Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish

Yang, Liandong; Irwin, David M.; He, Shunping

doi:10.1016/j.gene.2015.02.055

Cited by 8 publications

(5 citation statements)

References 78 publications

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“…We suggested that this may because the incomplete annotation of teleost genomes. Moreover, we identified 15 teleost-specific miRNAs, in consistent with recent studies [ 40 , 41 ]. For instance, miR-722 identified by our and others, was confirmed to function in immune system development and immune response [ 41 ].…”

Section: Discussionsupporting

confidence: 89%

“…The miRNA showed higher level of conservation than protein-coding sequence, which had been confirmed by previous studies [ 20 , 31 , 40 , 42 ]. There are two important implications in this study.…”

Section: Discussionsupporting

confidence: 84%

“…In general, abundant miRNAs play fundamental and broader regulatory functions [ 32 , 40 , 45 ]. We did not identify many highest expressed miRNAs and only 85 miRNAs occurred (over 10,000 read counts).…”

Section: Discussionmentioning

confidence: 99%

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The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

et al. 2017

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Tibetan naked carp Gymnocypris przewalskii is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in G. przewalskii, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of G. przewalskii to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionsupporting

confidence: 84%

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The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

et al. 2017

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“…The 3′ UTR sequences derived in this study represented only 17 % of the Atlantic cod genes ( 40 ) . The analysis of teleost-specific miRNA generated 155·32 targets/miRNA on average ( 41 ) , whereas in this study the average number of targets for differentially expressed miRNA was 53·25 with a minimum of 12 and a maximum of 112/miRNA (online Supplementary Table S3). Aside from the incomplete set of 3′ UTR used, low number of significantly enriched pathways could result from diverse roles of differentially expressed miRNA in various biological pathways and/or functional redundancy of miRNA.…”

Section: Discussionmentioning

confidence: 62%

First feed affects the expressions of microRNA and their targets in Atlantic cod

et al. 2016

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To our knowledge, there is no report on microRNA (miRNA) expression and their target analysis in relation to the type of the first feed and its effect on the further growth of fish. Atlantic cod (Gadus morhua) larvae have better growth and development performance when fed natural zooplankton as a start-feed, as compared with those fed typical aquaculture start-feeds. In our experiment, two groups of Atlantic cod larvae were fed reference feed (zooplankton, mostly copepods, filtered from a seawater pond) v. aquaculture feeds: enriched rotifers (Brachionus sp.) and later brine shrimp (Artemia salina). We examined the miRNA expressions of six defined developmental stages as determined and standardised by body length from first feeding for both diet groups. We found eight miRNA (miR-9, miR-19a, miR-130b, miR-146, miR-181a, miR-192, miR-206 and miR-11240) differentially expressed between the two feeding groups in at least one developmental stage. We verified the next-generation sequencing data using real-time RT-PCR. We found 397 putative targets (mRNA) to the differentially expressed miRNA; eighteen of these mRNA showed differential expression in at least one stage. The patterns of differentially expressed miRNA and their putative target mRNA were mostly inverse, but sometimes also concurrent. The predicted miRNA targets were involved in different pathways, including metabolic, phototransduction and signalling pathways. The results of this study provide new nutrigenomic information on the potential role of miRNA in mediating nutritional effects on growth during the start-feeding period in fish larvae.

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“…By targeting mRNAs, miRNAs regulate more than 60% of human protein-coding genes (He and Hannon 2004). This group of new regulatory molecules has a conservative function in vertebrates, and the gene regulatory mechanism has also been illustrated in teleosts (Tanzer and Stadler 2004;Wienholds et al 2005;Yang et al 2015).…”

Section: Introductionmentioning

confidence: 99%

MicroRNA Alternations in the Testes Related to the Sterility of Triploid Fish

Tao

Zhou

et al. 2018

Mar Biotechnol

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The knowledge of understanding the molecular traits of the sterile triploid fish is sparse. Herein, we analyzed the microRNA (miRNA) alternations in the testes of the sterile triploid fish produced by crossing the tetraploid fish with the diploid fish, compared with those of tetraploids and diploids used as the controls. A total of 136, 134, and 142 conserved miRNAs and 105, 112, and 119 novel miRNAs were identified in the diploid, triploid, and tetraploid fish, respectively. The genes targeted by the differentially expressed miRNAs were identified and were enriched in the GO term cell surface receptor signaling pathway, cellular process, G-protein coupled receptor signaling pathway, and metabolic process. KEGG pathway enrichment was also assessed to evaluate the target genes with differentially expressed miRNAs and these genes were enriched in four pathways (synthesis and degradation of ketone bodies, pentose and glucuronate interconversions, cyanoamino acid metabolic process, and ascorbate and aldarate metabolism). Nine differentially expressed miRNAs were verified by quantitative real-time PCR analysis (qPCR). The upregulated miRNAs in triploids, including miR-101a, miR-199-5p, miR-214, miR-222, and miR-193a, showed the same results with high-throughput sequencing. Among the selected downregulated miRNAs, miR-7b and miR-153b had significantly lower expression levels in triploids. Dnah3 and Tekt1 genes targeted by miR-199-5p showed lower expression in triploids by qPCR. These verified differentially expressed miRNAs may participate in testicular development and sperm activity by targeting functional genes, which were identified with differential expression in the triploid. This evidence provides insights into the epigenetic regulatory mechanisms of sterility in triploid cyprinids.

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Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish

Cited by 8 publications

References 78 publications

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

First feed affects the expressions of microRNA and their targets in Atlantic cod

MicroRNA Alternations in the Testes Related to the Sterility of Triploid Fish

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