MicroRNA roles and their potential use as selection tool to cold tolerance of domesticated teleostean species: A systematic review

Blödorn, Eduardo B.; Domingues, William Borges; Nunes, Leandro S.; Komninou, Eliza Rossi; Pinhal, Danillo; Campos, Vinicius F.

doi:10.1016/j.aquaculture.2021.736747

Cited by 14 publications

(10 citation statements)

References 75 publications

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“…In the gonads, it was detected in mature sharpsnout seabream (Diplodus puntazzo) but not in the marine medaka [95,98]. Strikingly, miRNA122 was reported to be sensitive to cold temperatures in the Senegalese sole (Solea senegalensis) [24,99], thus the role of this miRNA as a thermal recorder is worth further exploring. Regarding miR-146b in humans, it plays a role in the innate immune response [100] and is involved in gliomas and ovarian cancers [101,102].…”

Section: Discussionmentioning

confidence: 99%

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

Gelderen

Montfort

Álvarez‐Dios

et al. 2021

Preprint

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MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression in a wide variety of physiological processes, including those related to the reproductive system. Although in the last decade a plethora of miRNAs has been reported, the miRNA alterations occurred by environmental cues and their biological functions have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation (18-32 days post fertilization, dpf), a treatment that results in male-skewed sex ratios. Once the fish reached adulthood (90 dpf), ovaries and testes were sequenced by high-throughput technologies. About 101 million high-quality reads were obtained from gonadal samples. Analyses of the expression levels of the miRNAs identified a total of 23 and 1 differentially expressed (DE) miRNAs in ovaries and testes, respectively, two months after the heat treatment. Most of the identified miRNAs were involved in human sex-related cancer. After retrieving 3’ UTR regions, ~400 predicted targets of the 24 DE miRNAs were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of them, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the predicted sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected miRNAs (miR-122-5p and miR-146-5p) showed exclusive expression in the ovarian germ cells. The present study expands the catalog of sex-specific miRNAs and deciphers, for the first time, thermosensitive miRNAs in the zebrafish gonads that might be used as potential epimarkers to predict environmental past events.

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Section: Discussionmentioning

confidence: 99%

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

Gelderen

Montfort

Álvarez‐Dios

et al. 2021

Preprint

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“…In 2015, MirGeneDB was created and covers a breadth of metazoan species, but this database provides miRNA annotation for only one fish species, zebrafish ( Fromm et al 2020 ). miRNAs, however, are of great interest in fish research with studies ranging from genomic evolution ( Xiong et al 2019 ; Desvignes et al 2021 ), development ( Giraldez et al 2006 ; Kasper et al 2017 ; Gay et al 2018 ), medical models ( Hsu et al 2017 ), aquaculture ( Herkenhoff et al 2018 ; Blödorn et al 2021 ; Cardona et al 2021 ), pathology ( Andreassen and Høyheim 2017 ; Wang et al 2018 ), toxicology ( Goodale et al 2019 ; Ahkin Chin Tai and Freeman 2020 ), to adaptation, and speciation ( Franchini et al 2019 ; Kelley et al 2021 ). In most fish miRNA studies, the lack of consistent annotation resources leads to using, by default, combinations of annotations existing in other, often distantly related species, or to de novo prediction of miRNAs using different algorithms in different research groups, leading to inconsistent results among species.…”

Section: Introductionmentioning

confidence: 99%

FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes

Desvignes

Bardou

Montfort

et al. 2022

Molecular Biology and Evolution

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microRNAs are important post-transcriptional regulators of gene expression involved in countless biological processes and are widely studied across metazoans. While miRNA research continues to grow, the large community of fish miRNA researchers lacks exhaustive resources consistent among species. To fill this gap, we developed FishmiRNA, an evolutionarily supported microRNA annotation and expression database for ray-finned fishes: www.fishmirna.org. The self-explanatory database contains detailed, manually-curated miRNA annotations with orthology relationships rigorously established by sequence similarity and conserved syntenies, and expression data provided for each detected mature miRNA. In just few clicks, users can download the annotation and expression database in several convenient formats either in its entirety or a subset. Simple filters and BLAST search options also permit the simultaneous exploration and visual comparison of expression data for up to any ten mature miRNAs across species and organs. FishmiRNA was specifically designed for ease of use to reach a wide audience.

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“…Thus, resolving cold-tolerance mechanisms can help improve cold-tolerance of fish and decrease winter-time aquaculture costs. Many studies have been conducted recently that primarily focus on polar (Chen et al, 2008;Coppe et al, 2013;Todgham et al, 2017;Blödorn et al, 2021) and model fish (Yang et al, 2011;Hu et al, 2016;Nitzan et al, 2019). In contrast, much less is known about other Schizothoracine fish species (Tong et al, 2017ab;Tong et al, 2017ab Zhou et al, 2020Yang et al, 2021), thus confounding an understanding of their cold responses and cold adaptation metabolisms have developed a series of adaptation mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Insights Into miRNA-mRNA Regulatory Mechanisms of Cold Adaptation in Gymnocypris eckloni: Ubiquitin-Mediated Proteolysis Is Pivotal for Adaptive Energy Metabolism

Nie

Wang

et al. 2022

Front. Genet.

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This study aimed to understand cold stress adaptations mechanism in fish. Thus, the transcriptional response to cold conditions in Gymnocypris eckloni was evaluated using RNA-seq and microRNA (miRNA)-seq analyses. Low-temperature (LT) group G. eckloni was cultivated outdoors in waters cooled to 2–4°C for 3 weeks, while individuals in the control temperature (CT) group were exposed to 14–16°C. Significantly different responses were observed in both mRNA and miRNA expression profiles, with more mRNAs (1,833 and 1,869 mRNAs were up- and downregulated, respectively) and fewer miRNAs (15 and 6 were up- and downregulated, respectively) observed in the LT group individuals relative to the CT group individuals. A miRNA-mRNA network involved in the regulation of G. eckloni responses to cold stress was constructed; this network included ubiquitin-mediated proteolysis, protein processing, and oxidative phosphorylation. These results provided new insights into mechanisms of cold tolerance by fish, including decreased metabolic activity in addition to proteolysis.

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MicroRNA roles and their potential use as selection tool to cold tolerance of domesticated teleostean species: A systematic review

Cited by 14 publications

References 75 publications

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes

Insights Into miRNA-mRNA Regulatory Mechanisms of Cold Adaptation in Gymnocypris eckloni: Ubiquitin-Mediated Proteolysis Is Pivotal for Adaptive Energy Metabolism

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