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

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.

miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data

“…This data variation was explained as differences in the experimental design [24]. These results indicate that the miRNA identification method (for more details, see Pinhal and Bovolenta et al [24]) was consistent with the other studies and that the number of Nile tilapia miRNAs annotated is within those expected for Teleostei species. In addition, the miRTil database expands the repertoire of novel miRNAs.…”

“…However, putative novel miRNAs in miRTil increases this number to up to 368 miRNAs loci, a significant increase over Brawand et al, who discovered 40 putative novel miRNAs [21]. This data variation was explained as differences in the experimental design [24]. These results indicate that the miRNA identification method (for more details, see Pinhal and Bovolenta et al [24]) was consistent with the other studies and that the number of Nile tilapia miRNAs annotated is within those expected for Teleostei species.…”

“…Initially, we might choose miRNAs among 16 expression sample profiles (as described in Pinhal and Bovolenta et al [24]) by selecting the tissue or developmental stage, gender (male, female, or sex mixed, described as "pool"), and age of individuals used for the miRNA-seq ( Figure S5). In this case study, we selected "white muscle" as the sample, "male" as gender, and "Adult" (260 days) as individual age; in this example, we retrieved a total of 532 mature miRNAs expressed in male white skeletal muscle, partially represented in Figure S6.…”

“…miRNAs have been associated with economically relevant Nile tilapia traits, such as sexual differentiation [14][15][16][17], muscle growth, and disease resistance [18][19][20]. However, most of Nile tilapia-specific miRNA data is available only in textual form in biomedical literature [15][16][17][18][21][22][23][24]; therefore, scientists must use non-automated workflows to establish relationships between miRNA expression profiles and economically relevant traits. To facilitate the implementation of automated workflows and other large scale analysis, it is imperative to provide Nile tilapia-specific miRNA data in an open-access and user-friendly database.…”

Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication

“…Cytosine methylation could interact with histone modifiers or regulate miRNA to control the growth. Indeed, the importance of miRNA in growth of Nile tilapia has already been shown [68] and some miRNA features (e.g., arm-switching) can be sex-dependent in this species [69].…”