ArticleNature methods2010
A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Ageing induces tissue-specific transcriptomic changes in Caenorhabditis elegans.The EMBO journal · 2022Article
- Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading.Nature communications · 2021Article
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- Application of targeted mass spectrometry in bottom-up proteomics for systems biology research.Journal of proteomics · 2018Review
- Expanding the horizons of microRNA bioinformatics.RNA (New York, N.Y.) · 2018Article
- Recent Molecular Genetic Explorations ofGenetics · 2018Article
- High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature.Scientific reports · 2017Article
- Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Pairing beyond the Seed Supports MicroRNA Targeting Specificity.Molecular cell · 2016Article
- Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry.International journal of molecular sciences · 2015Review
- Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.Genome research · 2015Article
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- Identification and functional analysis of novel and conserved microRNAs in tomato.Molecular biology reports · 2014Article
- RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans.Open biology · 2013Article
- MicroRNA regulation of T-cell differentiation and function.Immunological reviews · 2013Review
- Proteomics for understanding miRNA biology.Proteomics · 2013Review
- Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans.PLoS genetics · 2013Article
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Abstract
Efficient experimental strategies are needed to validate computationally predicted microRNA (miRNA) target genes. Here we present a large-scale targeted proteomics approach to validate predicted miRNA targets in Caenorhabditis elegans. Using selected reaction monitoring (SRM), we quantified 161 proteins of interest in extracts from wild-type and let-7 mutant worms. We demonstrate by independent experimental downstream analyses such as genetic interaction, as well as polysomal profiling and luciferase assays, that validation by targeted proteomics substantially enriched for biologically relevant let-7 interactors. For example, we found that the zinc finger protein ZTF-7 was a bona fide let-7 miRNA target. We also validated predicted miR-58 targets, demonstrating that this approach is adaptable to other miRNAs. We propose that targeted mass spectrometry can be applied generally to validate candidate lists generated by computational methods or in large-scale experiments, and that the described strategy should be readily adaptable to other organisms.
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