Analysis of miRNA transcriptome in the cardiac muscle of Nile Tilapia fish using RNA-seq and comparative genomics

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs (~ 22 nucleotides) that regulate post-transcriptionally the expression of target RNAs thus controlling protein production. In vertebrates, the involvement of miRNAs in controlling the growth, development, stress response and regeneration, among other essential processes have been demonstrated in several organs, including the heart. Moreover, the observed association between miRNAs abundance and diversity and the increased complexity of the taxonomic group became miRNAs relevant elements both for understanding the evolution of genes and regulatory mechanisms, through intraspecific genomic analyzes, as well as phylogenetic markers in comparative genomic investigations. In fish, the largest group of living vertebrates, among the ~ 30,000 known species only a small fraction was investigated regarding the miRNAs composition and expression profiles. In this project we propose the use of high-performance sequencing ("deep sequencing" or RNA-seq) analysis combined with comparative genomics aiming to determine the overall composition and genomic research organization, diversity and evolutionary dynamics of families of miRNAs expressed in the tissue heart, using as a model biological Nile tilapia (Oreochromis niloticus), which has complete genome sequenced. From these experiments, it will be possible to identify combinations of miRNAs and target mRNAs and link them to the evolution of genomes and to the regulation of specific biological processes. (AU)