Yang Kun, Sablok Gaurav, Qiao Guang, Nie Qiong, Wen Xiaopeng
Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region - Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China; College of Life Sciences, Guizhou UniversityGuiyang, China.
Climate Change Cluster (C3), University of Technology Sydney Sydney, NSW, Australia.
Front Plant Sci. 2017 Mar 21;8:322. doi: 10.3389/fpls.2017.00322. eCollection 2017.
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://github.com/347033139/isomiR2Function.
在植物中，非编码RNA（ncRNA），特别是微小RNA（miRNA，19 - 24个核苷酸）介导的转录后调控参与了植物发育、生物和非生物相互作用中转录图谱的调控。在过去几年中，人们相当关注于描绘和解读miRNA及其典型异源异构体（isomiR）在植物中的作用。然而，考虑到我们定义isomiR的相关特征，如模板化或非模板化，对植物isomiR进行恰当分类和准确预测仍然缺乏相关方法。在本研究中，我们展示了isomiR2Function，这是一个易于部署的独立工具，可用于可靠且高通量地发现模板化和非模板化isomiR。此外，isomiR2Function能够识别差异表达的isomiR，并基于转录本或PARE - Seq，使用Targetfinder或Cleaveland进行并行的靶标预测。isomiR2Function还能使用TopGO软件包对检测到的靶标进行功能富集分析。与之前开发的isomiR预测工具相比，isomiR2Function的基准测试显示其对isomiR的预测和分类具有高度准确性。此外，其附加功能的下游实现方式使isomiR2Function可被归类为一个从发现到功能角色的isomiR分析的单一独立工具。总而言之，isomiR2Function能够以最小的工作量对miRNA测序进行简化处理，以识别和表征isomiR。可通过https://github.com/347033139/isomiR2Function访问isomiR2Function。
