A real-time PCR method for the quantitative analysis of RNA editing at specific sites

In this study, a quantitative PCR (qPCR) method was developed to determine the A-to-I RNA editing frequencies at specific sites. The A-to-I RNA editing of nuclear transcripts exerts profound effects on the biological activities of gene products. RNA editing of nuclear gene transcripts have been shown to be developmentally regulated and tissue specific, and alternations of RNA editing activities have been observed under pathological conditions. Two sites of ionotropic glutamate receptor subunits, the Q/R site of zebrafish gria2alpha and the Y/C site of grik2alpha, were chosen in this study to demonstrate the applicability of the SYBR Green detection-based real-time PCR method to measure RNA editing activities during zebrafish development. The results obtained by qPCR were consistent with those obtained by the limited primer extension. However, the qPCR method has the advantages of easy handling and low cost.