Gene Expression and Epigenetics

Gene expression can be regulated at multiple levels:

1. Transcriptional level — controlling whether a gene is transcribed into mRNA (most important)
2. Post-transcriptional level — mRNA processing (alternative splicing)
3. Translational level — controlling whether mRNA is translated into protein
4. Post-translational level — modifying proteins after translation

Transcription factors are proteins that bind to specific DNA sequences near genes to regulate transcription.

Activators

• Bind to enhancer sequences (sometimes far from the gene)
• Stimulate RNA polymerase to bind to the promoter and begin transcription
• Increase the rate of transcription

Repressors

• Bind to silencer sequences or directly to the promoter region
• Prevent RNA polymerase from binding
• Decrease or stop transcription

How Transcription Factors Work

1. A signalling molecule (e.g., hormone) binds to a receptor on the cell surface or enters the cell directly (steroid hormones are lipid-soluble)
2. This triggers a signal transduction pathway inside the cell
3. The pathway activates or releases a transcription factor
4. The transcription factor enters the nucleus and binds to the appropriate DNA sequence
5. Gene expression is turned on (activator) or off (repressor)

Example: Oestrogen

• Oestrogen is a steroid hormone that passes through the cell membrane
• Inside the cell, it binds to an oestrogen receptor (which is a transcription factor)
• The hormone-receptor complex enters the nucleus
• It binds to a specific DNA sequence (oestrogen response element)
• This activates transcription of target genes involved in female sexual development

Epigenetics is the study of heritable changes in gene expression that do NOT involve changes to the DNA base sequence.

DNA Methylation

• Methyl groups ($-CH_3$) are added to cytosine bases in DNA (usually at CpG sites)
• Methylation silences genes — prevents transcription factors and RNA polymerase from binding
• Heavily methylated genes are typically not expressed
• Patterns of methylation can be inherited during cell division
• Environmental factors (diet, stress, toxins) can alter methylation patterns

Histone Modification

• DNA in eukaryotes is wrapped around histone proteins, forming nucleosomes
• Histones can be chemically modified:
  • Acetylation of histones → DNA loosens (euchromatin) → genes are accessible for transcription → increased expression
  • Deacetylation → DNA tightly packed (heterochromatin) → genes are inaccessible → reduced expression
  • Methylation of histones can either activate or silence genes depending on the location

Significance of Epigenetics

• Explains how identical twins can develop different phenotypes over time
• Epigenetic changes can be influenced by environmental factors (nutrition, stress, chemicals, age)
• Some epigenetic marks can be passed to offspring (transgenerational epigenetic inheritance)
• Abnormal epigenetic patterns are linked to diseases including cancer (e.g., silencing of tumour suppressor genes)

RNA interference is a mechanism that silences gene expression after transcription.

1. Double-stranded RNA (dsRNA) is produced (from certain genes or introduced artificially)
2. An enzyme called Dicer cuts the dsRNA into short fragments called small interfering RNA (siRNA)
3. siRNA binds to a protein complex called RISC (RNA-Induced Silencing Complex)
4. One strand of siRNA guides RISC to the complementary mRNA
5. RISC degrades the mRNA, preventing it from being translated into protein

Applications of RNAi

• Potential gene therapy — silencing disease-causing genes
• Research tool — "knocking down" specific genes to study their function
• Agricultural applications — creating pest-resistant crops

How Cells Differentiate

• All cells contain the same DNA (genome)
• Differentiation occurs because different genes are expressed in different cell types
• Transcription factors, epigenetic modifications, and signalling molecules determine which genes are active
• Once differentiated, most animal cells lose the ability to become other cell types (they become committed)

Totipotency, Pluripotency, and Multipotency

Induced Pluripotent Stem Cells (iPSCs)

• Yamanaka (2006) showed that adult cells can be reprogrammed back to a pluripotent state
• Done by introducing specific transcription factors (Oct4, Sox2, Klf4, c-Myc)
• iPSCs can then be differentiated into any cell type
• Avoids ethical issues of embryonic stem cells
• Potential for personalised medicine (cells from the patient → no immune rejection)

Hox Genes

• Homeobox genes (Hox genes) are a family of genes that control the body plan during embryonic development
• They determine the identity of body segments (e.g., where limbs, antennae, wings develop)
• Hox genes code for transcription factors containing a homeodomain — a protein region that binds to DNA
• Hox genes are highly conserved across species (similar sequences in flies, mice, and humans)
• Mutations in Hox genes can cause dramatic changes (e.g., legs growing where antennae should be in fruit flies)

Question: Explain how DNA methylation can lead to differences between genetically identical organisms. (4 marks)

Solution:

Genetically identical organisms (e.g., identical twins) have the same DNA base sequences. However, environmental factors (such as diet, stress, or exposure to toxins) can cause different patterns of DNA methylation in each organism. When methyl groups are added to cytosine bases, this prevents transcription factors from binding to those regions, silencing the associated genes. Different methylation patterns mean different genes are expressed in each organism, leading to different phenotypes (observable characteristics) despite identical genotypes. These epigenetic changes can accumulate over a lifetime, explaining why identical twins become increasingly different as they age.

• Gene expression is regulated at transcriptional, post-transcriptional, translational, and post-translational levels.
• Transcription factors (activators and repressors) control whether genes are transcribed.
• Epigenetics: DNA methylation silences genes; histone acetylation activates genes — changes are heritable but don't alter the DNA sequence.
• RNA interference silences genes post-transcriptionally by degrading mRNA using siRNA and RISC.
• Cell differentiation depends on differential gene expression; iPSCs can be reprogrammed from adult cells.
• Hox genes control body plan development through transcription factor activity.