Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).
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DOI：
10.1038/ncomms12339
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发表时间：
2016-08-17
影响因子：
16.6
通讯作者：
Harrow J
中科院分区：
文献类型：
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作者：
Lagarde J;Uszczynska-Ratajczak B;Santoyo-Lopez J;Gonzalez JM;Tapanari E;Mudge JM;Steward CA;Wilming L;Tanzer A;Howald C;Chrast J;Vela-Boza A;Rueda A;Lopez-Domingo FJ;Dopazo J;Reymond A;Guigó R;Harrow J
长链非编码RNA（lncRNA）构成了哺乳动物转录组的一个大的，但大部分未表征的部分。这种表征需要对其基因结构和边界进行全面，高质量的注释，这是目前缺乏的。在这里，我们描述了RACE-Seq，这是一种基于RACE（cDNA末端快速扩增）和长读段RNA测序的实验工作流程。我们将RACE-Seq应用于7种组织中的398个人类lncRNA基因，发现了2，556个靶向新转录本。约60%的靶位点在5′或3′端延伸，通常达到基因边界的基因组标志。对新转录本的分析表明，lncRNA与蛋白质编码基因一样长，具有同样多的外显子，并经历同样多的选择性剪接，与目前的假设相反。总的来说，我们表明RACE-Seq是注释生物体深层转录组的有效工具，并且与其他靶向测序技术相比具有优势。 长的非编码RNA越来越多地被认为是调节细胞过程的重要因素，并构成转录组的一大部分，但大多数是未表征的。在这里，作者介绍了RACE-Seq，一种改进和扩展低表达转录本注释的工具。
Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification of cDNA ends) and long-read RNA sequencing. We apply RACE-Seq to 398 human lncRNA genes in seven tissues, leading to the discovery of 2,556 on-target, novel transcripts. About 60% of the targeted loci are extended in either 5′ or 3′, often reaching genomic hallmarks of gene boundaries. Analysis of the novel transcripts suggests that lncRNAs are as long, have as many exons and undergo as much alternative splicing as protein-coding genes, contrary to current assumptions. Overall, we show that RACE-Seq is an effective tool to annotate an organism's deep transcriptome, and compares favourably to other targeted sequencing techniques. Long non-coding RNAs are increasingly recognised to be important factors in regulating cellular processes and comprise a large faction of the transcriptome, however most are uncharacterised. Here the authors present RACE-Seq, a tool to improve and extend the annotation of low-expression transcripts.