Table 3.
Common methodologies for epigenetic endpoints applied for nanomaterial studies.
| Epigenetic Endpoints | Specific Epigenetic Markers | Analytical Methods | References |
|---|---|---|---|
| DNA methylation | Global DNA methylation screening (5mc, 5hmC, 6mA, etc.) | HPLC/MS, ELISA, methylation-sensitive comet assay, pyrosequencing (repetitive sequences LINE-1 or Alu) | [121,122,123,124] |
| Gene-specific promoter methylation | Methylation-specific PCR | [121,125] | |
| Differentially methylated regions (whole-genome sequencing) | MPS, DNA methylation-specific microarrays, MeDIP followed by sequencing | [121,126] | |
| Histone modification | Whole genome (specific histone marker) | ChIP with DNA microarray, ChIP-Seq, ChIP-Chip | [127,128] |
| Gene-specific histone (specific) modification | ChIP-qPCR | [128,129] | |
| Global histone modification markers | HPLC/MS, ELISA, immunostaining, immunoblotting | [130,131] | |
| Noncoding RNAs | Whole genome | RNA-seq, microarray | [132,133] |
| Gene-specific | qPCR | [134] |
DNA: deoxyribonucleic acid; HPLC/MS: high-performance liquid chromatography–mass spectrometry; ELISA: enzyme-linked immunosorbent assay; 5mC: 5-methylcytosine; 5hmC: 5-hydroxymethyl cytosine; 6mA: 6-adenine methylation; PCR: polymerase chain reaction; MPS: massively parallel DNA sequencing; MeDIP: methylated DNA immunoprecipitation; ChIP: chromatin immunoprecipitation (ChIP); qPCR: quantitative PCR; RNA: ribonucleic acid.