Genome-wide identification and functional analysis of circRNAs in Zea mays

Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs, which increasingly drawn researchers' attention in recent years as their importance in regulating gene expression at the transcriptional and post-transcriptional levels. With the development of high-throughput sequencing and bioinformatics, circRNAs have been widely analysed in animals, but the understanding of characteristics and function of circRNAs is limited in plants, especially in maize. Here, 3715 unique circRNAs were predicted in Zea mays systematically, and 8 of 12 circRNAs were validated by experiments. By analysing circRNA sequence, the events of alternative circularization phenomenon were found prevailed in maize. By comparing circRNAs in different species, it showed that part circRNAs are conserved across species, for example, there are 273 circRNAs conserved between maize and rice. Although most of the circRNAs have low expression levels, we found 149 differential expressed circRNAs responding to heat, cold, or drought, and 1782 tissue-specific expressed circRNAs. The results showed that those circRNAs may have potential biological functions in specific situations. Finally, two different methods were used to search circRNA functions, which were based on circRNAs originated from protein-coding genes and circRNAs as miRNA decoys. 346 circRNAs could act as miRNA decoys, which might modulate the effects of multiple molecular functions, including binding, catalytic activity, oxidoreductase activity, and transmembrane transporter activity. In summary, maize circRNAs were identified, classified and characterized systematically. We also explored circRNA functions, suggesting that circRNAs are involved in multiple molecular processes and play important roles in regulating of gene expression. Our results provide a rich resource for further study of maize circRNAs.

环状RNA（Circular RNAs，circRNAs）是一类内源性非编码RNA，近年来因其在转录与转录后水平调控基因表达中的关键作用，愈发受到研究者的广泛关注。随着高通量测序（high-throughput sequencing）与生物信息学（bioinformatics）技术的发展，环状RNA已在动物中得到广泛分析，但目前学界对植物中环状RNA的特征与功能的认知仍较为有限，在玉米（Zea mays）中更是如此。本研究系统地在玉米中预测得到3715条独特的环状RNA，其中12条环状RNA中有8条通过实验得到了验证。通过对环状RNA序列的分析，本研究发现可变环化现象在玉米中广泛存在。通过跨物种的环状RNA比较分析，研究发现部分环状RNA在物种间具有保守性：例如玉米与水稻之间共存在273条保守环状RNA。尽管大多数环状RNA的表达水平较低，但本研究共鉴定出149条响应热、冷或干旱胁迫的差异表达环状RNA，以及1782条组织特异性表达的环状RNA。上述结果表明，这些环状RNA可能在特定生理条件下发挥潜在的生物学功能。最后，本研究采用两种不同的方法探究环状RNA的功能：一种基于源自蛋白编码基因的环状RNA，另一种将环状RNA作为miRNA诱饵（miRNA decoys）。共有346条环状RNA可作为miRNA诱饵，其可能调控多种分子功能相关的过程，包括结合、催化活性、氧化还原酶活性以及跨膜转运蛋白活性。综上，本研究系统地完成了玉米环状RNA的鉴定、分类与特征解析。本研究同时对环状RNA的功能进行了探究，结果表明环状RNA参与多种分子生物学过程，并在基因表达调控中发挥重要作用。本研究的结果为玉米环状RNA的后续研究提供了丰富的资源。