Current trends in the development and application of molecular technologies for cancer epigenetics

Table 1 DNA methylation analyses used in methyl-deficient model of hepatocarcinogenesis in rodents

Dietary component	Model	Observations	Methylation assay	Ref.
Amino acid-defined diet lacking choline, methionine, folic acid and vitamin B12	Rat	Depletion of SAdoMet and DNA hypomethylation	Liver DNA methyltransferase activity assay with labeled SAdoMet	[20]
Amino acid-defined diet lacking choline, methionine, folic acid and vitamin B12	Rat	Hypomethylation of CCGG site of c-myc, c-fos and c-Ha-ras	Enzyme digestion by HpaII/MspI	[21]
Diet low in methionine lacking in choline and folic acid	Rat	Hypermethylation of p16INK4A	MS-PCR	[94]
Diet low in methionine lacking in choline and folic acid	Rat	Decrease in the total percent of methylated CCGG sites in DNA	HpaII/MspI-based cytosine extension assay	[22]
Diet low in methionine lacking in choline and folic acid	Rat	Depletion of S-AdoMet, decrease in S-AdoMet/S-AdoHcy and global DNA hypomethylation	HpaII/MspI-based cytosine extension assay	[23]
Diet low in methionine lacking in choline and folic acid	Rat	Hypomethylation of ID element and LINE-1 in preneoplastic livers and liver tumors; Decrease in histone H4-Lys20 trimethylation and increase in histone H3-Lys9 trimethylation; Decrease in histone H4-Lys20 trimethylation at the LINE-1 regulatory region	ID methylation by methylation-sensitive McrBC-PCR array; LINE-1 methylation by COBRA-assay; global histone methylation by Western blotting; LINE-1-associated histone methylation by ChIP	[15]
Diet deficient in methionine lacking in choline and folic acid	Rat	Changes in the DNA methylation machinery	Indirect methods by DNA methyltransferases and Methyl CpG binding proteins	[24]
Amino acid-defined diet lacking choline	Rat	Hypermethylation of upstream of E-cadherin and Cx26	Bisulfite sequencing	[95]
Diet deficient in methionine lacking in choline and folic acid	Rat	global loss of DNA methylation; hypermethylation of CpG islands	Global DNA methylation by cytosine extension assay and [3H-methyl] incorporation; CpG island methylation by [32P]dGTP incorporation	[30]
Diet deficient in methionine lacking in choline and folic acid	Mouse	Global DNA hypomethylation; substantial loss of repetitive sequences (LINE-1, SINES, IAP elements) cytosine methylation. Increase in histone H3-Lys9 trimethylation and decrease in histone H4-Lys20 trimethylation	Global DNA methylation by cytosine extension assay; methylation-sensitive McrBC-qPCR assay; global histone modifications by Western blot	[96]
Diet deficient in methionine lacking in choline and folic acid	Mouse	Detection of CpG island methylation profiles	MeDIP	[97]

S-AdoMet: S-adenosylmethionine; ID: Identifier; LINE-1: Long interspersed nucleotide elements; SINES: Short interspersed nuclear elements; IAP: Intracisternal A-particle; MS-PCR: Methylation-specific polymerase chain reaction; ChIP: Chromatin immunoprecipitation; MeDIP: Methylated DNA immunoprecipitation.