物种的基因组注释中包含 RNA 切割和多聚腺苷酸化的位点。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。核糖体分析数据表明，其中许多亚型被翻译。通过将 TECtool 应用于单细胞测序数据，我们发现新鉴定的亚型在细胞亚群中表达。因此，TECtool 能够在研究充分的细胞系统和罕见的细胞类型中鉴定以前未知的亚型。
