Epigenetics
Epigenetics is the study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence. Epigenetic mechanisms control which genes are switched on or off in a given cell, and these changes can be influenced by the environment and, in some cases, passed to future generations. The field has emerged over the past three decades as a major frontier in molecular biology and medicine, providing molecular explanations for cellular memory in differentiation, for the inheritance of phenotypic states without DNA mutation, and for the contribution of environment to disease risk.
Spec mapping: This lesson sits in AQA 7402 Section 3.8.2 — Most of a cell's DNA is not translated. The specification expects candidates to describe how DNA methylation of cytosines at CpG sites and acetylation/deacetylation of histones modify gene expression, and to recognise that environmental factors can influence these modifications. (Refer to the official AQA specification document for exact wording.)
What Is Epigenetics?
Key Definition: Epigenetics refers to changes in gene expression that are heritable through cell division (and sometimes across generations) without any alteration to the DNA base sequence itself.
Key principles:
- Every cell in a multicellular organism contains the same DNA, but different cell types express different genes. Epigenetic mechanisms are responsible for this differential gene expression.
- Epigenetic changes are reversible — unlike mutations, they do not permanently alter the DNA sequence. This reversibility is the molecular feature that makes epigenetic marks therapeutically tractable: drugs that remove or restore them can in principle rewrite the expression state of a cell.
- Epigenetic modifications regulate gene expression by altering how accessible the DNA is to the transcription machinery. They do not change what the DNA encodes; they change what the cell does with what is encoded.
- Two main epigenetic mechanisms are studied at A-Level: DNA methylation and histone modification. A third — non-coding RNA-mediated silencing — is acknowledged but lies beyond the AQA specification.
The genetic vs epigenetic distinction is sharp and central to A* answers:
| Property | Genetic change | Epigenetic change |
|---|
| Affects DNA sequence | Yes — bases replaced, inserted or deleted | No — sequence is unchanged |
| Reversible | Generally no (except by repair before replication) | Yes — actively removed by enzymes |
| Heritable through mitosis | Yes | Yes (most marks) |
| Heritable through meiosis | Yes (germline) | Limited — most marks are reprogrammed in gametogenesis |
| Tissue-specific | No (the genome is the same in every cell) | Yes — different cell types have different epigenomes |
| Detectable by sequencing | Yes — read directly from the sequence | Requires specialised techniques (bisulphite sequencing, ChIP-seq) |
Chromatin Structure and Gene Expression
To understand epigenetics, it is important to understand how DNA is packaged:
- DNA is wrapped around proteins called histones to form nucleosomes — the basic unit of chromatin.
- Eight histone proteins (two each of H2A, H2B, H3 and H4) form a histone octamer, and approximately 147 base pairs of DNA are wrapped around each octamer in ~1.65 turns of a left-handed superhelix.
- Nucleosomes are linked by stretches of "linker DNA" (~20–80 bp) and a fifth histone, H1, binds linker DNA and stabilises higher-order chromatin folding.
- The degree of chromatin compaction affects gene expression:
- Euchromatin — loosely packed chromatin. DNA is accessible to RNA polymerase and transcription factors. Genes in euchromatin are more likely to be actively transcribed.
- Heterochromatin — tightly packed chromatin. DNA is less accessible. Genes in heterochromatin are generally silenced (not transcribed).
Key Definition: Chromatin is the complex of DNA and histone proteins found in the nucleus. Its structure can be modified to regulate gene expression.
Histone tails as the substrate of epigenetic modification
Each core histone has a flexible N-terminal "tail" that protrudes from the nucleosome. These tails are the substrate for most histone modifications: acetylation and methylation of specific lysines, phosphorylation of specific serines and threonines, and ubiquitination of specific lysines. The combinatorial pattern of these modifications is sometimes referred to as the histone code, and it is read by chromatin-binding proteins that recognise specific marks.
DNA Methylation
Key Definition: DNA methylation is the addition of a methyl group (–CH₃) to a cytosine base in DNA, typically at CpG sites (where a cytosine is followed by a guanine). This modification generally silences gene expression.
