RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2012 
FD July 01 
VO 22 
IS 7 
SP 1360 
OP 1371 
DO 10.1101/gr.133330.111 
UL http://genome.cshlp.org/content/22/7/1360.abstract 
AB 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.