Epigenetics and Gene Regulation

Gene Expression and Its Regulation

Every cell in a multicellular organism contains the same genome, yet cells are highly specialised (differentiated) — a neurone is radically different from a liver cell or a white blood cell. This is because different genes are expressed (switched on) in different cell types. Gene regulation determines which genes are transcribed and translated, when, and how much protein is produced.

Levels of Gene Regulation

Gene expression can be regulated at multiple levels:

Level	Mechanism	Examples
Transcriptional	Control of whether a gene is transcribed into mRNA	Transcription factors, epigenetic modifications
Post-transcriptional	Control of mRNA processing and stability	Alternative splicing, mRNA degradation, siRNA
Translational	Control of whether mRNA is translated	Initiation factor regulation
Post-translational	Control of protein activity and lifespan	Phosphorylation, ubiquitination, proteolysis

Transcriptional regulation is the most important and most commonly examined at A-Level.

Transcription Factors

Transcription factors are proteins that bind to specific DNA sequences near a gene and either promote or inhibit transcription.

• Activators bind to enhancer sequences and stimulate RNA polymerase binding to the promoter, increasing transcription
• Repressors bind to silencer sequences or directly to the promoter, blocking RNA polymerase and reducing/preventing transcription

Transcription factors respond to signals — hormones, growth factors, environmental stimuli — allowing the cell to adjust gene expression to changing conditions.

Oestrogen as a Transcription Factor Example

Oestrogen is a steroid hormone that acts as a transcription factor:

1. Being lipid-soluble, oestrogen crosses the cell membrane by diffusion

2. It binds to an intracellular oestrogen receptor in the cytoplasm

3. The hormone-receptor complex enters the nucleus

4. It acts as a transcription factor, binding to specific DNA sequences called oestrogen response elements (EREs) in the promoter regions of target genes

5. This stimulates transcription of genes involved in female sexual development, the menstrual cycle, and bone maintenance

The Lac Operon: Prokaryotic Gene Regulation

The lac operon in E. coli is the classic model of gene regulation and is specified by AQA. It controls the expression of genes needed to metabolise lactose.

Structure of the Lac Operon

The operon consists of:

• Promoter — where RNA polymerase binds to begin transcription
• Operator — a DNA sequence between the promoter and structural genes; acts as a molecular switch
• Structural genes:
• lacZ — encodes β-galactosidase, which hydrolyses lactose into glucose and galactose
• lacY — encodes lactose permease, which transports lactose into the cell
• lacA — encodes transacetylase
• Regulatory gene (lacI) — located upstream; codes for the lac repressor protein (constitutively expressed)

Regulation of the Lac Operon

When lactose is ABSENT:

1. The lac repressor protein (produced by lacI) binds to the operator

2. This blocks RNA polymerase from transcribing the structural genes

3. β-galactosidase and permease are NOT produced

4. The operon is switched off — an example of negative regulation

When lactose is PRESENT:

1. Lactose (or its isomer allolactose) acts as an inducer

2. Allolactose binds to the lac repressor protein, causing a conformational change

3. The altered repressor can no longer bind to the operator

4. RNA polymerase is free to bind to the promoter and transcribe the structural genes

5. β-galactosidase and permease are produced

6. The operon is switched on

This is an efficient system — the enzymes for lactose metabolism are only produced when lactose is available, conserving cellular resources.

Epigenetics

Epigenetics is the study of heritable changes in gene expression that do NOT involve changes to the base sequence of DNA. Epigenetic modifications alter how genes are read without altering the genetic code itself. They can be:

• Reversible — unlike mutations
• Heritable — passed on during cell division (and sometimes between generations)
• Influenced by environmental factors — diet, stress, toxins, ageing

DNA Methylation

DNA methylation is the addition of a methyl group (-CH₃) to cytosine bases in DNA, typically at CpG dinucleotides (where cytosine is followed by guanine). This is catalysed by DNA methyltransferase enzymes.

Effects:

• Methylation of a gene's promoter region inhibits transcription — the methyl groups physically block transcription factor binding or recruit proteins that condense the chromatin
• Heavily methylated genes are effectively silenced
• Methylation patterns are copied during DNA replication by maintenance methyltransferases, ensuring the epigenetic state is inherited by daughter cells

Examples:

• X-inactivation — in female mammals, one X chromosome in each cell is heavily methylated and condensed into a Barr body, silencing most of its genes. This is random and occurs early in development, producing a mosaic pattern (visible in tortoiseshell cats)
• Genomic imprinting — certain genes are expressed from only the maternal or paternal allele, depending on methylation patterns set during gamete formation
• Tumour suppressor gene silencing — aberrant methylation of tumour suppressor gene promoters (e.g. BRCA1, p16) can silence them, contributing to cancer

Histone Modification

DNA in eukaryotes is wrapped around histone proteins, forming nucleosomes. The tails of histone proteins can be chemically modified, altering how tightly DNA is packaged:

Histone acetylation:

• Acetyl groups are added to histone tails by histone acetyltransferases (HATs)
• Acetylation reduces the positive charge on histones, weakening their attraction to the negatively charged DNA
• Chromatin becomes less condensed (euchromatin) → DNA is more accessible to transcription factors and RNA polymerase → gene expression increases
• Removal of acetyl groups by histone deacetylases (HDACs) causes chromatin to condense (heterochromatin) → gene expression decreases

Histone methylation:

• Can either activate or repress transcription depending on which amino acid residue is methylated and how many methyl groups are added
• Adds another layer of regulatory complexity

Epigenetics and the Environment

Environmental factors can alter epigenetic marks:

• Diet — folate and other methyl donors in the diet can influence DNA methylation patterns. The classic example is the Agouti mouse study: genetically identical mice with different coat colours and body weights depending on maternal diet during pregnancy
• Stress — chronic stress can alter methylation patterns in genes related to the stress response (e.g. the glucocorticoid receptor gene), potentially increasing susceptibility to mental health disorders
• Toxins — smoking, alcohol, and environmental pollutants can cause epigenetic changes associated with disease
• Ageing — methylation patterns change with age, and these changes are predictable enough to be used as an "epigenetic clock"

Transgenerational Epigenetic Inheritance

Some epigenetic modifications can be passed to subsequent generations through the germline, though most are reprogrammed (erased and reset) during early embryonic development and gametogenesis. Evidence for transgenerational effects includes:

• The Dutch Hunger Winter study — children of women who were pregnant during the 1944-45 famine in the Netherlands showed altered methylation patterns and increased rates of obesity and cardiovascular disease decades later; some effects persisted into the grandchildren's generation

Exam Tips

• AQA expects detailed knowledge of the lac operon — be able to draw and label it, and describe what happens both with and without lactose
• For epigenetics, always state that the DNA base sequence is NOT changed — marks are given for this distinction
• Link methylation to gene silencing and acetylation to gene activation — these are common mark-scheme points
• When discussing epigenetics and environment, use named examples (Agouti mice, Dutch Hunger Winter) for full marks
• Remember: epigenetic changes are potentially reversible and heritable — both features distinguish them from mutations