Table 1.
Types of chromatin alterations that regulate gene expression
| Chromatin alteration1 | Subtype | Acts upon | Mechanism | Outcome for transcription |
|---|---|---|---|---|
| Histone Modifications | Ubiquitination | Lysine (K) | distances histones from DNA (bulky moiety) | Activation (H2B) or repression (H2A)2 |
| Methylation | Lysine, Arginine (R) | Recruitment of other chromatin regulators | Activation (H3K4, H3K363) or repression (H3K93, H3K27, H4K20, H4R3) | |
| Acetylation | Lysine | Charge neutralization4, recruitment of other chromatin regulators | Activation | |
| Phosphoryation | Serine (S), Threonine (T) | Charge neutralization4, recruitment of other chromatin regulators | Activation | |
| Chromatin5 remodeling | SWI/SNF | Nucleosome position and occupancy2 | Sliding to new position, histone octamer eviction2 | Actvation and repression |
| SWR1 | Histone exchange | H2A.Z histone variant incorporation | Activation | |
| DNA methylation | CG and non-CG | Promoter | Inhibition of transcription factor binding | Repression |
| CG | Gene (less at 5′ and 3′ ends) | May reduce transcription elongation | Repression |
1
These and additional chromatin alterations also play a role in heterochromatic silencing of repetitive DNA and transposons, genome integrity, and chromosome stability, which are reviewed elsewhere [24,49,51].
2
Not yet demonstrated for plants.
3
May activate transcription when localized in transcribed region, but repress transcription when localized in the promoter region.
4
Charge neutralization decreases the affinity of positively charged histones for negatively charged DNA.
5
For simplicity, only a subset of the chromatin remodeling complexes that regulate transcription are listed here.