TY  - JOUR
A1  - Jovanovic, Marko
A1  - Reiter, Lukas
A1  - Clark, Alejandra
A1  - Weiss, Manuel
A1  - Picotti, Paola
A1  - Rehrauer, Hubert
A1  - Frei, Andreas
A1  - Neukomm, Lukas J.
A1  - Kaufman, Ethan
A1  - Wollscheid, Bernd
A1  - Simard, Martin J.
A1  - Miska, Eric A.
A1  - Aebersold, Ruedi
A1  - Gerber, André P.
A1  - Hengartner, Michael O.
T1  - RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans
Y1  - 2012/07/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1360 
EP  - 1371 
DO  - 10.1101/gr.133330.111 
VL  - 22 
IS  - 7 
UR  - http://genome.cshlp.org/content/22/7/1360.abstract 
N2  - 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. 
ER  -