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Computational Identification of Novel MicroRNAs and Their Targets in Vigna unguiculata

DOI: 10.1155/2010/128297

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Abstract:

MicroRNAs (miRNAs) are a class of endogenous, noncoding, short RNAs directly involved in regulating gene expression at the posttranscriptional level. High conservation of miRNAs in plant provides the foundation for identification of new miRNAs in other plant species through homology alignment. Here, previous known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS) databases of Vigna unguiculata, and according to a series of filtering criteria, a total of 47 miRNAs belonging to 13 miRNA families were identified, and 30 potential target genes of them were subsequently predicted, most of which seemed to encode transcription factors or enzymes participating in regulation of development, growth, metabolism, and other physiological processes. Overall, our findings lay the foundation for further researches of miRNAs function in Vigna unguiculata. 1. Introduction MicroRNAs (miRNAs) are a class of endogenous, small, noncoding, single-stranded RNAs that act as posttranscriptional regulators in eukaryotes [1]. They have been reported to be located mostly within noncoding regions of genomes, and usually transcribed from RNA polymerase II promoters [2, 3]. The generation of mature miRNA is a complicated enzyme-catalyzed process, from the initial transcript pri-miRNA to the precursor (pre-miRNA) with a characteristic hairpin structure, then a miRNA duplex (miRNA?:?miRNA*) [4]. In the end, it is assembled to the RNA-induced silencing complex (RISC) to direct its activity on a target mRNA, depending on the degree of base-pairing between the miRNA and the responsive element and results in either cleavage or translational repression of the target mRNA. Perfect complementarity generally results in cleavage, such as in plants, whereas imperfect base-pairing leads to translational repression [4, 5]. MiRNA genes represent about 1%-2% of the known eukaryotic genomes and constitute an important class of fine-tuning regulators that are involved in several physiological or disease-associated cellular processes [6]. For example, studies in plants have revealed the key roles of miRNAs in diverse regulatory pathways, including growth, development, and defense response against every sort of stress [7–17]. Considering the importance of miRNAs in gene regulation, two major categories of approaches have been applied for miRNA investigation [1]. Compared to the experimental approaches, computation (bioinformatics) methods have been proved to be faster, more affordable, and more effective, contributing mostly to today’s plentiful storage

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