title: RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.
abstract: 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.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
authors.forename: Marko
authors.initials: M
authors.lastname: Jovanovic
authors.forename: Lukas
authors.initials: L
authors.lastname: Reiter
authors.forename: Alejandra
authors.initials: A
authors.lastname: Clark
authors.forename: Manuel
authors.initials: M
authors.lastname: Weiss
authors.forename: Paola
authors.initials: P
authors.lastname: Picotti
authors.forename: Hubert
authors.initials: H
authors.lastname: Rehrauer
authors.forename: Andreas
authors.initials: A
authors.lastname: Frei
authors.forename: Lukas J
authors.initials: LJ
authors.lastname: Neukomm
authors.forename: Ethan
authors.initials: E
authors.lastname: Kaufman
authors.forename: Bernd
authors.initials: B
authors.lastname: Wollscheid
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Simard
authors.forename: Eric A
authors.initials: EA
authors.lastname: Miska
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: André P
authors.initials: AP
authors.lastname: Gerber
authors.forename: Michael O
authors.initials: MO
authors.lastname: Hengartner
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified / Q000235:genetics / Q000378:metabolism; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D003433:Crosses, Genetic; D007158:Immunologic Techniques / Q000379:methods; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis; D040901:Proteomics / Q000379:methods*; D034622:RNA Interference; D020871:RNA Stability; D018510:RNA, Helminth / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D019076:Transgenes
chemical_list: D035683:MicroRNAs; D018510:RNA, Helminth; D012333:RNA, Messenger; D016601:RNA-Binding Proteins