Header

UZH-Logo

Maintenance Infos

RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulated bantam/miR58 targets in C. elegans


Jovanovic, Marko; Reiter, Lukas; Clark, Alejandra; Weiss, Manuel; Picotti, Paola; Rehrauer, Hubert; Frei, Andreas; Neukomm, Lukas; Kaufman, Ethan; Wollscheid, Bernd; Simard, Martin J; Miska, Eric; Aebersold, Ruedi; Gerber, Andre P; Hengartner, Michael O (2012). RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulated bantam/miR58 targets in C. elegans. Genome Research, 22(7):1360-1371.

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, RIPchipSRM (RNA binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo highconfidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA induced silencing complexes from wildtype and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homologue miR58. Comparison of total mRNA and protein abundance changes in mir58 mutant and wildtype animals indicated that the direct bantam/miR58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.

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, RIPchipSRM (RNA binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo highconfidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA induced silencing complexes from wildtype and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homologue miR58. Comparison of total mRNA and protein abundance changes in mir58 mutant and wildtype animals indicated that the direct bantam/miR58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.

Statistics

Citations

11 citations in Web of Science®
12 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

336 downloads since deposited on 26 Apr 2012
29 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
07 Faculty of Science > Institute of Molecular Life Sciences
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Language:English
Date:2012
Deposited On:26 Apr 2012 06:47
Last Modified:07 Dec 2017 13:52
Publisher:Cold Spring Harbor Laboratory Press
ISSN:1088-9051
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1101/gr.133330.111
PubMed ID:22454234

Download

Download PDF  'RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulated bantam/miR58 targets in C. elegans'.
Preview
Content: Published Version
Filetype: PDF
Size: 1MB
View at publisher