Abstract
Objective: To establish a protocol to determine the structure of RNA 5' end cap by using coimmunoprecipitation( Co-IP) in conjunction with microarray technology. Methods: Total RNAs isolated from Caenorhabditis elegans were precipitated with the antibody against M3G cap structure. For Microarray analysis, the probes were designed for 127 non-coding RNAs( ncRNAs) of C. elegans. The cap structure was determined and RNA transcription was also analyzed. Results: 37 ncRNAs was isolated and identified as containing m3G cap structure. This number is similar with other species,for which m3G cap RNAs have been found. Conclusions: It is feasible and effective to determine the structure of ncRNA 5' end cap by using Co-IP followed by Microarray analysis. This method is of great specificity and high sensitivity,which maybe applied to the large-scale RNA cap structure identification,the discovery of novel RNA and the identification of RNA functions.
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