Gene Control – Transcription Factors
Learning Objective
State that transcription factors (TFs) are proteins that bind specific DNA sequences and control gene expression in eukaryotes by decreasing or increasing the rate of transcription.
Key Terminology (Glossary)
- cis‑regulatory element – DNA sequence (promoter, enhancer, silencer) that controls transcription of a nearby gene.
- general transcription factor (GTF) – Non‑DNA‑binding proteins (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH) required for assembly of the pre‑initiation complex.
- activator / repressor transcription factor – TFs that increase or decrease transcription, respectively.
- co‑activator / co‑repressor – Proteins that do not bind DNA directly but are recruited by activators or repressors to modulate the transcriptional machinery.
- chromatin‑remodelling complex – Protein machines that reposition nucleosomes or modify histones, altering DNA accessibility.
- RNA polymerase II (Pol II) – Enzyme that synthesises messenger RNA in eukaryotes.
- pre‑initiation complex (PIC) – Assembly of Pol II, GTFs and associated factors at the core promoter ready to start transcription.
- reporter‑gene assay – Experimental technique in which a regulatory DNA fragment is fused to a detectable gene (e.g., luciferase) to measure TF activity.
1. Core Transcription Process (Context for TFs)
Cambridge A‑Level expects you to know the six‑step model of Pol II transcription. The steps are shown below with the key DNA elements and proteins involved.
- Promoter recognition – General transcription factors bind core promoter elements:
- TATA box (≈‑30 bp upstream of the transcription start site)
- Initiator (Inr) (covers the start site)
- BRE (TFIIB‑recognition element)
- Pre‑initiation complex (PIC) formation – GTFs (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH) assemble on the promoter and recruit Pol II.
- Initiation – TFIIH helicase activity unwinds ~12 bp of DNA, Pol II synthesises a short RNA (≈10‑12 nt) and clears the promoter.
- Promoter clearance & early elongation – Phosphorylation of the Pol II C‑terminal domain (CTD) allows transition to productive elongation.
- Elongation – Pol II moves along the template, synthesising pre‑mRNA; elongation factors (e.g., DSIF, NELF) assist.
- Termination – Poly‑adenylation signal (AAUAAA) and associated factors cause release of the nascent transcript.
2. General Transcription Factors (GTFs)
| GTF | Main Function in PIC |
|---|
| TFIIA | Stabilises TFIID‑DNA interaction; prevents repressor binding. |
| TFIIB | Positions Pol II at the start site; interacts with BRE. |
| TFIID (contains TBP) | Recognises the TATA box; nucleates PIC assembly. |
| TFIIE | Recruits and regulates TFIIH. |
| TFIIF | Associates with Pol II and promotes its recruitment to the promoter. |
| TFIIH | Helicase activity (DNA unwinding) and CTD kinase activity (phosphorylation of Pol II). |
3. What Transcription Factors Do
- Bind specific DNA motifs within cis‑regulatory elements using DNA‑binding domains (zinc finger, helix‑turn‑helix, leucine zipper, etc.).
- Act as activators to increase transcription or repressors to decrease transcription.
- Recruit co‑activators/co‑repressors, the basal transcription machinery, and/or chromatin‑remodelling complexes.
- Are often regulated post‑translationally (phosphorylation, ligand binding, proteolysis) so that gene expression can respond rapidly to cellular signals.
4. Mechanisms by Which TFs Influence Transcription
- DNA binding – Specific domains recognise short consensus sequences (e.g., Sp1 binds 5′‑GGGCGG‑3′).
- Recruitment of the transcriptional machinery
- Activators attract co‑activators (e.g., histone acetyltransferases) and help stabilise the PIC.
- Repressors can block activator sites, hinder PIC assembly, or recruit co‑repressors that impede Pol II progression.
- Chromatin remodelling
- Acetylation of histone tails by HATs (often recruited by activators) neutralises positive charge, loosening DNA‑histone interactions → DNA more accessible.
