Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts
Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts
复制标题
通过 5’-Cap 捕获进行长读长直接 RNA 测序揭示了 Piwi 对蝗虫中转座元件广泛外显化的影响
DOI：
10.1080/15476286.2019.1602437
复制
发表时间：
2019-04-15
期刊：
影响因子：
4.1
通讯作者：
Kang, Le
中科院分区：
文献类型：
--
作者：
Jiang, Feng;Zhang, Jie;Kang, Le
飞蝗（Locusta migratoria）基因组的大基因组中积累了大量的转座因子（transposable elements，TEs），这些转座因子具有内在的转录活性。阻碍精确确定全长RNA转录物序列的能力是外显子化的TE，其产生难以使用短读段测序技术解析的许多高度相似的片段。在这里，我们应用了一个5 MODIFIER LETTER PRIME-Cap捕获方法，使用Nanopore长读直接RNA测序来表征其天然RNA形式的全长转录本，并分析蝗虫转录组中的TE外显子化模式。我们的研究结果揭示了广泛建立的TE外显子和大量的贡献，TEs的蝗虫转录组中的RNA剪接。受Piwi表达影响的转录组谱的结果表明，TE衍生序列是Piwi介导的抑制的主要靶点。此外，我们的研究表明，Piwi表达调节含有TE衍生序列的RNA转录物的长度，从而产生替代UTR用途。总的来说，我们的研究结果揭示了转录组的特点TE外显子组的物种，其特点是大的和重复的基因组。
The large genome of the migratory locust (Locusta migratoria) genome accumulates massive amount of accumulated transposable elements (TEs), which show intrinsic transcriptional activities. Hampering the ability to precisely determine full-length RNA transcript sequences are exonized TEs, which produce numerous highly similar fragments that are difficult to resolve using short-read sequencing technology. Here, we applied a 5MODIFIER LETTER PRIME-Cap capturing method using Nanopore long-read direct RNA sequencing to characterize full-length transcripts in their native RNA form and to analyze the TE exonization pattern in the locust transcriptome. Our results revealed the widespread establishment of TE exonization and a substantial contribution of TEs to RNA splicing in the locust transcriptome. The results of the transcriptomic spectrum influenced by Piwi expression indicated that TE-derived sequences were the main targets of Piwi-mediated repression. Furthermore, our study showed that Piwi expression regulates the length of RNA transcripts containing TE-derived sequences, creating an alternative UTR usage. Overall, our results reveal the transcriptomic characteristics of TE exonization in the species characterized by large and repetitive genomes.