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.

Table 2 A summary of selected evidence for effects of butyrate in histone modification and histone modification assays in cancer cell culture models

Dietary component	Cell culture model	Observations	Histone modification assay	Ref.
Sodium butyrate	SW620 human colon carcinoma cells	Increased global histone H4 acetylation	Western blot	[70]
Sodium butyrate	A375 human melanoma and S91 mouse melanoma	Increased global histone H4 acetylation	Western blot	[98]
Sodium butyrate	Colo-320 human colon cancer cells	Increased acetylation of histone H3 and H4 within CDKN1A promoter site	ChIP	[64]
Sodium butyrate	EBC-1 human lung epithelial cells	Increased histone H3 and H4 acetylation associated with promoter of cathelicidin	ChIP	[99]
Sodium butyrate	HepG2 human hepatocarcinoma	Increased global histone H3 and H4 acetylation; Genome-wide changes in acetylation of DNA-bound histones	Western blot; ChIP-chip (ChIP and microarray hybridization)	[100]

CDKN1A: Cyclin-dependent kinase inhibitor 1A; ChIP: Chromatin immunoprecipitation.