Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development

Author(s)

Pinhal, Danillo ^[1] ; Bovolenta, Luiz A. ^[2] ; Moxon, Simon ^[3] ; Oliveira, Arthur C. ^[1] ; Nachtigall, Pedro G. ^[1] ; Acencio, Marcio L. ^[4] ; Patton, James G. ^[5] ; Hilsdorf, Alexandre W. S. ^[6] ; Lemke, Ney ^[2] ; Martins, Cesar ^[7]

Affiliation

^[1] Sao Paulo State Univ UNESP, Inst Biosci Botucatu, Dept Genet, Botucatu, SP - Brazil

^[2] Sao Paulo State Univ UNESP, Inst Biosci Botucatu, Dept Phys & Biophys, Botucatu, SP - Brazil

^[3] UEA, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk - England

^[4] Norwegian Univ Sci & Technol NTNU, Dept Clin & Mol Med, Trondheim - Norway

^[5] Vanderbilt Univ, Stevenson Ctr, 221 Kirkland Hall, Nashville, TN 37235 - USA

^[6] Univ Mogi das Cruzes, Unit Biotechnol, Mogi Das Cruzes, SP - Brazil

^[7] Sao Paulo State Univ UNESP, Inst Biosci Botucatu, Dept Morphol, Botucatu, SP - Brazil

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 8, MAY 29 2018.
• Web of Science Citations: 4

Abstract

MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs. (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
• FAPESP's process: 12/15589-7 - Investigation of the composition, function and evolutionary dynamics of microRNAs in fish genomes using RNA-Seq and reverse genetics
• Grantee: Danillo Pinhal
• Support Opportunities: Regular Research Grants
• FAPESP's process: 15/16661-1 - Sex and B chromosome enigmas: model systems for the study of chromosome and genome evolution
• Grantee: César Martins
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 15/19176-7 - Discovering variations and functions from non-coding Small RNAs in Oreochromis niloticus
• Grantee: Luiz Augusto Bovolenta
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 11/06465-0 - Genome-wide identification and characterization of micro-RNAs in the fish Nile tilapia, Oreochromis niloticus
• Grantee: César Martins
• Support Opportunities: Regular Research Grants
• FAPESP's process: 13/06864-7 - Functional analysis of microRNAs in cardiac development of fish species by RNA-Seq and reverse genetics
• Grantee: Pedro Gabriel Nachtigall
• Support Opportunities: Scholarships in Brazil - Doctorate