Mechanism
- The enzyme DNA methyltransferase (DNMT) catalyses the addition of a methyl group to the 5' position of cytosine, producing 5-methylcytosine (5mC). The methyl donor is S-adenosylmethionine (SAM), a metabolite whose abundance depends on dietary methyl donors (folate, vitamin B12, methionine, choline).
- Methylation occurs predominantly at CpG dinucleotides (a cytosine followed by guanine, linked by a phosphodiester bond). The "p" denotes the phosphodiester bond and distinguishes a CpG from a C-G base pair.
- Regions of DNA with a high density of CpG sites are called CpG islands and are often found in or near promoter regions. Approximately 60–70% of human gene promoters overlap a CpG island.
Effects on Gene Expression
- Methylation of CpG islands in a gene's promoter region typically inhibits transcription because:
- Methyl groups can directly block the binding of transcription factors to the promoter.
- Methylated DNA recruits methyl-CpG-binding proteins (e.g. MeCP2), which in turn recruit histone-modifying enzymes (HDACs and methyltransferases that mark H3K9) that compact the chromatin into a heterochromatic state.
- Methylation within the gene body (the transcribed region) can sometimes be associated with active transcription — the relationship is more complex than a simple "methylation = off" rule.
- DNA methylation patterns are maintained through cell division by the enzyme maintenance methyltransferase (DNMT1), which recognises hemi-methylated DNA (where one strand is methylated and the newly synthesised strand is not) and methylates the new strand. De novo methyltransferases (DNMT3A, DNMT3B) establish new methylation patterns, primarily during development.
- Removal of methylation can be passive (failure of DNMT1 to re-methylate during replication) or active (oxidation of 5mC to 5-hydroxymethylcytosine by TET enzymes, followed by repair).
Examples
- X-chromosome inactivation: In female mammals, one of the two X chromosomes is extensively methylated and condensed into a Barr body. Most genes on the inactivated X chromosome are silenced. This is a form of dosage compensation, ensuring that females (XX) do not produce twice as much X-linked gene product as males (XY). The choice of which X to inactivate is random in each cell early in development, but once established it is heritable through all subsequent divisions — producing the mottled coat patterns of tortoiseshell cats (X-linked coat colour alleles expressed in patches according to which X is inactive).
- Genomic imprinting: Certain genes are expressed from only one parental allele (either the maternal or paternal copy), with the other copy being silenced by methylation. An example is the IGF2 gene (insulin-like growth factor 2), which is expressed only from the paternal allele. Loss of imprinting underlies the Prader-Willi (paternal deletion of 15q11–13) and Angelman (maternal deletion of the same region) syndromes — same chromosomal change, opposite parental origin, completely different clinical phenotypes.
- Cancer: Abnormal methylation patterns are a hallmark of many cancers. Hypermethylation of tumour suppressor gene promoters (e.g. CDKN2A, MLH1) can silence these genes, contributing to uncontrolled cell division. Conversely, global hypomethylation of repetitive sequences destabilises the genome and can de-repress oncogenes. The role of methylation in tumour suppressor silencing is developed in detail in Lesson 3 (Oncogenes, Tumour Suppressors and Cancer).
Mermaid: DNA methylation gating gene expression
flowchart LR
A["Unmethylated CpG island promoter"] -->|TF binds freely| B["RNA polymerase II recruited"]
B --> C["Gene transcribed (ON)"]
A -.->|DNMT3A/3B add methyl groups| D["Methylated CpG island"]
D --> E["TF binding blocked"]
D --> F["MeCP2 recruits HDAC + H3K9 methyltransferase"]
F --> G["Chromatin compacted (heterochromatin)"]
E --> H["Gene silenced (OFF)"]
G --> H
Histone Modification
Key Definition: Histone modification refers to the addition or removal of chemical groups to the amino acid tails of histone proteins, which alters chromatin structure and thereby regulates gene expression.
