An estimate of the total number of true human miRNAs.
Julia Alles,Tobias Fehlmann,Ulrike Fischer,Christina Backes,Galata,Marie Minet,Martin Hart,Masood Abu-Halima,Friedrich A. Grässer,Hans-Peter Lenhof,Andreas Keller,Eckart Meese +11 more
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TLDR
The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNA candidates, 1115 of which are currently annotated in miRBase V22.Abstract:
While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.read more
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MicroRNAs: Target Recognition and Regulatory Functions
TL;DR: In this article, a review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
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MirGeneDB 2.0: the metazoan microRNA complement
Bastian Fromm,Bastian Fromm,Diana Domanska,Eirik Høye,Eirik Høye,Vladimir Ovchinnikov,Vladimir Ovchinnikov,Wenjing Kang,Ernesto Aparicio-Puerta,Morten Johansen,Kjersti Flatmark,Kjersti Flatmark,Anthony Mathelier,Anthony Mathelier,Eivind Hovig,Eivind Hovig,Michael Hackenberg,Marc R. Friedländer,Kevin J. Peterson +18 more
TL;DR: This work extensively expands the curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution and shows that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs.
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miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.
Fabian Kern,Tobias Fehlmann,Jeffrey Solomon,Louisa Schwed,Nadja Grammes,Christina Backes,Kendall Van Keuren-Jensen,David Craig,Eckart Meese,Andreas Keller,Andreas Keller +10 more
TL;DR: The miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs is presented, supporting miRNA input from ten frequently investigated organisms and implementing novel categories like annotation confidence level or localisation in biological compartments.
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miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database.
Tim Kehl,Fabian Kern,Christina Backes,Tobias Fehlmann,Daniel Stöckel,Eckart Meese,Hans-Peter Lenhof,Andreas Keller,Andreas Keller +8 more
TL;DR: The updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.
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Salivary exosomal miR-24-3p serves as a potential detective biomarker for oral squamous cell carcinoma screening.
TL;DR: Salivary exosomal miR-24-3p is a potential novel diagnostic biomarker for OSCC, and miR+3p can maintain the proliferation of OSCC cells through targeting PER1, and dual luciferase reporter assay indicated that miR&D can interact with PER1 directly.
References
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Circulating serum miRNAs as potential biomarkers for nephroblastoma
Nicole Ludwig,Nasenien Nourkami-Tutdibi,Christina Backes,Hans-Peter Lenhof,Norbert Graf,Andreas Keller,Eckart Meese +6 more
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Impact of host genes and strand selection on miRNA and miRNA* expression.
Marta Biasiolo,Gabriele Sales,Marta Lionetti,Luca Agnelli,Katia Todoerti,Andrea Bisognin,Alessandro Coppe,Chiara Romualdi,Antonino Neri,Stefania Bortoluzzi +9 more
TL;DR: The results point out the regulatory importance of post-transcriptional phases of miRNAs biogenesis, reinforcing the role of such layer of miRNA biogenesis in miRNA-based regulation of cell activities.
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Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.
TL;DR: This study integrated the small RNA sequencing datasets in Caenorhabditis elegans and Drosophila melanogaster and devised an analytical pipeline coupled with detailed manual inspection to curate miRNA annotation systematically in miRBase, finding that, whereas MC miRNAs are often co-expressed at multiple developmental stages, LC mi RNAs tend to be expressed specifically at fewer stages.
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Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants.
TL;DR: A structure- and expression-based strategy to validate a set of defined miRNA genes, or even to annotate novel ones based on currently available sRNA HTS data sets is proposed.
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Assessment of isomiR Discrimination Using Commercial qPCR Methods
TL;DR: It is found that although these miRNA qPCR methods possess high sensitivity for specific sequences, they also pick up background signals from closely related isomiRs, which influences the reliable quantification of individual isomiR.