Identify intronic microRNA with bioinformatics.

Chih-Hao Kuo, Mark D Goldberg, Shi-Lung Lin, Shao-Yao Ying, Jiang F Zhong

Department of Cell and Neurobiology, University of Southern California, Los Angeles, CA, USA.

Methods in molecular biology (Clifton, N.J.) 2013

filter terms:

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 identified 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 difficult. The cell type and developmental-specific expression of miRNA make the experimental approach even more difficult. 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 specific introns. Intronic miRNA may directly regulate the expression of its target genes during development. The reported bioinformatics approach not only identifies 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.

Citation

Chih-Hao Kuo, Mark D Goldberg, Shi-Lung Lin, Shao-Yao Ying, Jiang F Zhong. Identify intronic microRNA with bioinformatics. Methods in molecular biology (Clifton, N.J.). 2013;936:77-82