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Validation of human microRNA target pathways enables evaluation of target prediction tools.

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Date

2020-11-13

Authors

Kern, Fabian
Krammes, Lena
Danz, Karin
Diener, Caroline
Kehl, Tim
Küchler, Oliver
Fehlmann, Tobias
Kahraman, Mustafa
Rheinheimer, Stefanie
Aparicio-Puerta, Ernesto

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Oxford University Press
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Abstract

MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.

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MeSH Terms

1-Methyl-4-phenylpyridinium
3' Untranslated Regions
Cell Line, Tumor
Gene Expression Regulation
High-Throughput Screening Assays
Humans
MicroRNAs
Neuroblastoma
Parkinson Disease
Predictive Value of Tests
Signal Transduction
Transcriptome
Tumor Necrosis Factor-alpha

DeCS Terms

1-Metil-4-fenilpiridinio
Enfermedad de Parkinson
Ensayos analíticos de alto rendimiento
Factor de necrosis tumoral alfa
Línea celular tumoral
MicroARNs
Neuroblastoma
Regiones no traducidas 3'
Regulación de la expresión génica
Transcriptoma
Transducción de señal
Valor predictivo de las pruebas

CIE Terms

Keywords

Cell Line, Genes, Reporter, Mesencephalon, Neurons, Sensitivity and Specificity, Transforming Growth Factor beta

Citation

Kern F, Krammes L, Danz K, Diener C, Kehl T, Küchler O, et al. Validation of human microRNA target pathways enables evaluation of target prediction tools. Nucleic Acids Res. 2021 Jan 11;49(1):127-144.