Journal
GENOME RESEARCH
Volume 22, Issue 7, Pages 1360-1371Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.133330.111
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Funding
- University of Zurich Research Priority Program in Systems Biology/Functional Genomics
- Swiss National Science Foundation [SNF 31003A-130530]
- European Research Council [ERC-2008-AdG 233226]
- GEBERT RUF Foundation
- SystemsX
- Swiss Initiative for Systems Biology
- Ernst Hadorn Foundation
- ETH Zurich
- Human Frontier Science Program Organization
- Bonizzi-Theler Foundation
- Natural Sciences and Engineering Research Council of Canada
- Programme Grant from the Cancer Research UK
- Research Foundation of the University of Zurich
- Roche Research Foundation
- Marie Curie Intra-European fellowship
- Cancer Research UK [11832] Funding Source: researchfish
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MicroRNAs (miRNAs) are small, noncoding RNAs that negatively regulate gene expression. As miRNAs are involved in a wide range of biological processes and diseases, much effort has been invested in identifying their mRNA targets. Here, we present a novel combinatorial approach, RIP-chip-SRM (RNA-binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo high-confidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homolog miR-58. Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.
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