Transcription factors are proteins that bind specific DNA sequences and control whether, when and how much RNA polymerase transcribes a gene. General transcription factors (TFIID, TFIIB, TFIIF, TFIIE and TFIIH) assemble with RNA polymerase II at the core promoter of protein-coding genes: TFIID's TATA-binding protein (TBP) recognizes the TATA box, and TFIIH unwinds the DNA (helicase) and phosphorylates the polymerase's C-terminal domain (kinase) so it can leave the promoter. Specific transcription factors bind promoter-proximal elements, enhancers and silencers to turn particular genes up or down. Step 1 tests DNA-binding motifs, nuclear hormone receptors and the drugs that hit them, and single-gene diseases such as p53 (Li-Fraumeni), FOXP3 (IPEX) and AIRE (APS-1).
General vs specific transcription factors
| General (basal) transcription factors | Specific transcription factors | |
|---|---|---|
| Job | Position RNA polymerase II, open the DNA, release the polymerase into elongation | Raise or lower transcription of particular genes in particular cells |
| Where they bind | Core promoter, e.g., the TATA box (present in many genes) about 25-35 bp upstream of the start site | Promoter-proximal elements (CAAT box, GC box), enhancers, silencers |
| Which genes | Essentially every RNA polymerase II gene | Selected genes, responding to hormones, cytokines or stress |
| Examples | TFIID (with TBP), TFIIB, TFIIF, TFIIE, TFIIH | p53, MYC, CREB, NF-κB, steroid and thyroid hormone receptors, FOXP3, AIRE |
How RNA polymerase II gets started, step by step
- TFIID binds the TATA box (when the promoter has one) through its TBP subunit, sharply distorting the DNA. TBP is also needed by RNA polymerases I and III.
- TFIIB binds next and bridges to RNA polymerase II, which arrives with TFIIF; TFIIE and TFIIH then complete the preinitiation complex.
- TFIIH does two jobs: two of its subunits are helicases that unwind DNA at the start site, and another is a kinase that phosphorylates the repeated sequences of the polymerase's C-terminal domain (CTD), releasing the polymerase into elongation.
- Activators bound at enhancers communicate with the polymerase through the Mediator complex and recruit chromatin remodeling complexes and histone acetylases.
Memory hook: TFIID Docks first, on the TATA box; TFIIH is the Helicase that also hits the tail (CTD) with phosphate.
Clinical tie-in: TFIIH also works in nucleotide excision repair. Its XPD subunit (ERCC2) is a helicase, and ERCC2 mutations cause xeroderma pigmentosum, trichothiodystrophy and an XP/Cockayne syndrome overlap (see the DNA repair mechanisms cheat sheet).
Enhancers, silencers and chromatin
- Promoter-proximal elements: the CAAT box (5'-CCAAT-3') and GC box (5'-GGGCGG-3', bound by Sp1), usually within about 100 bp upstream of the TATA box.
- Enhancers can sit upstream, downstream, inside the gene or thousands of nucleotides away; DNA looping lets activators on the enhancer reach the machinery at the promoter.
- Repressors bind promoter or enhancer regions (silencers are the DNA elements that recruit them) and block transcription.
- Chromatin decides access. Acetylation makes histones less positive and relaxes their grip on DNA, opening genes to transcription factors and RNA polymerase; deacetylated histones are tightly coiled and silent; methylated CpG-island promoters are usually silenced.
DNA-binding motifs
| Motif | What it looks like | Classic examples |
|---|---|---|
| Zinc finger | A Zn²⁺ ion held by cysteine and histidine side chains stabilizes a small fold that binds the major groove; the Cys2-Cys2 type marks steroid receptors | Glucocorticoid and estrogen receptors and other steroid receptors |
| Leucine zipper (bZIP) | Leucines at every 7th position of an α-helix zip two proteins together; the zipper is a dimerization motif, and the basic region beside it binds DNA | CREB, which binds the cAMP response element |
| Helix-loop-helix (bHLH) | A basic DNA-binding helix, a loop, then a second helix; also pairs into dimers | MYC |
| Helix-turn-helix | Two α-helices joined by a short turn, with one helix reading the major groove | Bacterial and phage repressors (λ repressor, Cro); the eukaryotic homeodomain (HOX proteins) binds DNA through a helix-turn-helix structure |
Exam pattern: "zinc finger protein that binds a hormone response element after ligand binding" is a nuclear receptor.
Nuclear receptors: ligand-activated transcription factors
Lipid-soluble hormones (steroids, thyroid hormone, vitamin D) diffuse across the plasma membrane and bind intracellular receptors: steroid receptors in the cytoplasm or nucleus, and thyroid hormone and vitamin D receptors in the nucleus. The hormone-receptor complex binds DNA and raises or lowers transcription of target genes.
