The big idea: Every cell in your body carries the same DNA — yet a nerve cell, a muscle cell and a skin cell all look and behave completely differently.
Why the cells differ
- Each cell switches different genes ON and OFF.
- The DNA letters are identical; what changes is which genes are expressed.
- Epigenetics is the study of these switches.
- An epigenetic change alters gene expression without changing the DNA base sequence.
- The change can be inherited by daughter cells when the cell divides.
The base sequence is identical in both panels — only the epigenetic switches differ. GENE OFF (silenced): methyl (CH₃) groups are added to the DNA and the DNA/histones are tightly packed, so RNA polymerase cannot bind and no mRNA is made. GENE ON: the DNA is open, so it can be transcribed.
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- Epigenetics
- Heritable changes in gene expression that do NOT change the DNA base sequence (the A, T, C, G order stays the same).
- Gene expression
- Whether a gene is switched on (transcribed into mRNA and used) or off.
- Heritable
- Passed on — here, copied to the daughter cells when a cell divides, so the same genes stay on or off.
- Methyl group
- A small chemical tag, written CH₃, that can be attached to cytosine bases in DNA or to amino acids in histones.
- Histone
- A protein that DNA is wound around; how tightly the DNA wraps controls whether genes can be read.
Epigenetic ≠ mutation: A mutation changes the actual DNA base sequence (it rewrites the letters).
An epigenetic change does not touch the sequence — it only changes whether a gene is read, like a sticky note on a page rather than crossing words out.
Where the word comes from: epi- means 'on top of' — epigenetic marks sit on top of the DNA, they don't rewrite it.
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There are two main epigenetic mechanisms, and both work by controlling whether the transcription machinery can reach a gene.
Read each as a chain of cause and effect: a chemical mark is added, that changes how the DNA is exposed, and that decides whether the gene is read or silenced.
1 — DNA methylation (usually SILENCES a gene)
- Methyl groups (CH₃) are attached to the DNA, on cytosine bases, often in the gene's promoter (the start signal).
- The methyl marks block RNA polymerase from settling on the promoter.
- With the start signal blocked, the gene cannot be transcribed — no mRNA is made.
- So methylation at a promoter usually switches the gene OFF (silenced).
Focus on the lower panel: methyl (CH₃) groups on the DNA plus tightly packed DNA/histones keep RNA polymerase out — the gene is silenced. Remove those marks and loosen the packing and the same gene can be read again.
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2 — Histone modification (changes how tightly DNA is packed)
- DNA is wound around histone proteins; chemical tags added to the histones change how tightly it wraps.
- Tightly packed (condensed) DNA is hidden — RNA polymerase cannot reach the gene, so it is OFF.
- Loosely packed (open) DNA is exposed — RNA polymerase can reach the gene, so it is ON.
- So the packing state set by histone tags decides whether a gene is accessible and expressed. Methyl tags on histone amino acids can either repress or activate transcription, depending on where they are added.
| DNA packing | Is the gene accessible? | Can RNA polymerase bind? | Gene state |
|---|---|---|---|
| Loosely packed (open) | Yes — the DNA is exposed | Yes | ON (expressed) |
| Tightly packed (condensed) | No — the DNA is hidden | No | OFF (silenced) |
Both come down to one thing: access: Both mechanisms control whether RNA polymerase can reach the gene.
Methylation blocks the promoter directly; tight histone packing hides the whole stretch of DNA. Either way, a blocked or hidden gene is silenced (OFF).
Open, unmethylated DNA is accessible, so the gene is expressed (ON).
The sequence never changes: Crucially, in none of this does the base sequence change — and the marks can be copied to daughter cells, so the same genes stay on or off after division (heritable).
| DNA methylation | Histone modification | |
|---|---|---|
| What is added/changed | Methyl (CH₃) groups are attached to the DNA, often at a gene's promoter | Chemical tags are added to the histone proteins that DNA is wound around |
| What it changes | Whether RNA polymerase can read the gene | How tightly the DNA is packed around the histones |
| Effect on the gene | Methylation at a promoter usually SILENCES the gene (transcription blocked) | Tightly packed (condensed) = gene OFF; loosely packed = gene ON |
| Does the base sequence change? | No — the A, T, C, G order is untouched | No — the base sequence is untouched |
| Reversible / heritable? | Reversible, and can be copied to daughter cells (heritable) | Reversible, and can be copied to daughter cells (heritable) |
Why this matters: These switches are how one genome produces many cell types — every cell keeps all the genes, but each expresses a different subset.
Because epigenetic marks are reversible, they also let cells respond to the environment and, in some cases, change which genes are on across a lifetime — without ever altering the DNA sequence itself.
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The big idea: Epigenetic tags are chemical groups added to DNA or to histones. Methyl tags on a promoter switch a gene off; methyl tags on histones can switch genes off or on.
The points to remember
- Methyl groups can be added to cytosine bases in the DNA of a promoter.
- A methylated promoter represses transcription: RNA polymerase cannot bind, so the gene is off.
- In the nucleus, DNA is wound around histones; each unit is a nucleosome.
- Methylation of histone amino acids can repress or activate transcription.
- The tags never change the base sequence.
Remember it as: Promoter tags: off. Histone tags: off or on.
Real example: tortoiseshell cats. In each cell of a female mammal one X chromosome is switched off, partly by methylation of its DNA. In tortoiseshell cats a fur-colour gene sits on the X, so patches of fur show which X is switched off.
How it is asked: 1A items reading data on methylation and transcription, short answers on how histone methylation affects transcription, and longer answers comparing promoter and histone tags.
Explain how methylation of the promoter of a gene affects its expression.
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Histone tags work both ways: Promoter methylation only switches genes off; histone methylation can switch them off or on.