Improved definition of the mouse transcriptome via targeted RNA sequencing.
Improved definition of the mouse transcriptome via targeted RNA sequencing.
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通过靶向的RNA测序改善了小鼠转录组的定义。
DOI：
10.1101/gr.199760.115
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发表时间：
2016-05
期刊：
影响因子：
7
通讯作者：
Enright AJ
中科院分区：
文献类型：
--
作者：
Bussotti G;Leonardi T;Clark MB;Mercer TR;Crawford J;Malquori L;Notredame C;Dinger ME;Mattick JS;Enright AJ
靶向RNA测序（CaptureSeq）使用寡核苷酸探针捕获RNA进行测序，提供丰富的读段覆盖率，精确测量基因表达和定量表达数据。我们应用CaptureSeq在当前鼠GRCm38组装中改进转录本注释。超过23，000个对应于推定或注释的长非编码RNA（lncRNA）的区域和154，281个已知的剪接连接位点被选择用于跨5个小鼠组织和3个脑亚区的靶向测序。结果表明，小鼠转录组比以前认为的要复杂得多。我们组装了比GENCODE更完整的转录本亚型，扩展了转录本边界，并连接了散布的映射读段岛。我们描述了一种新的过滤管道，识别以前未注释的，但高质量的转录异构体。在这个集合中，911个GENCODE邻近基因被浓缩成400个扩展的基因模型。此外，594个GENCODE lncRNA在其结构用CaptureSeq延伸时获得开放阅读框（ORF）。最后，我们使用当前的FANTOM和Mouse ENCODE资源验证我们的观察结果。
Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.