A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

Yang, Liandong; He, Shunping

doi:10.1016/j.gene.2013.09.060

Cited by 12 publications

(8 citation statements)

References 69 publications

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“…However, in the identified wheat pre-miRNAs, the GC content (37.39 ± 13.47%) was significantly lower than the AU content (61.40 ± 13.56%) ( t -test, P < 1 e − 5) (Table 2; Figure 2(d)). Our results were consistent with previous findings on Asiatic cotton [52] and rainbow trout [53] where more than half of the total number of nucleotides was A or U. In this study, we also determined the A/U and C/G ratio to be 0.96 and 1.00, respectively, which suggest the presence of more U and C nucleotides in precursor sequences.…”

Section: Resultssupporting

confidence: 92%

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Kumar

Singh

Kanodia

et al. 2014

Journal of Nucleic Acids

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MicroRNAs are endogenous small noncoding RNAs which play critical roles in gene regulation. Few wheat (Triticum aestivum L.) miRNA sequences are available in miRBase repertoire and knowledge of their biological functions related to biotic stress is limited. We identified 52 miRNAs, belonging to 19 families, from next-generation transcriptome sequence data based on homology search. One wheat specific novel miRNA was identified but could not be ascribed or assigned to any known miRNA family. Differentially expressed 22 miRNAs were found between susceptible and resistant wheat near-isogenic lines inoculated with leaf rust pathogen Puccinia triticina and compared with mock inoculated controls. Most miRNAs were more upregulated in susceptible NIL compared to resistant NIL. We identified 1306 potential target genes for these 52 miRNAs with vital roles in response to stimuli, signaling, and diverse metabolic and cellular processes. Gene ontology analysis showed 66, 20, and 35 target genes to be categorized into biological process, molecular function, and cellular component, respectively. A miRNA-mediated regulatory network revealed relationships among the components of the targetome. The present study provides insight into potential miRNAs with probable roles in leaf rust pathogenesis and their target genes in wheat which establish a foundation for future studies.

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Section: Resultssupporting

confidence: 92%

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Kumar

Singh

Kanodia

et al. 2014

Journal of Nucleic Acids

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“…The genes targeted by miR-4785 and miR-6352 were predicted using TargetScan64 and miRanda65 with default parameters. For TargetScan, we used TargetScan human and TargetScan mouse to predict miR-4785 and miR-6352 targets, respectively.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

Bouchareb

Cam

Montfort

et al. 2017

Sci Rep

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MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary. Of the miRNAs exhibiting the highest overabundance in the ovary, 20 were selected for further analysis. Using a combination of QPCR and in silico analyses, we identified 8 novel miRNAs that are predominantly expressed in the ovary, including 2 miRNAs (miR-4785 and miR-6352) that exhibit strict ovarian expression. Of these 8 miRNAs, 7 were previously uncharacterized in fish. The strict ovarian expression of miR-4785 and miR-6352 suggests an important role in oogenesis and/or early development, possibly involving a maternal effect. Together, these results indicate that, similar to protein-coding genes, a significant number of ovarian-predominant miRNA genes are found in fish.

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“…Rainbow trout is a commercially important cold‐water fish in the world (Mennigen et al 2013; Yang & He 2014). miRNAs in the species were first systematically investigated in 2014 through the well‐developed comparative genome‐based homologue search, and a total of 196 potential miRNAs belonging to 124 miRNA families have been identified (Yang & He 2014). These miRNA targets have been predicted to regulate 105 pathways, including those of purine metabolism, nitrogen metabolism, oxidative phosphorylation and immune responses (Yang & He 2014).…”

Section: Mirnas Associated With Immune Responses In Teleost Fishmentioning

confidence: 99%

MicroRNA regulation of Toll‐like receptor, RIG‐I‐like receptor and Nod‐like receptor pathways in teleost fish

Chu

2020

Reviews in Aquaculture

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The innate immune system is the first‐line defence against invading pathogens, and the main molecules involved in recognizing invading pathogens are the pattern recognition receptors. Accumulating evidences have demonstrated that activation and termination of the immune responses are regulated by various layers of regulators and mechanisms. MicroRNAs (miRNAs) are a group of small non‐coding RNAs that emerged as critical component of the complex regulatory networks in fish immune responses. In this review, we have summarized miRNA regulation in teleost fish, which can provide new insights into the regulation of innate immune receptor pathways in fish. Meanwhile, we comprehensively discuss the recent researches on how teleost miRNAs respond to the signalling pathways of innate immune receptors, including Toll‐like receptors, retinoic acid‐inducible gene‐I‐like receptors and Nod‐like receptors.

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A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

Cited by 12 publications

References 69 publications

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

MicroRNA regulation of Toll‐like receptor, RIG‐I‐like receptor and Nod‐like receptor pathways in teleost fish

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