- Deacetylation by HDACs (recruited by repressors) restores positive charge, compacting chromatin → transcription reduced.
- ATP‑dependent remodelers (SWI/SNF, ISWI) can slide or evict nucleosomes, providing additional control.
- Signal‑dependent regulation
- Phosphorylation (e.g., MAPK‑mediated phosphorylation of Elk‑1) changes TF conformation and DNA‑binding affinity.
- Ligand binding (e.g., steroid hormone receptors) causes nuclear translocation and DNA binding.
- Proteolytic cleavage (e.g., SREBP) releases an active DNA‑binding fragment.
5. Typical Structure of a Transcription Factor
| Domain | Function |
|---|
| DNA‑binding domain | Recognises a specific nucleotide motif (e.g., zinc finger). |
| Activation / repression domain | Interacts with co‑activators, co‑repressors, or the basal transcription machinery. |
| Regulatory domain | Receives signals (phosphorylation, ligand binding, proteolysis) that modify TF activity. |
6. Representative Eukaryotic Transcription Factors
- Sp1 – Binds GC‑rich promoters; strong activator of many housekeeping genes.
- p53 – Tumour‑suppressor; activates genes for cell‑cycle arrest or apoptosis and can repress proliferation genes.
- NF‑κB – Activated by cytokine signalling; induces transcription of immune‑response genes.
- Oct‑4 – Maintains pluripotency in embryonic stem cells by activating stem‑cell‑specific genes.
- Steroid‑hormone receptors (e.g., estrogen receptor) – Ligand‑dependent nuclear TFs that regulate development and metabolism.
7. Predicting the Effect of Mutations in Regulatory Regions (AO2)
Use the table to practice interpreting how changes affect transcription rates.
| Mutation | Location | Predicted Effect on Transcription |
|---|
| Deletion of TATA box | Core promoter | Severe reduction – PIC cannot form efficiently. |
| Point mutation in Sp1 binding site | Promoter (GC‑rich region) | Reduced basal expression of housekeeping gene. |
| Insertion of an enhancer with a high‑affinity NF‑κB site | 1 kb upstream | Up‑regulation (up to 10‑fold) when NF‑κB is activated. |
| Silencer mutation that abolishes a HDAC‑recruiting motif | Intron downstream | Loss of repression → higher transcription than normal. |
8. Experimental Investigation of TF Activity (AO3)
Reporter‑gene assay example
- Clone a candidate enhancer (or promoter) upstream of a luciferase reporter gene in a plasmid.
- Transfect cultured eukaryotic cells with the construct together with:
- Expression vector for the TF of interest (or an empty vector as control).
- Optional co‑activator or co‑repressor plasmids.
- Treat cells with a stimulus that activates the TF (e.g., TNF‑α for NF‑κB).
- Measure luciferase activity. An increase compared with control indicates activation; a decrease indicates repression.
- Controls: promoter‑less reporter (background), mutant binding‑site reporter (specificity), and a constitutive‑expression control for transfection efficiency.
This simple assay demonstrates how TFs modulate transcription rates and provides data that can be interpreted in exam questions.
9. Diagram Suggestion (for teachers / students)
A schematic should show two parallel scenarios:
- Activator pathway: Enhancer → Activator TF → co‑activator (HAT) → open chromatin → PIC formation → Pol II recruitment → ↑ transcription.
- Repressor pathway: Silencer → Repressor TF → co‑repressor (HDAC) → closed chromatin → blocked PIC → ↓ transcription.
Summary
Transcription factors are essential regulatory proteins that bind defined DNA sequences and modulate the rate of transcription in eukaryotic cells. They work in concert with general transcription factors, RNA polymerase II, co‑activators/co‑repressors, and chromatin‑remodelling complexes. By acting as activators or repressors, and by being subject to rapid signal‑dependent regulation, TFs provide the flexible control required for development, cellular homeostasis, and environmental responses—core ideas examined throughout the Cambridge International AS & A Level Biology syllabus.