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, such as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics researchers from Sao Paulo State University 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 were 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. The researchers 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, these 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.



Genome organization of miRNAs genes in Nile tilapia genome. Black: known miRNAs. Red: novel miRNAs described in current study. Green: novel miRNAs described previously by Huang et al.36 and Yan et al.40; MiRNAs in brackets: clustered miRNAs.


D. Pinhal, L. A. Bovolenta, S. Moxon, A. C. Oliveira, P. G. Nachtigall, M. L. Acencio, J. G. Patton, A. W. S. Hilsdorf, N. Lemke, C. Martins (2018) Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased arm switching and increasing complexity of expression throughout development Scientific Reports volume 8, Article number: 8248 [article]

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