Transcriptome-wide investigation of circular RNAs in rice.
Transcriptome-wide investigation of circular RNAs in rice.
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水稻环状RNA的全转录组研究
DOI：
10.1261/rna.052282.115
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发表时间：
2015-12
期刊：
影响因子：
--
通讯作者：
Han B
中科院分区：
文献类型：
--
作者：
Lu T;Cui L;Zhou Y;Zhu C;Fan D;Gong H;Zhao Q;Zhou C;Zhao Y;Lu D;Luo J;Wang Y;Tian Q;Feng Q;Huang T;Han B
通过高通量深度测序和对大量转录数据的分析，新近发现了各种稳定的环状RNA(CircRNAs)，它们是在古生物、秀丽线虫、小鼠和人类中丰富的非编码RNA。CircRNAs在miRNA的功能和转录调控中发挥着重要作用，它作为竞争的内源RNAs或其亲本编码基因的正调控因子。然而，对植物中的CircRNA知之甚少。在这里，我们报告了2354个水稻CircRNAs，它们是通过对ssRNA-seq数据的深度测序和计算分析而鉴定出来的。其中1356个为外显子环状RNA。一些CircRNAs表现出组织特异性表达。水稻CircRNA有相当多的异构体，包括选择性后剪接和选择性剪接环化模式。具有多个外显子的亲本基因优先循环。只有484个CircRNA具有源自已知剪接位点的反向剪接。此外，只有92个CircRNA被发现富含侧翼序列中的微型反向重复转座元件(Me)或与至少18个碱基的侧翼内含子序列互补，这表明除了直接反向剪接外，水稻还存在其他一些产生机制。水稻CircRNAs对miRNA靶点没有明显的富集性。一项转基因研究表明，与空载体对照植物相比，在转基因植物中过表达CircRNA可以降低其亲本基因的表达水平。这表明CircRNA及其线性形式可能是其亲本基因的负调控因子。总体而言，这些分析揭示了CircRNAs在水稻中的普遍存在，并为研究水稻CircRNAs提供了新的生物学见解。
Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs.