ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA

Hu, Xiang; Chen, Wen; Li, Jing; Huang, Shulan; Xu, Xuling; Zhang, Xuan; Xiang, Sheng; Liu, Changning

doi:10.1093/database/bay114

Cited by 35 publications

(39 citation statements)

References 45 publications

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“…The ZFLNC database is the most comprehensive database of zebrafish lncRNAs to date. The data consists of resources from NCBI, ENSEMBL, NONCODE, zflncRNApedia, and literature [17]. Thus, the transcripts without a BLAST hit against the ZFLNC data were considered as “novel”.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, the RepeatMasker tool was utilized to identify the sequences with repetitive regions, and those transcripts were excluded. The total lncRNAs obtained were matched against the lncRNAs from the ZFLNC database [17] using BLASTN (coverage ≥ 55% and E value ≤ 1e −5 ), and those without a match were deemed as candidate novel lncRNAs in zebrafish brain regions. Multiple lncRNAs located in intronic regions of a single gene were also discarded to produce final list of novel lncRNA transcripts.…”

Section: Methodsmentioning

confidence: 99%

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Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Banerjee

Koner

Karasik

et al. 2020

Preprint

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Long non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer's disease (AD). However, no data are available on the roles of lncRNAs and their target genes under hypoxia in the zebrafish brain. From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified 8114, 7775, and 7816 novel lncRNA transcripts in the Fb, Mb, and Hb regions, respectively. In comparison to the normoxic group, hypoxic fish showed differential expression of 357, 553, and 786 novel lncRNA genes in the Fb, Mb, and Hb regions, respectively. Co-expression network analysis identified a series of lncRNA-mRNA pairs in all the regions, which were enriched for AD. In conclusion, functional annotation of lncRNAs induced by hypoxia provided knowledge on potential regulators for genes participating in AD pathogenesis.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Banerjee

Koner

Karasik

et al. 2020

Preprint

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“…Thus far, only lncRNA THOR has been reported to have an oncogenic role in tumorigenesis via a zebrafish model [17]. However, the homologies of most human lncRNAs cannot be found in zebrafish, which limits the application of zebrafish genetic models for tumor-related lncRNA research [18]. Zebrafish xenograft models offer the in vivo conditions of human cancer cells and do not have such restrictions, which prompts us to explore whether such models can be used to study the roles of human lncRNAs in cancer.…”

Section: Bioinformaticsmentioning

confidence: 99%

Zebrafish xenograft model of human lung cancer for studying the function of LINC00152 in cell proliferation and invasion

Shen

Sun

et al. 2020

Cancer Cell Int

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Background: Numerous studies have shown that long noncoding RNAs play important roles in human cancer progression. Although zebrafish xenografts have recently become a novel in vivo model for human cancer research, whether such models can be used to study the function of long noncoding RNAs remains unknown. Methods: In vitro studies validated the roles of LINC00152 in the proliferation and invasion of lung cancer cells. In vivo studies of zebrafish xenografts also confirmed these roles of LINC00152. In vivo confocal imaging was used to more accurately evaluate the function of LINC00152 in cell proliferation and migration. Pharmacological experiments were further performed to study the potential ability of LINC00152 downregulation combined with an EGFR inhibitor to treat tumors in cultured cells and the zebrafish xenograft model. Results: Silencing of LINC00152 suppressed cell proliferation and invasion in SPCA1 and A549 lung cancer cell lines in vitro. In the zebrafish xenograft model, knockdown of LINC00152 reduced the proliferation and migration of lung cancer cells, as indicated by the two imaging methods at different magnifications. Moreover, the knockdown of LINC00152 enhanced the inhibition effect of afatinib for lung cancer progression in cultured cells and the zebrafish xenograft model. Conclusion: Our study reveals the oncogenic roles and potential for LINC00152 to be a target for tumor treatment in lung cancer using zebrafish xenograft models, and the findings suggest that this model could be used for functional and application studies of human long noncoding RNAs in tumor biology.

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“…Finally, the protein-protein interaction network and the regulatory network of lncRNAs-mRNA were established via Cytoscape software (http://www.cytoscape.org/) [41]. We used the ZFLNC database to conduct a conservative analysis of lncRNA [46].…”

Section: Protein-protein Interaction Network and Lncrna-gene Co-exprementioning

confidence: 99%

Transcriptome profiling analysis of sex-based differentially expressed mRNAs and lncRNAs in the brains of mature zebrafish (Danio rerio)

Yuan

Jiang

Sun

et al. 2019

Preprint

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Background: Similar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the brain of male and female zebrafish are lacking. Results: In this study, the mRNA and lncRNAs expression profiles were obtained from the brain tissue samples of the three male and three female zebrafish by high-throughput transcriptome sequencing. We identified a total of 108 mRNAs and 50 lncRNAs with sex-based differential expression. We randomly selected four differentially expressed genes for RT-qPCR verification and the results certified that the expression pattern showed a similar trend between RNA-seq and RT-qPCR results. Protein-protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to obtain the biological significance of differentially expressed mRNA in the brain dimorphism of zebrafish. Finally, a Pearson correlation analysis was performed to construct the co-expression network of the mRNAs and lncRNAs. Conclusions: We found that 12 new lncRNAs not only have significant gender specificity in the brain of zebrafish, and this finding may provide a clue to further study of the functional difference between male and female zebrafish brain.

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ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA

Cited by 35 publications

References 45 publications

Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Zebrafish xenograft model of human lung cancer for studying the function of LINC00152 in cell proliferation and invasion

Transcriptome profiling analysis of sex-based differentially expressed mRNAs and lncRNAs in the brains of mature zebrafish (Danio rerio)

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