Spreadsheet-Based Program for the Analysis

Methylation of DNA in CpG dense r e gions of gene promoters (CpG islands) i s important for transcriptional inactivation o f selective genes in normal and neoplasti c cells. Here, we present a spreadsheet-base d program adapted from Microsof t ® Exce l ® that is useful for identifying CpG island s and for assisting in the laboratory analysi s of DNA methylation of these regions. Upo n execution of the program, a customize d workbook analyzes an entered DNA s e quence for the total number and percentag e cytosine and guanine nucleotides, the tota l number and percentage of CpG sites, and a CpG:GpC ratio. The program also display s the distribution of CpG sites in a visual fo r mat as well as in two different graphica l formats. Finally, the program assists in la b oratory studies of DNA methylation tha t employ bisulfite modification of DNA b y displaying methylation-dependent effects o f bisulfite treatment on DNA sequences.