The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China.
Sci Rep. 2017 Dec 7;7(1):17135. doi: 10.1038/s41598-017-16861-w.
MicroRNAs (miRNAs) are known to play important roles in various cellular processes and stress responses. MiRNAs can be identified by analyzing reads from high-throughput deep sequencing. The reads realigned to miRNA precursors besides canonical miRNAs were initially considered as sequencing noise and ignored from further analysis. Here we reported a small-RNA species of phased and half-phased miRNA-like RNAs different from canonical miRNAs from cassava miRNA precursors detected under four distinct chilling conditions. They can form abundant multiple small RNAs arranged along precursors in a tandem and phased or half-phased fashion. Some of these miRNA-like RNAs were experimentally confirmed by re-amplification and re-sequencing, and have a similar qRT-PCR detection ratio as their cognate canonical miRNAs. The target genes of those phased and half-phased miRNA-like RNAs function in process of cell growth metabolism and play roles in protein kinase. Half-phased miR171d.3 was confirmed to have cleavage activities on its target gene P-glycoprotein 11, a broad substrate efflux pump across cellular membranes, which is thought to provide protection for tropical cassava during sharp temperature decease. Our results showed that the RNAs from miRNA precursors are miRNA-like small RNAs that are viable negative gene regulators and may have potential functions in cassava chilling responses.
微小 RNA（miRNA）在各种细胞过程和应激反应中发挥着重要作用。miRNA 可以通过分析高通量深度测序的读取来识别。除了经典 miRNA 之外，与 miRNA 前体重新对齐的读取最初被认为是测序噪声，并从进一步的分析中忽略。在这里，我们报道了一种不同于经典 miRNA 的小 RNA 种，即来自四个不同冷胁迫条件下的木薯 miRNA 前体的相位和半相位 miRNA 样 RNA。它们可以形成大量沿着前体排列的多个小 RNA，呈串联、相位或半相位排列。其中一些 miRNA 样 RNA 通过重新扩增和重新测序得到了实验验证，并且与它们的同源经典 miRNA 具有相似的 qRT-PCR 检测比例。那些相位和半相位 miRNA 样 RNA 的靶基因在细胞生长代谢过程中发挥作用，并在蛋白激酶中发挥作用。半相位 miR171d.3 被证实对其靶基因 P-糖蛋白 11 具有切割活性，P-糖蛋白 11 是一种广泛的跨细胞膜底物外排泵，被认为在热带木薯急剧降温时提供保护。我们的研究结果表明，miRNA 前体的 RNA 是 miRNA 样小 RNA，是可行的负基因调节剂，可能在木薯冷胁迫反应中具有潜在功能。
