Table
- From genome to epigenome

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Table 1. Comparison of current methodologies for use in high-throughput epigenome profiling

	Pretreatment of material	Detection	Prior sequence selection	Global (G)/individual (I) CpG mapping	Whole genome coverage	Quantifiable

DNA methylation maps	Bisulphite treatment of DNA	PCR and sequencing	Y	I	N	N
		Pyrosequencing/MALDI-MS	Y	I	N	Y
		Q-PCR	Y	I	N	Y
		Hybridization to CpG and TpG oligo microarrays	Y	I	N	Y
	Restriction enzyme techniques
	RLGS	Cloning into libraries and sequencing	N	G	Y	N
	McrBC/Meth sensitive RE	Hybridization to genomic microarrays	N	G	M	Y
	MS-RDA
	ChIP with antibodies to MBDs	Cloning into libraries and sequencing	N	G	Y	N
		Hybridization to genomic microarrays	N	G	M	Y
Histone modification maps	ChIP	Hybridization to genomic/amplicon/oligo microarrays (ChIP-chip)	N		M
		Cloning into libraries and sequencing	N		Y
		ChIP-BS	Y		N
Physical chromatin structure	Chromatin fractionation	Hybridization to genomic/amplicon/oligo microarrays	N		M

Y, yes; N, no; M, maybe depending on the coverage of the microarray.

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Source: Human Molecular Genetics 2005 14(suppl_1):R3-R10

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