ArticlePloS one2013
Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- High cholesterol intake remodels cholesterol turnover and energy homeostasis in Nile tilapia (Marine life science & technology · 2023Article
- Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome forBiology · 2022Article
- Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon.BMC genomics · 2017Article
- In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data.Genomics data · 2016Article
- Article
- Expression of microRNA‑26b and identification of its target gene EphA2 in pituitary tissues in Yanbian cattle.Molecular medicine reports · 2015Article
- A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2015Review
- Identification and analysis of genetic variations in pri-miRNAs expressed specifically or at a high level in sheep skeletal muscle.PloS one · 2015Article
- Validation of miRNA genes suitable as reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar).BMC research notes · 2014Article
- MicroRNA in teleost fish.Genome biology and evolution · 2014Review
- Differential expression profiling of spleen microRNAs in response to two distinct type II interferons in Tetraodon nigroviridis.PloS one · 2014Article
- Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus.PloS one · 2014Article
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4 authors.
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Abstract
backgroundmicroRNAs (miRNAs) are implicated in regulation of many cellular processes. miRNAs are processed to their mature functional form in a step-wise manner by multiple proteins and cofactors in the nucleus and cytoplasm. Many miRNAs are conserved across vertebrates. Mature miRNAs have recently been characterized in Atlantic halibut (Hippoglossus hippoglossus L.). The aim of this study was to identify and characterize precursor miRNA (pre-miRNAs) and miRNA targets in this non-model flatfish. Discovery of miRNA precursor forms and targets in non-model organisms is difficult because of limited source information available. Therefore, we have developed a methodology to overcome this limitation.
methodsGenomic DNA and small transcriptome of Atlantic halibut were sequenced using Roche 454 pyrosequencing and SOLiD next generation sequencing (NGS), respectively. Identified pre- miRNAs were further validated with reverse-transcription PCR. miRNA targets were identified using miRanda and RNAhybrid target prediction tools using sequences from public databases. Some of miRNA targets were also identified using RACE-PCR. miRNA binding sites were validated with luciferase assay using the RTS34st cell line.
resultsWe obtained more than 1.3 M and 92 M sequence reads from 454 genomic DNA sequencing and SOLiD small RNA sequencing, respectively. We identified 34 known and 9 novel pre-miRNAs. We predicted a number of miRNA target genes involved in various biological pathways. miR-24 binding to kisspeptin 1 receptor-2 (kiss1-r2) was confirmed using luciferase assay.
conclusionThis study demonstrates that identification of conserved and novel pre-miRNAs in a non-model vertebrate lacking substantial genomic resources can be performed by combining different next generation sequencing technologies. Our results indicate a wide conservation of miRNA precursors and involvement of miRNA in multiple regulatory pathways, and provide resources for further research on miRNA in non-model animals.
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