Bioinformatic prediction of microRNAs and their target genes in maize

Abstract

MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Identification of miRNAs and their target genes is essential to understand the regulation network of miRNAs in gene expression. With the method of bioinformatic computation, we used previously deposited miRNA sequences from Arabidopsis, rice, and other plant species to blast the databases of maize expressed sequence tags and genomic survey sequence that do not correspond to protein coding genes. A total of 11 novel miRNAs were identified from maize following a range of filtering criteria. All the potential miRNA precursors can be folded into the typical secondary structure of miRNA family, despite of variation in length and structure. Using these miRNAs sequences, we further blasted the databases of maize mRNAs and identified 26 target genes for seven of the eleven newly identified miRNAs. These genes encode twenty-six proteins involved in metabolism, signal transduction, transcriptional regulation, transmembrane transport, biostress, and abiostress responses, as well as chloroplast assembly. The identification of these novel miRNAs is a useful complement to the maize miRNA database.