Identify Intronic MicroRNA with bioinformatics

Abstract

MicroRNAs (miRNAs) are single-strand nonprotein coding RAN with 18 to 25-nucleotides long. With complementary sequence to target messenger RNA (mRNA), miRNA regulates mRNA degradation and protein translation. miRNAs have been identi fi ed in various organisms ranging from virus to human. Increasing evidence indicates that mammalian gene regulation has multiple layers and the availability of mRNA is not the sole regulation mechanism. The evolutionally conserved miRNA may be a primary regulation mechanism of gene expression. Its role in directing embryo development and stem cell differentiation should not be underestimated. Due to the small size of miRNA, identifying it with experimental approach (e.g., direct cloning) is dif fi cult. The cell type and developmental-speci fi c expression of miRNA make the experimental approach even more dif fi cult. Consequently, bioinformatics approaches have been developed to identify novel miRNA. In human miRNA study, many studies search for the mostly complete human genomic sequence. Here, we report a rapid bioinformatics approach to mine miRNA from gene speci fi c introns. Intronic miRNA may directly regulate the expression of its target genes during development. The reported bioinformatics approach not only identi fi es the potential miRNA, but also provides the intron location of these miRNA like sequence. This information is critical for studying the gene-gene interaction via miRNA, and facilitates the study of miRNA in gene expression regulation. © Springer Science+Business Media, LLC 2013.