Existence of Internal N7-Methylguanosine Modification in mRNA Determined by Differential Enzyme Treatment Coupled with Mass Spectrometry Analysis

The recent discovery of reversible chemical modifications on mRNA has opened a new era of post-transcriptional gene regulation in eukaryotes. Among the 15 types of modifications identified in mRNA of eukaryotes, N7-methylguanosine (m(7)G) is unique owing to its presence in the 5' cap structure. It remains unknown whether m(7)G is also present internally in mRNA, and this is largely attributed to the lack of an appropriate analytical method to differentiate internal m(7)G in mRNA from that in the 5' cap. To address this analytical challenge, we developed a novel strategy of combining differential enzymatic digestion with liquid chromatography tandem mass spectrometry analysis to quantify the levels of these two types of m(7)G modifications in mRNA. In particular, we found that Si nuclease and phosphodiesterase I exhibit differential activities toward internal and 5'-terminal m(7)G. By using this method, we found that internal m(7)G was present in mRNA of cultured human cells as well as plants and rat tissue. In addition, our results showed that plants contain higher levels of internal m(7)G in mRNA than mammals. We also observed that exposure of rice to cadmium (Cd) stimulated marked diminution in the levels of m(7)G at both the S' cap and internal positions of mRNA, which was correlated with the Cd-induced elevated expression of m(7)G-decapping enzymes. Taken together, we reported here a strategy to distinguish internal and 5'-terminal m(7)G in mRNA, and by using this method, we demonstrated the prevalence of internal m(7)G modification in mRNA, which we believe will stimulate future functional studies of m(7)G on post-transcriptional gene regulation in eukaryotes.