Histone Acetylation
- Acetylation is the addition of an acetyl group (–COCH₃) to lysine residues in the N-terminal tails of histones (e.g. H3K9ac, H3K27ac, H4K16ac).
- Catalysed by enzymes called histone acetyltransferases (HATs) such as p300, CBP and GCN5. The acetyl donor is acetyl-CoA — linking histone acetylation directly to cellular metabolic state.
- Acetylation reduces the positive charge on histones (lysine is positively charged; adding acetyl groups neutralises this charge).
- Since DNA is negatively charged (due to phosphate groups), reducing the positive charge on histones weakens the electrostatic interaction between histones and DNA.
- The chromatin becomes less condensed (more "open"), making the DNA more accessible to RNA polymerase and transcription factors.
- Acetyl-lysines are also recognised by bromodomain-containing reader proteins (such as the BET family) that further recruit the transcription machinery.
- Therefore, histone acetylation is generally associated with increased gene expression (gene activation).
Histone Deacetylation
- Deacetylation is the removal of acetyl groups from histones.
- Catalysed by histone deacetylases (HDACs) — a family of around 18 enzymes in humans, divided into four classes.
- Restores the positive charge on histones, strengthening the histone-DNA interaction.
- Chromatin becomes more condensed (compacted), reducing accessibility.
- Associated with decreased gene expression (gene silencing).
Other Histone Modifications
- Methylation of histones (different from DNA methylation) — can activate or repress transcription depending on which amino acid is methylated and how many methyl groups are added. H3K4 trimethylation marks active promoters; H3K27 trimethylation and H3K9 trimethylation mark repressed regions. The "rules" of histone-methylation logic are part of the histone code.
- Phosphorylation — addition of phosphate groups by kinases; involved in chromatin condensation during cell division (H3 serine 10 phosphorylation accompanies mitosis) and DNA damage signalling (γH2AX marks double-strand breaks).
- Ubiquitination of histone tails (e.g. H2AK119ub) — typically associated with repression.
Reciprocal logic of acetylation and methylation
| Modification | Charge effect | Chromatin state | Transcription |
|---|
| H3/H4 lysine acetylation | Neutralises + charge | Open (euchromatin) | Active |
| H3/H4 lysine deacetylation | Restores + charge | Compact (heterochromatin) | Silent |
| H3K4 trimethylation | No charge effect | Open at active promoters | Active |
| H3K9 trimethylation | No charge effect | Compact (constitutive heterochromatin) | Silent |
| H3K27 trimethylation | No charge effect | Compact (facultative heterochromatin) | Silent (Polycomb) |
| CpG methylation (DNA) | n/a (chemical mark on cytosine) | Recruits MeCP2 → HDAC → compact | Silent |
Environmental Influences on Epigenetics
Epigenetic modifications can be influenced by the environment, providing a molecular mechanism by which experience and exposure can leave durable marks on gene expression.
- Diet: Folate, vitamin B12, methionine and choline are methyl donors that feed into the SAM pool used by DNMTs. Diets deficient or rich in these nutrients can shift methylation patterns. The Agouti mouse experiment demonstrated that maternal diet rich in methyl donors could alter the coat colour and obesity of offspring by changing methylation of the Agouti gene's regulatory region.
- Stress: Chronic stress has been shown to alter DNA methylation patterns in the brain, affecting expression of genes involved in the stress response (e.g., the glucocorticoid receptor gene NR3C1 in studies of maternal care in rats).
- Smoking: Tobacco smoke alters methylation patterns, increasing the risk of cancer. Smoking during pregnancy affects the methylation patterns of the developing foetus.
- Toxins and pollutants: Exposure to chemicals such as bisphenol A (BPA) and certain pesticides can alter epigenetic marks.
These mechanisms create a route by which an organism's history can influence its gene expression without genetic mutation — a phenomenon that has reshaped thinking about gene-environment interaction.
Transgenerational Epigenetic Inheritance
One of the most intriguing — and contested — aspects of epigenetics is the possibility that epigenetic changes can be inherited across generations.