| Citation | Wright JE, Gaidatzis D, Senften M, Farley BM, Westhof E, Ryder SP, Ciosk R. A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1. EMBO J, 2011. |
| PubMed ID | 21169991 |
| Short Description | A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1. GEO Record: GSE21591 Platform: GPL200 Download gene-centric, log2 transformed data: WBPaper00037901.ce.mr.csv |
| # of Conditions | 15 |
Full Description
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RNA-binding proteins (RBPs) are critical regulators of gene expression. To understand and predict the outcome of RBP-mediated regulation a comprehensive analysis of their interaction with RNA is necessary. The signal transduction and activation of RNA (STAR) family of RBPs includes developmental regulators and tumour suppressors such as Caenorhabditis elegans GLD-1, which is a key regulator of germ cell development. To obtain a comprehensive picture of GLD-1 interactions with the transcriptome, we identified GLD-1-associated mRNAs by RNA immunoprecipitation followed by microarray detection. Based on the computational analysis of these mRNAs we generated a predictive model, where GLD-1 association with mRNA is determined by the strength and number of 7-mer GLD-1-binding motifs (GBMs) within UTRs. We verified this quantitative model both in vitro, by competition GLD-1/GBM-binding experiments to determine relative affinity, and in vivo, by 'transplantation' experiments, where 'weak' and 'strong' GBMs imposed translational repression of increasing strength on a non-target mRNA. This study demonstrates that transcriptome-wide identification of RBP mRNA targets combined with quantitative computational analysis can generate highly predictive models of post-transcriptional regulatory networks. Experimental Details: WBPaper00037901:Input_rep1 WBPaper00037901:Input_rep2 WBPaper00037901:Input_rep3 WBPaper00037901:aMYC_rep1 WBPaper00037901:aMYC_rep2 WBPaper00037901:aMYC_rep3 WBPaper00037901:aFLAG_rep1 WBPaper00037901:aFLAG_rep2 WBPaper00037901:aFLAG_rep3 WBPaper00037901:N2_aFLAG_rep1 WBPaper00037901:N2_aFLAG_rep2 WBPaper00037901:N2_aFLAG_rep3 WBPaper00037901:GGF_aFLAG_rep1 WBPaper00037901:GGF_aFLAG_rep2 WBPaper00037901:GGF_aFLAG_rep3. |
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