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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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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]
Total Authors: 10
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
Total Affiliations: 7
Document type: Journal article
Source: SCIENTIFIC REPORTS; v. 8, MAY 29 2018.
Web of Science Citations: 3
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: 15/16661-1 - Sex and B chromosome enigmas: model systems for the study of chromosome and genome evolution
Grantee:César Martins
Support type: Research Projects - Thematic Grants
FAPESP's process: 12/13450-1 - Large scale exploratory analysis of Nile Tilapia's miRNA expression using bioinformatics tools
Grantee:Luiz Augusto Bovolenta
Support type: 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 type: Regular Research Grants
FAPESP's process: 15/19176-7 - Discovering variations and functions from non-coding Small RNAs in Oreochromis niloticus
Grantee:Luiz Augusto Bovolenta
Support type: 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 type: 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 type: Scholarships in Brazil - Doctorate