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

• Grant number: 12/13450-1
• Support Opportunities: Scholarships in Brazil - Doctorate
• Effective date (Start): October 01, 2012
• Effective date (End): December 31, 2016
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Ney Lemke
• Grantee: Luiz Augusto Bovolenta
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Associated scholarship(s): 15/19176-7 - Discovering variations and functions from non-coding Small RNAs in Oreochromis niloticus, BE.EP.DR

Abstract

MicroRNAs (miRNAs) are small RNA molecules (~20 nucleotides) that post-transcriptionally regulate the expression of endogenous 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 somewhat restricted to a few species and only a fraction of the predicted miRNAs targets has been functionally characterized. In this sense, the use of next generation sequencing technology coupled with gene expression analysis by RT-qPCR enable both the identification of the microRNome and the experimental validation of miRNA gene targets in a species. The Nile Tilapia, Oreochromis niloticus, can be considered an excellent biological model for miRNAs investigation in vertebrates due to its economic importance and fully sequenced genome. To produce a functional annotation of the tilapia microRNome, this project aims to (i) organize the sequence data of expressed miRNAs, (ii) develop an open-access database of Nile tilapia miRNAs, (iii) integrate information of this database with other relevant databases, (iv) create hypotheses about physiologically relevant actions of these miRNAs by analyzing the miRNAs clusters induced by their similar expression profiles in different types of tissue (white muscle, red muscle, gonads, brain etc..) and different stages of development, (v) predict the miRNAs targets, and finally, (vi) determine the chromosomal location of expressed miRNAs on the 22 chromosomes of tilapia in order to build genomic maps of microRNA genes.

Scientific publications

(6)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

PINHAL, DANILLO; BOVOLENTA, LUIZ A.; MOXON, SIMON; OLIVEIRA, ARTHUR C.; NACHTIGALL, PEDRO G.; ACENCIO, MARCIO L.; PATTON, JAMES G.; HILSDORF, ALEXANDRE W. S.; LEMKE, NEY; MARTINS, CESAR. Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. SCIENTIFIC REPORTS, v. 8, MAY 29 2018. (12/13450-1, 12/15589-7, 15/16661-1, 15/19176-7, 11/06465-0, 13/06864-7)

OLIVEIRA, ARTHUR C.; BOVOLENTA, LUIZ A.; NACHTIGALL, PEDRO G.; HERKENHOFF, MARCOS E.; LEMKE, NEY; PINHAL, DANILLO. Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses. FRONTIERS IN GENETICS, v. 8, MAY 16 2017. (14/03062-0, 13/06864-7, 12/13450-1, 15/19176-7)

ACENCIO, MARCIO LUIS; BOVOLENTA, LUIZ AUGUSTO; CAMILO, ESTHER; LEMKE, NEY. Prediction of Oncogenic Interactions and Cancer-Related Signaling Networks Based on Network Topology. PLoS One, v. 8, n. 10, OCT 25 2013. (13/02018-4, 12/00741-8, 10/20684-3, 12/13450-1)

OLIVEIRA, UR C.; BOVOLENTA, LUIZ A.; ALVES, LUCAS; FIGUEIREDO, LUCAS; RIBEIRO, AMANDA O.; CAMPOS, VINICIUS E.; LEMKE, NEY; PINHAL, DANILLO. Understanding the Modus Operandi of MicroRNA Regulatory Clusters. CELLS, v. 8, n. 9, SEP 2019. (18/05484-0, 18/26409-6, 12/13450-1, 12/15589-7, 15/19176-7, 17/17510-2)

BOVOLENTA, LUIZ AUGUSTO; PINHAL, DANILLO; ACENCIO, MARCIO LUIS; DE OLIVEIRA, ARTHUR CASULLI; MOXON, SIMON; MARTINS, CESAR; LEMKE, NEY. miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data. CELLS, v. 9, n. 8, AUG 2020. (10/20684-3, 12/13450-1, 12/15589-7, 14/08420-1, 15/19176-7, 11/06465-0, 13/03644-6)

CAMILO, ESTHER; BOVOLENTA, LUIZ A.; ACENCIO, MARCIO L.; RYBARCZYK-FILHO, JOSE L.; CASTRO, MAURO A. A.; MOREIRA, JOSE C. F.; LEMKE, NEY. GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks. Bioinformatics, v. 29, n. 19, p. 2505-2506, OCT 1 2013. (13/02018-4, 12/00741-8, 10/20684-3, 12/13450-1)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

BOVOLENTA, Luiz Augusto. Large scale exploratory analysis of Nile tilapia's miRNA expression using bioinformatics tools. 2016. Doctoral Thesis - Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu Botucatu.