Discovering variations and functions from non-coding Small RNAs in Oreochromis niloticus

• Grant number: 15/19176-7
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Effective date (Start): October 15, 2015
• Effective date (End): March 28, 2016
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Ney Lemke
• Grantee: Luiz Augusto Bovolenta
• Supervisor: Simon Moxon
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Research place: Genome Analysis Centre, England
• Associated to the scholarship: 12/13450-1 - Large scale exploratory analysis of Nile tilapia's miRNA expression using bioinformatics tools., BP.DR

Abstract

The Nile tilapia is an important African cichlid fish with rapid adaptive radiation and valuable economic production in worldwide aquaculture, mainly in Brazilian aquaculture. Different morphological and physiological features of Nile tilapia can influence its aquacultural production, such as gender, tolerance to poor quality water and feeding behavior. Non-coding small RNAs can be key factors underlying these characteristics influencing the aquaculture of Nile tilapia. While some non-coding small RNAs types can regulate gene expression (microRNAs [miRNAs]), others can prevent the occurrence of mutations in the germ line genomes caused by harmful mobile (transposable) elements (PIWI-interacting RNAs [piRNAs]). Therefore, to understand how miRNAs and piRNAs impact the morphological and physiological aspects of adult fishes and the developmental stages of embryos is paramount to tilapia aquaculture. For these reasons, we propose in this project the construction of a large scale catalogue of miRNAs and piRNAs along with their tissue and embryonic gene expression signatures and putative functions. Regarding specifically miRNAs, we will analyze isoforms and occurrence of arm switching events. In piRNAs, we will firstly determine how to identify, classify and quantify these molecules prior to the construction of this catalogue. To achieve the above mentioned goals, we will use bioinformatics approaches such as clustering, graph-based and functional enrichment analyses. Furthermore, for identification of piRNAs we will use previously developed machine learning methods. Finally, we expect to provide a catalogue of miRNAs and piRNAs that can be used to gain insights into the influence of small RNAs on the morphological and physiological aspects of tilapia and to improve the tilapia production. (AU)

Scientific publications

(4)

(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, 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)

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)