ArticleScientific reports2019
miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 63 citations in OpenAlex.
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- Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.PLoS genetics · 2025Article
- Identification of sex-biased MiRNA markers informative of heat-past events.BMC genomics · 2025Article
- The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback.BMC biology · 2025Article
- Gonadal miRNomes and transcriptomes in infected fish reveal sexually dimorphic patterns of the immune response.Functional & integrative genomics · 2025Article
- A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome.G3 (Bethesda, Md.) · 2024Article
- Plasma cortisol and production of miRNAs in red drum (Sciaenops ocellatus) exposed to three distinct challenges.Fish physiology and biochemistry · 2024Article
- The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch (International journal of molecular sciences · 2023Article
- Circulating MicroRNAs Indicative of Sex and Stress in the European Seabass (Dicentrarchus labrax): Toward the Identification of New Biomarkers.Marine biotechnology (New York, N.Y.) · 2023Article
- Deciphering sex-specific miRNAs as heat-recorders in zebrafish.Scientific reports · 2022Article
- An ancient truncated duplication of the anti-Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family.Molecular ecology resources · 2022Article
- Physical Enrichment Triggers Brain Plasticity and Influences Blood Plasma Circulating miRNA in Rainbow Trout (Biology · 2022Article
- Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Effects of salinity acclimation on histological characteristics and miRNA expression profiles of scales in juvenile rainbow trout (Oncorhynchus mykiss).BMC genomics · 2022Article
- FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes.Molecular biology and evolution · 2022Article
- Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome forBiology · 2022Article
- miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies.F1000Research · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Global MicroRNA Profiling of Vascular Endothelial Cells.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Circulating miRNA repertoire as a biomarker of metabolic and reproductive states in rainbow trout.BMC biology · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
MicroRNAs (miRNAs) can have organ-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variation. It remains unclear, however, which mechanisms of miRNA production or modification are organ-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, helps quantify mature miRNAs, accounts for post-transcriptional processing, such as nucleotide editing, and identifies mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Our results provided evidence for the existence of 286 miRNA genes and 382 unique mature miRNAs (excluding mir430 gene duplicates and the vaultRNA-derived mir733), which doesn't represent a miRNAome larger than other teleost miRNomes. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, many of which are evolutionarily-conserved in the brain and heart in both species. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms may regulate post-transcriptional variations in miRNA sequence. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide changes in the seed sequence with organ specific editing rates, highest in the brain. In summary, Prost! is a new tool to identify and understand small RNAs, to help clarify a species' miRNA biology as shown here for an important model for the evolution of developmental mechanisms, and to provide insight into organ-enriched expression and the evolutionary conservation of miRNA post-transcriptional modifications.
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