Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.
College of Life Sciences, Shaanxi Normal University, Xi'an, China.
PLoS One. 2018 Dec 11;13(12):e0202375. doi: 10.1371/journal.pone.0202375. eCollection 2018.
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（circRNAs）是一类内源性非编码 RNA，近年来，它们在转录和转录后水平调节基因表达的重要性引起了研究人员的广泛关注。随着高通量测序和生物信息学的发展，circRNAs 在动物中得到了广泛分析，但在植物中，尤其是在玉米中，对 circRNAs 的特征和功能的认识还很有限。在这里，我们系统地预测了玉米中有 3715 个独特的 circRNAs，其中 12 个 circRNAs 的 8 个通过实验得到了验证。通过分析 circRNA 序列，发现玉米中存在广泛的选择性环化现象。通过比较不同物种的 circRNAs，表明部分 circRNAs 在物种间是保守的，例如，玉米和水稻之间有 273 个保守的 circRNAs。尽管大多数 circRNAs 的表达水平较低，但我们发现了 149 个对热、冷或干旱有响应的差异表达 circRNAs 和 1782 个组织特异性表达的 circRNAs。结果表明，这些 circRNAs 在特定情况下可能具有潜在的生物学功能。最后，我们使用两种不同的方法来搜索 circRNA 的功能，一种是基于来源于蛋白编码基因的 circRNAs，另一种是基于 circRNAs 作为 miRNA 诱饵。有 346 个 circRNAs 可以作为 miRNA 诱饵，可能调节多个分子功能的作用，包括结合、催化活性、氧化还原酶活性和跨膜转运体活性。综上所述，我们系统地鉴定、分类和描述了玉米 circRNAs。我们还探索了 circRNA 的功能，表明 circRNAs 参与了多个分子过程，并在基因表达调控中发挥着重要作用。我们的结果为进一步研究玉米 circRNAs 提供了丰富的资源。
