A Protocol for the Determination of the Methylation Status of Gingival Tissue DNA at Specific CpG Islands

Tissue biopsies are very precious. A method that allows the isolation of a high quality and quantity of genomic DNA, total RNA, and total protein from a single biopsy that is suitable for downstream applications (e.g., DNA methylation analysis, quantitative PCR, and gel electrophoresis techniques) is very desirable. The method described here combines a tissue stabilization reagent combined with a spin-column method for the simultaneous purification of gingival tissue DNA, RNA, and protein. The genomic DNA is then used for quantitative analysis of DNA methylation using real-time PCR (the qAMP method). Subsequent data analysis is very straightforward using online software. Future analyses may include the RNA transcript analysis as well as protein expression levels of genes identified as differentially methylated.