MicroRNAs (miRNAs) regulate gene expression for diverse functions, but only a limited number of mRNA targets have been experimentally identified. We show that GW182 family proteins AIN-1 and AIN-2 act redundantly to regulate the expression of miRNA targets, but not miRNA biogenesis. Immunoprecipitation (IP) and mass spectrometry indicate that AIN-1 and AIN-2 interact only with miRNA-specific Argonaute proteins ALG-1 and ALG-2 and with components of the core translational initiation complex. Known miRNA targets are enriched in AIN-2 complexes, correlating with the expression of corresponding miRNAs. Combining IP with pyrosequencing and microarray analysis of RNAs associated with AIN-1/AIN-2, we identified 106 previously annotated miRNAs plus 9 new candidate miRNAs, but nearly no siRNAs, and more than 3500 potential miRNA targets including nearly all known ones. Our results demonstrate an effective biochemical approach to systematically identify miRNA targets and provide valuable insights regarding the properties of miRNA effector complexes. Keywords: IP microarray of miRNA targets
Illumina Genome Analyzer II paired end sequencing; Illumina sequencing of C. elegans dauer exit daf-2(el370) sample 2 DauerExitDAF2-2 polyA+ RNAseq random fragment library RW0001
Illumina Genome Analyzer II paired end sequencing; Illumina sequencing of C. elegans dauer entry daf-2(el370) sample 2 DauerEntryDAF2-2 polyA+ RNAseq random fragment library RW0001
Illumina Genome Analyzer II paired end sequencing; Illumina sequencing of C. elegans dauer daf-2(el370) sample 2 DauerDAF2-2 polyA+ 76bp SE RNAseq random fragment library RW0001
Illumina HiSeq 2000 paired end sequencing; Illumina sequencing of C. elegans dauer daf-2(el370) sample 2-1 DauerDAF2-2-1 polyA+ 100bp PE RNAseq random fragment library RW0001