Validation of human microRNA target pathways enables evaluation of target prediction tools
Metadatos
Mostrar el registro completo del ítemEditorial
OXFORD UNIV PRESS
Fecha
2021Referencia bibliográfica
Fabian Kern, Lena Krammes, Karin Danz, Caroline Diener, Tim Kehl, Oliver Küchler, Tobias Fehlmann, Mustafa Kahraman, Stefanie Rheinheimer, Ernesto Aparicio-Puerta, Sylvia Wagner, Nicole Ludwig, Christina Backes, Hans-Peter Lenhof, Hagen von Briesen, Martin Hart, Andreas Keller, Eckart Meese, Validation of human microRNA target pathways enables evaluation of target prediction tools, Nucleic Acids Research, Volume 49, Issue 1, 11 January 2021, Pages 127–144, https://doi.org/10.1093/nar/gkaa1161
Patrocinador
Michael J. Fox foundation 14446; Internal funds of Saarland University; Instituto de Salud Carlos III European Commission IFI16/00041 MV19/00058Resumen
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 TGFBsignaling, 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.