Frydrych Capelari Érika, da Fonseca Guilherme Cordenonsi, Guzman Frank, Margis Rogerio
Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil.
Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil.
Plants (Basel). 2019 Aug 26;8(9):302. doi: 10.3390/plants8090302.
Competing endogenous RNAs (ceRNAs) are natural transcripts that can act as endogenous sponges of microRNAs (miRNAs), modulating miRNA action upon target mRNAs. Circular RNAs (circRNAs) are one among the various classes of ceRNAs. They are produced from a process called back-splicing and have been identified in many eukaryotes. In plants, their effective action as a miRNA sponge was not yet demonstrated. To address this question, public mRNAseq data from Argonaute-immunoprecipitation libraries (AGO-IP) of flowers were used in association with a bioinformatics comparative multi-method to identify putative circular RNAs. A total of 27,812 circRNAs, with at least two reads at the back-splicing junction, were identified. Further analyses were used to select those circRNAs with potential miRNAs binding sites. As AGO forms a ternary complex with miRNA and target mRNA, targets count in AGO-IP and input libraries were compared, demonstrating that mRNA targets of these miRNAs are enriched in AGO-IP libraries. Through this work, five circRNAs that may function as miRNA sponges were identified and one of them were validated by PCR and sequencing. Our findings indicate that this post-transcriptional regulation can also occur in plants.
竞争性内源RNA（ceRNA）是一类天然转录本，可作为微小RNA（miRNA）的内源海绵，调节miRNA对靶mRNA的作用。环状RNA（circRNA）是ceRNA的不同类别之一。它们通过一种称为反向剪接的过程产生，并已在许多真核生物中被鉴定出来。在植物中，它们作为miRNA海绵的有效作用尚未得到证实。为了解决这个问题，我们使用了来自花朵的AGO免疫沉淀文库（AGO-IP）的公共mRNAseq数据，并结合生物信息学比较多方法来鉴定假定的环状RNA。共鉴定出27812个环状RNA，其反向剪接连接处至少有两个读数。进一步的分析用于筛选那些具有潜在miRNA结合位点的环状RNA。由于AGO与miRNA和靶mRNA形成三元复合物，因此比较了AGO-IP文库和输入文库中的靶标数量，结果表明这些miRNA的mRNA靶标在AGO-IP文库中富集。通过这项工作，鉴定出了5个可能作为miRNA海绵发挥作用的环状RNA，其中一个通过PCR和测序得到了验证。我们的研究结果表明，这种转录后调控也可能发生在植物中。
