Chen Gang, Cui Jiawen, Wang Li, Zhu Yingfang, Lu Zhaogeng, Jin Biao
College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China.
College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.
Front Plant Sci. 2017 Sep 27;8:1678. doi: 10.3389/fpls.2017.01678. eCollection 2017.
Circular RNAs (circRNAs) are a family of transcripts with covalently closed circular structures and still largely unknown functions. Large numbers of circRNAs have been found in various biological processes in humans and animals, but fewer circRNAs have been identified in plants. We performed a genome-wide analysis of circRNAs in via deep sequencing. We constructed 14 strand-specific libraries from 13 samples of plants from four developmental stages, four stress treatments, and five organs and a mixed sample across the lifespan. In total, we identified 5861 circRNAs, including 1275 novel ones, using the strict threshold of at least two unique back-spliced supporting reads. The circRNAs were non-randomly distributed in all chromosomes; most were exonic. Sequence similarity analysis of circRNAs between and four other species showed that some circRNAs are conserved in plants. Functional annotation indicated that many parent genes of circRNAs are involved in many fundamental processes including plant development, reproduction, and response to stimulus. In addition, a small proportion of circRNAs was shown to be potential targets of miRNAs, indicating that the circRNAs could interact with miRNAs to regulate gene expression. qRT-PCR analysis revealed that circRNAs displayed diverse expression patterns at different growth stages. Our results provide an important resource for continuing circRNA research in , and should enhance our understanding of circRNAs in plants.
环状RNA（circRNAs）是一类具有共价闭合环状结构且功能仍 largely未知的转录本。在人类和动物的各种生物过程中已发现大量circRNAs，但在植物中鉴定出的circRNAs较少。我们通过深度测序对[具体植物名称未给出]中的circRNAs进行了全基因组分析。我们从处于四个发育阶段、四种胁迫处理、五个器官的13个植物样本以及一个整个生命周期的混合样本构建了14个链特异性文库。总共，我们使用至少两个独特的反向剪接支持读数的严格阈值鉴定出5861个circRNAs，其中包括1275个新的circRNAs。circRNAs在所有染色体中呈非随机分布；大多数是外显子的。[具体植物名称未给出]与其他四个物种之间的circRNAs序列相似性分析表明，一些circRNAs在植物中是保守的。功能注释表明，许多circRNAs的亲本基因参与了包括植物发育、繁殖和对刺激的反应等许多基本过程。此外，一小部分circRNAs被证明是miRNAs的潜在靶标，这表明circRNAs可以与miRNAs相互作用以调节基因表达。qRT-PCR分析表明，circRNAs在不同生长阶段表现出不同的表达模式。我们的结果为在[具体植物名称未给出]中继续进行circRNA研究提供了重要资源，并应增强我们对植物中circRNAs的理解。
