Table 1.

Comparison of different DNA Methylation measuring methods.

				Base conversion
Category	Endonuclease digestion	Affinity enrichment		Bisulfite-dependent		Bisulfite-free
Methods	MRE-seq	MeDIP-seq	MBD-seq	RRBS	WGBS	TAPS	EM-seq
Resolution	Single-base	150–300 bp		Single-base
Coverage	–	+/–		+ +
DNA input	+	+		+ +		–
Cost	–	–		+ +		–
Application	Site-specific studies	Low-resolution, large-scale studies		High resolution, whole-genome studies
Pros	Cost-effective, user-friendly	High sensitivity, low cost		Detect whole-genome methylation at single-base
Cons	Enzyme-dependent methylation detection; incomplete digestion	Low resolution; biased towards highly methylated regions		DNA degradation; high cost; reduced sequence complexity		Unsuitable for single cells; Large investment

EM-seq = Enzymatic Methyl-seq, MBD = methyl-CpG-binding domain protein, MeDIP = methylated DNA immunoprecipitation, MRE = methylation sensitive restriction enzyme, RRBS = reduced representation bisulfite sequencing, -seq = sequencingg, TAPS = TET-assisted pyridine borane sequencing, WGBS = whole-genome bisulfite sequencin.

Coverage, DNA input and cost in table 1 are divided into 5 levels, followed by + + > + > +/– > – > – –.