see Messerschmidt Review (2014)
- undetectable in certain yeast, nematode, and fly species
- in mamamals, DNA methylation is vital
- mostly in symmetrical CpG context
- single CpGs typically hypermethylated vs. unmethylated CpG islands --> low CpG density promoters are generally hypermethylated, yet active vs. high CpG density promoters that are inactive if methylated
- transposons are repressed if methylated (esp. LINEs, LTRs), so are pericentromeric repeats
- imprinted genes show parent-of-origin-specific DNA methylation (introduced during gamete differentiation) and subsequently allele-specific gene expression
--> Dnmt3a, Dnmt3b
- maternally provided (Dnmt3a)
--> Dnmt1
- high affinity for hemimethylation
- its deletion in mESCs causes hypotmethylation, but not a complete loss (lethal effect, though)
Dnmt2 is a misnomer: it methylates RNA, not DNA
| LMR | UMR | IMR | PMD | |
|---|---|---|---|---|
| me level | 10-50% | 0-10% | mean: 57% | 0-100%, seemingly disordered |
| size | 271 bp | 150 kb | ||
| abundance | 20-40% of the genome | |||
| tissue-specific? | yes | yes, mostly | yes (not present in ESC) | |
| CpG content | low | high | not defined | variable |
| localization | DHS overlap | mostly promoters, CGIs | mostly intragenic | heterochromatin |
| reference | Stadler (2011) | Stadler (2011) | Elliott (2015) | Lister (2009), Gaidatzis (2014) |