Genes wrap around histone protein spools (nucleosomes) to form chromatin. Chemical tags added to DNA and histones — without changing the DNA sequence — control how tightly that chromatin is packed, and therefore how easily the transcription machinery can reach the gene.
E = clamp( (1 - M) * (0.35 + 0.65*A) - 0.5*C , 0, 1 )
M = methylation fraction (0-1)
A = histone acetylation (0 = off, 1 = on)
C = chromatin condensation (rises with M, falls with A)
E = relative gene expression rate
- DNA methylation — adds methyl groups to CpG sites (red beads); higher values recruit repressor proteins and silence the gene.
- Environmental stress — diet, toxins and stress hormones drift the methylation level over time.
- Histone acetylation — loosens histone-DNA grip, opening chromatin even under some methylation.
- Reset chromatin — returns the locus to an unmarked, moderately open baseline state.