miRNA identification and target gene prediction in the turbot, Scophthalmus maximus

MARTIN, ANA PAULA; ÁLVAREZ-DIOS, JOSÉ A.; FERNÁNDEZ, CARLOS; SCIARA, ANDRÉS A.; PARDO, BELÉN G.; BOUZA, CARMEN; MARTÍNEZ PORTELA, PAULINO

Praga

Congreso; AQUA 2012; 2012

World Aquaculture Society and European Aquaculture Society

MicroRNAs (miRNAs) are non-coding RNA molecules of 22nts length. They are important gene regulators that downregulate gene expression at the post-transcriptional level in eukaryotes. They control a variety of critical biological processes, including early embryo development, cell proliferation, differentiation, apoptosis and metabolism. The sequence of many miRNAs is found to be conserved in their mature form even among highly divergent organisms. In addition, the evolutionary appearance of multicellular organisms appears to be correlated with the appearance of specifi miRNA pathways regulating gene expression. MiRNAs recognize specifi partially complemented sequences on their messenger RNA (mRNAs) targets and exert their activity by regulating their deadenylation, translation, and degradation. In metazoans, miRNA-target recognition site usually are in the 3? untranslated regions (3?UTR) and typically encompasses the first 2 to 7 bases of the 5? end of the microRNA, called the microRNA seed region. The localization of a target site in this region, its proximity to other sites and its local secondary structure also inflence the miRNA activity. Computational and experimental analyses indicate that, in animals, one miRNA can target many different sites on the same mRNA or on many different mRNAs. A comprehensive and reliable catalogue of miRNAs and miRNA gene targets is critical to understand the gene regulatory networks and the biological processes where they participate. Though experimental approaches have been used to identify miRNAs and their target genes, currently miRNA and target identifiation still largely relies on computational algorithms due to the low-cost effiiency of this strategy. Here, we use the existing expressed sequence tag (EST) database comprising around 70.000 unique sequences from most turbot tissues to identify miRNAs and their target genes using a bioinformatic approach. Several widely used bioinformatics tools for miRNAs and gene targets that take advantage of the unique characteristics of miRNA?mRNA interactions, experimental validation, as well as the integration of sequence-based evidence and microarray expression data were used for this purpose. A sequential bioinformatic pipeline was developed for automatic integration of this information to explore the most relevant miRNA features. Furthermore, given the importance of miRNAs in regulating gene expression, elucidating the expression of miRSNPs or miR-polymorphisms related to quantitative trait loci will help us to improve our understanding of complex traits and their application for undergoing genetic breeding programs in this species.