Deciphering Squamous Cell Carcinoma Using Multidimensional Genomic Approaches

Table 2

Techniques for genome-wide analysis of the methylome.

Bisulfite Conversion . Sodium bisulfite treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unaffected. This change in sequence can be discriminated using the techniques listed here, and relative methylation can be quantified relative to reference DNA.
Applications coupled with bisulfite conversion	References
Whole-genome sequencing	[40]
Illumina platforms	[41]
Bisulfite microarray (BS chip)	[41]
Methylation-specific quantum dot fluorescence resonance energy transfer (MS-qFRET)*	[42]
Bisulfite padlock probes (BSPPs)	[43]
Methylated DNA Precipitation . DNA is fractionated and methylated DNA sequences are subsequently eluted through the use of specific antibodies or methyl binding proteins. Following completion of the applications listed below, precipitated DNA can be analyzed using CpG island or promoter microarray hybridization, or sequenced.
Applications Coupled with Methylated DNA Precipitation	References
Methylated DNA immunoprecipitation (MeDIP) and (mDIP). Methylation-specific antibodies are utilized to immunoprecipitate methylated DNA fragmented by sonication.	[26, 34, 44]
Comprehensive high throughput arrays for relative methylation (CHARM). Custom tiling array used in conjunction with a genome-weighted smoothing algorithm.	[45]
Antibodies specific to 5-methyl-cytosine or methyl binding proteins are used to immunoprecipitate fragments of methylated DNA.	[27]
Methylated-CpG island recovery assay (MIRA). A matrix of methyl binding proteins is used to elute methylated DNA.	[46]
Methylation-sensitive Enzymes. The sensitivity of certain restriction endonucleases (REs) to DNA methylation is exploited to differentially digest DNA.
Applications coupled with restriction enzymes	References
Methyl-sensitive cut counting (MSCC)	[43]
HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) differentially amplifies methylated DNA	[47]
Restriction landmark genome scanning for screening methylated sites (RGLS-M)	[48]
Comprehensive high throughput arrays for relative methylation (CHARM)	[46]