Methods in DNA methylation profiling

Abstract

Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic patterns and offer a perspective on the ever-expanding literature, which we hope will be useful for investigators who are new to this area. The historical aspects that we cover will be helpful in interpreting this literature and we hope that our discussion of the newest analytical methods will stimulate future progress. We emphasize that no single approach can provide a complete view of the overall methylome, and that combinations of several modalities applied to the same sample set will give the clearest picture. Given the unexpected epigenomic patterns and new biological principles, as well as new disease markers, that have been uncovered in recent studies, it is likely that important discoveries will continue to be made using genome-wide DNA methylation profiling.

Keywords: CpG island; DNA methylation; bisulfite sequencing; differential methylation hybridization; methylated CpG island recovery assay; methylated DNA immunoprecipitation; methylation profiling; methylation-sensitive SNP chip analysis; next-generation DNA sequencing.

Figure 1. Methodologies based on methylation-sensitive restriction

(A) DMH methodology; (B) McrBC methodology. DMH: Differential methylation hybridization; McrBC: A methylation-sensitive restriction enzyme that cleaves two closely spaced (55–100 bp) methylated cytosines and preferentially digests densely methylated DNA sequences.

Figure 2. Affinity purification of hypermethylated DNA

(A) MeDIP methodology; (B) MIRA methodology. MBD: Methyl-binding domain; MeDIP: Methylated DNA immunoprecipitation; MIRA: Methylated CGI recovery assay.

Figure 3. High-throughput bisulfite sequencing

(A) RRBS methodology; (B) Padlock probes methodology. RRBS: Reduced representation bisulfite sequencing.