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首页> 外文期刊>Journal of structural and functional genomics >Computational identification of microRNAs and their targets from the expressed sequence tags of horsegram (Macrotyloma uniflorum (Lam.) Verdc.)
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Computational identification of microRNAs and their targets from the expressed sequence tags of horsegram (Macrotyloma uniflorum (Lam.) Verdc.)

机译：从horsgram（Macrotyloma uniflorum（Lam。）Verdc。）的表达序列标签中对microRNA及其靶标进行计算鉴定。

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摘要

MicroRNAs (miRNAs) are a class of naturally occurring and small non-coding RNA molecules of about 21–25 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. To predict new miRNAs in plants different computational approaches have been developed. In the present study, an EST based approach has been used to identify novel miRNAs in horsegram. Identification of miRNAs was initiated by mining the EST database available at NCBI. Total of 989 ESTs were obtained for the identification of miRNAs. These ESTs were subjected to CAP3 assembly to remove the redundancy. This resulted in an output of 72 contigs and 606 singletons as non redundant datasets. The miRNAs were then predicted by using miRNA-finder. A total of eight potential miRNAs were predicted and named as hor-miR1 to hor-miR8. None of identified miRNAs showed significant homology with the previously reported in plants and therefore should be considered novel. These miRNAs were inputted to miRU2 program to predict their targets. The target mRNAs for these miRNAs mainly belong to zinc finger, chromosome condensation, protein kinase, abscisic acid-responsive, calcineurin-like phosphoesterase, disease resistance and transcriptional factor family proteins. These targets appeared to be involved in plant growth and development and environmental stress responses.
机译：MicroRNA（miRNA）是一类天然的小非编码RNA分子，长度约为21–25个核苷酸。它们的主要功能是以不同方式下调基因表达，例如翻译抑制，mRNA切割和表观遗传修饰。为了预测植物中的新miRNA，已经开发了不同的计算方法。在本研究中，基于EST的方法已被用于识别马图中的新型miRNA。通过挖掘NCBI提供的EST数据库来启动miRNA的鉴定。总共获得989个EST来鉴定miRNA。这些EST经过CAP3组装以消除冗余。这导致输出72个重叠群和606个单例作为非冗余数据集。然后使用miRNA-finder预测miRNA。预测了总共八个潜在的miRNA，并将其命名为hor-miR1至hor-miR8。没有鉴定出的miRNA与先前报道的植物具有显着同源性，因此应被认为是新颖的。这些miRNA被输入到miRU2程序中以预测其靶标。这些miRNA的靶mRNA主要属于锌指，染色体缩合，蛋白激酶，脱落酸应答，钙调磷酸酶样磷酸酯酶，抗病性和转录因子家族蛋白。这些目标似乎与植物的生长发育和环境胁迫响应有关。

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