Large scale exploratory analysis of Nile tilapia's miRNA expression using bioinformatics tools

Author(s)

Luiz Augusto Bovolenta

• Document type: Doctoral Thesis
• Press: Botucatu. 2017-01-23.
• Institution: Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu
• Defense date: 2016-12-12
• Advisor: Ney Lemke; Danillo Pinhal; Marcio Luis Acencio

Abstract

MicroRNAs (miRNAs) are small RNA molecules that post-transcriptionally regulate the expression of genes, shaping the transcriptome and protein production. In general, miRNAs are highly conserved in the genome of eukaryotes and considered important elements in many biological processes during development, such as cell growth, differentiation and death. The large diversity of miRNAs identified is restricted to a few species and only a fraction of the predicted miRNAs targets has been functionally characterized. The use of high throughput sequencing technology coupled with gene expression analysis by RT-qPCR enable the characterization of the microRNome. The Nile tilapia, Oreochromis niloticus, can be considered an excellent biological model for miRNAs investigation in vertebrates due to its economic and evolutionary importance. To produce a functional annotation of the tilapia microRNome, this work organized the sequence data of expressed miRNAs, developed an open-access database of Nile tilapia miRNAs, integrated information of this database with other relevant databases, created hypotheses about physiologically relevant actions of these miRNAs by analyzing the miRNAs clusters induced by their similar expression profiles in six types of tissue (white muscle, red muscle, testis, ovary, liver, eye, brain and heart) and different stages of development (2, 3, 4, 5 and 10 days post-fertilization), predicted the miRNAs targets, and finally, determined the chromosomal location of expressed miRNAs on the 22 linkage groups of tilapia in order to build genomic maps of microRNA genes. We identified 271 conserved and 97 novel pre-miRNAs together with its expression profiles. Specifically, the expression values were distinguished into the 5’ and 3’ mature miRNA. We measured miRNA expression diversity along development. The highest diversity was observed at the sample of 5o day post-fertilization, which shows the importance of miRNAs in the species ontogenetic control. We also made associations between miRNA regulatory role in the ontogenic period and the evolutionary scenario. Moreover, this work highlights the diversification and exchange of expression in the mature molecule the 5’ to 3’ of miRNAs among samples, called arm-switching event, the variability of the mature sequences of miRNAs known as isomiRs, what characterizes a new regulatory complexity of the miRNA functional roles. Among the identified arm-switching events, we highlighted the mir-145 arm-switch associated with sex-biased expression in gonads. Among isomiRs, we highlighted the tissue-specific patterns of isomiRs with exchange of nucleic bases. Finally, we created the mirTil database (<http://www.lbbc.ibb.unesp.br/mirtil>), an open access database that guarantees the reproducibility of these analyses that could be also used on the investigation of other eukaryotes. (AU)

• FAPESP's process: 12/13450-1 - Large scale exploratory analysis of Nile tilapia's miRNA expression using bioinformatics tools.
• Grantee: Luiz Augusto Bovolenta
• Support Opportunities: Scholarships in Brazil - Doctorate