Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
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ABSTRACT:
PROVIDER: PRJNA555064 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9697470.fastq.gz | Fastqsanger.gz | |||
| SRR9697465.fastq.gz | Fastqsanger.gz | |||
| SRR9697466.fastq.gz | Fastqsanger.gz | |||
| SRR9697467.fastq.gz | Fastqsanger.gz | |||
| SRR9697468.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNAs (miRNAs) play vital roles in various biological processes by leading to mRNA cleavage or translational repression, and are also involved in multiple stress conditions. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, high-throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28°C, 30 days) and cold-acclimation (18°C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, dre-miR-100-3p inhibitor or dre-miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. In summary, the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation.
2019-12-17 | GSE134399 | GEO
Project description:Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells
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Project description:Long non-coding RNAs (lncRNAs) are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far, no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells (ZF4) cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high-throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs, there are 347 lncRNAs up-regulated and 342 lncRNAs down-regulated in cold acclimated cells, compared with that of control cells at 28°C. Among differentially expressed lncRNAs, 74 and 61 were found only in control cells or in cold-acclimated cells, respectively. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport, cell adhesion, oxidation-reduction process, and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA, and constructed a complex interaction network. In summary, our genome-wide systematic identification and function prediction of lncRNAs in zebrafish cells, lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes.
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Project description:Experiment was designed to identify transcriptome changes during cold acclimation of Drosophila melanogaster male flies. Resistance to cold is often measured by recovery times from chill coma, which is induced almost immediately upon exposure to low but non-freezing temperatures (~0C), with flies becoming immobilised and losing motor activity. This paralysis is also ostensibly reversible upon return to normal temperatures, although again there can be longer term effects. Acclimation for increased cold resistance requires exposure periods ranging from hours or days to several weeks at low temperatures between 0C to 12C, and samples were taken during the cold acclimation period (1 hr, 2 hr, 3 hr, 6 hr, 12 hr, 24 hr, 36 hr and 48 hr).
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Project description:Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAs’ roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava.
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Project description:Ambient temperature affects organisms comprehensively, however cold responses are different among tissues. Here, we adopt a transcript screening approach to explore and compare the cold responses in zebrafish gills and brain. Zebrafish were exposed to cold and the oligonucleotide-based microarray was used to identify cold-induced genes. Principle component analysis (PCA) of the gene expression profiles indicated that gills develop different strategies for the increasing of exposure period while brain relatively remained stable. Combining statistic and clustering methods, we found that gills showed higher protein metabolism and cell activity while brain showed higher stress responses and detoxification during cold acclimation. According to the microarray data sets, we extended the study on ionocyte- and isotocin neuron-related genes in gills and brain, respectively, and found these genes were broadly stimulated by cold. These data suggest that cold activates specific physiological functions in different tissues. Taken together, our results provide molecular evidences to elucidate the cold acclimation in zebrafish gills and brain. Keywords: Time course, Tissue types
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