How is epigenetics different from genetics?

Genetics concerns changes in the DNA sequence itself—mutations, insertions, deletions. Epigenetics involves chemical modifications to DNA or its associated proteins that change which genes are expressed without changing the sequence. Epigenetic changes are often reversible and can be influenced by diet, stress, toxins, and age, whereas most DNA sequence mutations are permanent.

Can epigenetic changes be inherited by children?

In most cases, epigenetic marks are erased and reset during the formation of egg and sperm cells (epigenetic reprogramming). However, some marks escape this erasure and are transmitted to offspring—a phenomenon called transgenerational epigenetic inheritance. Evidence in plants is strong; in mammals it has been demonstrated in specific circumstances, such as the effects of famine or certain toxin exposures on multiple generations.

What is chromatin remodeling and why does it matter?

Chromatin remodeling is the repositioning or restructuring of nucleosomes (DNA-histone complexes) to control DNA accessibility. When chromatin is loosely packed (euchromatin), transcription factors can bind and genes are expressed. Tightly packed heterochromatin blocks access, silencing genes. Chromatin remodeling complexes use ATP hydrolysis to slide, eject, or restructure nucleosomes, making it one of the primary mechanisms for regulating developmental gene expression programs.

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🧬 Epigenetics

Interactive epigenetics simulation. Model DNA methylation, histone acetylation, H3K4 and H3K9 methylation. See how chromatin state controls gene expression for 4 genes in real time.

Genetics & Evolution3DAdvanced60 FPS

About this simulation

This model demonstrates how DNA methylation, histone acetylation and H3K4 methylation combine to set chromatin compaction and, in turn, the expression level of four real human genes — BRCA1, TP53, MYC and CDKN2A. Silencing and activating scores are weighted and summed to give each gene an expression probability between 0 and 1, whilst an inheritance probability estimates the likelihood that the current epigenetic state would persist through cell division.

🔬 What it shows

Four sliders drive a weighted silencing-versus-activation formula per gene. Methylated CpG sites and tight chromatin compaction push expression down; histone acetylation and H3K4 methylation push it up. An environmental signal adds a per-gene boost or penalty on top.

🎮 How to use

Drag the CpG methylation, histone acetylation, H3K4 methylation and chromatin compaction sliders, then choose an environmental signal (heat, cold, nutrient-rich or starvation) from the dropdown. Watch the nucleosome view and the four-gene expression bar chart update instantly, alongside overall expression, inheritance probability and chromatin state readouts.

💡 Did you know?

Roughly 60-70% of human gene promoters sit within CpG islands, and methylating these islands is one of the commonest ways tumour suppressor genes such as TP53 are silenced in cancer.

Frequently asked questions

Which genes does the simulation track?

Four real human genes: BRCA1, TP53, MYC and CDKN2A. Each has its own expression bar and responds differently to the same methylation, acetylation and compaction settings because environmental signals apply a distinct boost or penalty to each gene.

How is expression level calculated?

Silencing factors (methylation weighted highest, then compaction, then low H3K4) are combined and subtracted from activating factors (acetylation, H3K4 methylation and any environmental boost), then clamped between 0% and 100% to give the bar height for each gene.

What does the inheritance probability readout mean?

It combines acetylation, unmethylated CpG fraction and H3K4 methylation into a single score approximating how likely the current active or silenced state is to be copied faithfully onto daughter cells after division.

What determines whether chromatin is labelled euchromatin or heterochromatin?

The chromatin state readout checks compaction and acetylation together with methylation: high compaction above 70% gives heterochromatin, high acetylation with low methylation gives euchromatin, and everything else is labelled mixed.

What do the environmental signal options change?

Heat stress, cold stress, nutrient-rich and starvation each apply a fixed positive or negative boost to each of the four genes' activation score before the expression bars are redrawn, mimicking how real environmental cues can shift gene expression through epigenetic channels.

⚙ Under the hood

Drag CpG methylation and histone acetylation sliders, pick heat, cold or starvation, and watch genes switch on and off without changing DNA sequence.

epigeneticsgeneticsmethylationgene-regulation

3D · Three.js / WebGL renderer · 60 FPS target · runs fully client-side, no install