Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells

Ji, Xiangqin; Jiang, Penglei; Luo, Juntao; Li, Mengjia; Bai, Yajing; Zhang, Junfang; Han, Bingshe

doi:10.1371/journal.pone.0226905

Cited by 14 publications

(8 citation statements)

References 52 publications

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“…1 b). This feature was incredibly different from those of model organisms, which generally have demonstrated a peak at ~ 22 nt dominated by miRNAs in both the total and unique reads [ 29 – 31 ] and suggests that the composition of small RNAs in T. vaginalis might be divergent.…”

Section: Resultsmentioning

confidence: 74%

Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis

et al. 2021

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Background Small non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis, the causative agent of human sexually transmitted trichomoniasis, still remain to be determined. Methods Small RNA transcriptomes from Trichomonas trophozoites were deep sequenced using the Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs). The tsRNA candidates were confirmed by stem-loop quantitative reverse transcription-PCR, and motifs to guide the cleavage of tsRNAs were predicted using the GLAM2 algorithm. Results The miRNAs were found to be present in T. vaginalis but at an extremely low abundance (0.0046%). Three categories of endogenous Trichomonas tsRNAs were identified, namely 5′tritsRNAs, mid-tritsRNAs and 3′tritsRNAs, with the 5′tritsRNAs constituting the dominant category (67.63%) of tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRNA-derived fragments (tRFs) and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in the non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. The results prove the expression of tRFs and tRNA-halves in the T. vaginalis transcriptome. Conclusions This is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was barely detected. These results may promote further research aimed at gaining a better understanding of the evolution of small non-coding RNA in T. vaginalis and their functions in the pathogenesis of trichomoniasis.

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Section: Resultsmentioning

confidence: 74%

Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis

et al. 2021

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“…Some studies have addressed the temperature effects on different target tissues. miRNA expression changed in response to increasing natural temperatures in zebrafish embryonic fibroblast cells 19 and in rainbow trout liver 20 and head kidney 21 . Cold tolerance has been tested by detailing miRNA expression in Emerald rockcod ( Trematomus bernacchii ) gills 22 , in turbot ( Scophthalmus maximus ) brain, head kidney and liver 23 , and in sole ( Solea senegalensis ) embryos 24 .…”

Section: Introductionmentioning

confidence: 99%

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

Gelderen

Montfort

Álvarez‐Dios

et al. 2022

Sci Rep

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In the last decade, a plethora of microRNAs (miRNAs) has been reported in a wide variety of physiological processes, including reproduction, in many aquatic organisms. However, miRNAome alterations occurred by environmental cues due to water temperature increment have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, the animal model zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation, a treatment that results in male-skewed sex ratios in the adulthood. Once the fish reached adulthood, gonads were sequenced by high-throughput technologies and a total of 23 and 1 differentially expressed miRNAs in ovaries and testes, respectively, were identified two months after the heat treatment. Most of these heat-recorder miRNAs were involved in human sex-related cancer and about 400 predicted-target genes were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of the predicted target genes, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected heat-recorder 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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“…As an aquatic model, it also has advantages in terms of avoiding the ethical challenges associated with sentient organisms, supporting the transition to in vitro testing. In fact, zebrafish cells, such as embryonic zebrafish cells (ZF4) and zebrafish liver (ZFL) cells, have gained popularity in past years as a potential early-stage model, mainly for the assessment of toxicological and biological responses, including translational gene expression [21], bacterial invasion [22], assessment of pharmacological chemicals [23], and impacts from polystyrene [24,25] and metallic NPs [26][27][28]. To date, only a few studies have explored the trafficking and uptake mechanisms of nanomaterials in zebrafish cells, highlighting a key knowledge gap that needs to be urgently explored [24][25][26]28].…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of Silver Nanoparticle Uptake by Embryonic Zebrafish Cells

et al. 2021

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Evaluation of the uptake pathways in cells during exposure to nanoparticles (NPs) is key for risk assessment and the development of safer nanomaterials, as the internalisation and fate of NPs is linked to their toxicity and mode of action. Here, we determined the uptake mechanisms activated during the internalisation of 10, 30, and 100 nm AgNPs by embryonic zebrafish cells (ZF4). The uptake results demonstrated an NP size- and time-dependent uptake, showing the highest total silver uptake for the smallest AgNP (10 nm) at the lowest exposure concentration (2.5 μg/mL) after 2 h, while after 24 h, the highest exposure concentration (10 μg/mL) of the 10 nm AgNPs revealed the highest cellular load at 8 pg/cell. Inhibition of the caveolae, clathrin, and macropinocytosis endocytic pathways by pharmaceutical inhibitors (genistein, chlorpromazine, and wortmannin respectively) revealed that uptake was mainly via macropinocytosis for the 10 nm AgNPs and via the caveolae-mediated pathway for the 30 and 100 nm AgNPs. The induction of autophagy was also strongly related to the NP size, showing the highest percentage of induction for the 10 nm (around 3%) compared to naive cells, suggesting that autophagy can be activated along with endocytosis to deal with exposure to NPs. TEM imaging revealed the distribution of NPs across the cytoplasm inside intracellular vesicles. An increase in Early Endosome formation (EE) was observed for the 30 and 100 nm sizes, whereas the 10 nm AgNPs disrupted the activity of EE. The data supports the establishment of adverse outcome pathways by increasing knowledge on the link between a molecular initiating event such as receptor-mediated endocytosis and an adverse outcome, as well as supporting the reduction of animal testing by using alternative testing models, such as fish cell lines.

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Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells

Cited by 14 publications

References 52 publications

Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis

Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

Mechanisms of Silver Nanoparticle Uptake by Embryonic Zebrafish Cells

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