RT Journal Article
T1 Validation of human microRNA target pathways enables evaluation of target prediction tools.
A1 Kern, Fabian
A1 Krammes, Lena
A1 Danz, Karin
A1 Diener, Caroline
A1 Kehl, Tim
A1 Küchler, Oliver
A1 Fehlmann, Tobias
A1 Kahraman, Mustafa
A1 Rheinheimer, Stefanie
A1 Aparicio-Puerta, Ernesto
A1 Wagner, Sylvia
A1 Ludwig, Nicole
A1 Backes, Christina
A1 Lenhof, Hans-Peter
A1 von Briesen, Hagen
A1 Hart, Martin
A1 Keller, Andreas
A1 Meese, Eckart
K1 Cell Line
K1 Genes, Reporter
K1 Mesencephalon
K1 Neurons
K1 Sensitivity and Specificity
K1 Transforming Growth Factor beta
AB 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.
PB Oxford University Press
YR 2020
FD 2020-11-13
LK http://hdl.handle.net/10668/16774
UL http://hdl.handle.net/10668/16774
LA en
NO 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.
DS RISalud
RD Apr 10, 2025