IDENTIFYING 5-METHYLCYTOSINE AND RELATED MODIFICATIONS IN DNA GENOMES

Intense interest in the biological roles of DNA methylation, particula rly in eukaryotes, has produced at least eight different methods for i dentifying 5-methylcytosine and related modifications in DNA genomes, However, the utility of each method depends not only on its simplicity but on its specificity, resolution, sensitivity and potential artifac ts. Since these parameters affect the interpretation of data, they sho uld be considered in any application. Therefore, we have outlined the principles and applications of each method, quantitatively evaluated t heir specificity, resolution and sensitivity, identified potential art ifacts and suggested solutions, and discussed a paradox in the distrib ution of m(5)C in mammalian genomes that illustrates how methodologica l limitations can affect interpretation of data, Hopefully, the inform ation and analysis provided here will guide new investigators entering this exciting field.