| Receptor | Ligand or drug | High-yield point |
|---|---|---|
| PPARγ | Pioglitazone (thiazolidinedione) | Changes transcription of insulin-responsive genes, decreasing insulin resistance in the periphery and liver; needs endogenous insulin; boxed warning for heart failure |
| PPARα | Fibrates (fenofibrate) | Activates lipoprotein lipase and lowers apo C-III, so triglycerides fall; raises apo A-I, apo A-II and HDL |
| RARα | Retinoic acid; tretinoin (all-trans retinoic acid) | The t(15;17) PML-RARα fusion stalls white cells at the promyelocyte stage: acute promyelocytic leukemia, treated with tretinoin plus arsenic trioxide, which degrades the fusion protein (AML Q-bank breakdown) |
| Androgen receptor | Testosterone | Nonfunctional receptor causes complete androgen insensitivity (46,XY with typically female external features); a CAG repeat expansion causes spinal and bulbar muscular atrophy |
High-yield transcription factors and their diseases
| Factor | Normal job | When it fails (or misfires) |
|---|---|---|
| p53 (TP53) | After DNA damage, activates repair genes and p21 (CDKN1A), a CDK inhibitor that blocks entry into S phase, or triggers apoptosis (e.g., via BAX): the "guardian of the genome" | Germline: Li-Fraumeni syndrome (breast cancer, bone and soft-tissue sarcomas, brain tumors, adrenocortical carcinoma; often in children and young adults) |
| MYC | bHLH factor that activates growth-related genes | Burkitt lymphoma: t(8;14), or t(8;22) or t(2;8), places MYC next to an immunoglobulin locus |
| FOXP3 | Forkhead factor required for regulatory T cells | IPEX (X-linked recessive): autoimmune enteropathy with severe diarrhea in the first months, early type 1 diabetes, eczema, autoimmune thyroid disease |
| AIRE | In medullary thymic epithelial cells, switches on thousands of tissue-restricted self-antigens so self-reactive T cells are deleted | APS-1 (APECED) (autosomal recessive, starts in childhood or adolescence): at least 2 of chronic mucocutaneous candidiasis, hypoparathyroidism and adrenal insufficiency |
| NF-κB | Held in the cytoplasm by IκBα until signals trigger IκBα phosphorylation and degradation; then enters the nucleus to switch on immune, inflammatory and anti-apoptotic genes | IKBKG (NEMO) defects block its release: incontinentia pigmenti; anhidrotic ectodermal dysplasia with immune deficiency |
| SRY | Y-chromosome factor that starts testis development | Swyer syndrome (some cases; 46,XY, no testes, uterus present); 46,XX testicular difference of sex development (SRY moved onto an X) |
| HOX (homeobox) genes | Early embryonic patterning; HOXA13 shapes the limbs, urinary tract and genitals | Hand-foot-genital syndrome (HOXA13) |
| PAX3 | Directs neural crest cells to form melanocytes and some nerve tissue | Waardenburg syndrome types I and III (hearing loss, patchy depigmentation); PAX3-FOXO1 fusion in alveolar rhabdomyosarcoma |
| TBX5 | T-box factor for upper limb, cardiac septum and conduction system | Holt-Oram syndrome (upper-limb and heart defects) |
Oncogene vs tumor suppressor: MYC is gain of function, p53 loss of function; see the oncogenes vs tumor suppressors cheat sheet.
Prokaryotic vs eukaryotic transcription
| Feature | Prokaryotes | Eukaryotes |
|---|---|---|
| RNA polymerase | One core enzyme | Three: I = 28S, 18S, 5.8S rRNA (nucleolus); II = mRNA; III = tRNA, 5S rRNA |
| Promoter recognition | σ (sigma) factor, which lets go after about the first 10 nucleotides | General transcription factors; TFIID (TBP) binds the TATA box |
| Promoter elements | -10 (TATAAT, the Pribnow box) and -35 (TTGACA) | TATA box (-25 to -35), CAAT and GC boxes, distant enhancers |
| Classic regulation | Operons (genes for one pathway share a promoter and one mRNA). lac operon: repressor sits on the operator until allolactose binds it; CAP-cAMP activates when glucose is scarce. trp operon: tryptophan-bound repressor shuts it off | Activators, repressors and chromatin state |
| Location | Transcription and translation run at the same time in the cytoplasm | Transcription in the nucleus; RNA is capped, spliced and polyadenylated first (see RNA processing) |
| Inhibitor | Rifampin: bacterial RNA polymerase, sparing the mammalian enzyme | α-Amanitin: RNA polymerase II (pol III moderately sensitive, pol I insensitive) |
α-Amanitin: the death cap question
- Amanita phalloides (death cap) causes most fatal mushroom poisonings. Its amatoxins, chiefly α-amanitin, survive cooking, bind RNA polymerase II and halt protein synthesis.
- Hepatocytes can no longer transcribe protein-coding genes, giving centrilobular hepatic necrosis.
- Timeline: delayed gastroenteritis 6-24 hours after the meal, apparent recovery at 24-36 hours, then fulminant liver and multiorgan failure around days 3-5.
How USMLE tests it
- "Restores assembly of the basal transcription machinery at the promoter" means a general transcription factor (TFIID/TBP). Histone acetyltransferases act on chromatin, the spliceosome works after transcription, σ factor is bacterial, and ribosomal subunits belong to translation.
- Hormone with an intracellular receptor: the receptor itself is the transcription factor, acting on hormone response elements.
- FOXP3 vs AIRE: both prevent autoimmunity; FOXP3 builds regulatory T cells, AIRE drives thymic deletion of self-reactive T cells (compare them in the immune tolerance Q-bank breakdown).
Practice question
A 4-month-old boy is evaluated for failure to thrive. Since 3 weeks of age he has had profuse watery diarrhea despite formula changes. He has a widespread eczematous rash. Serum glucose is 386 mg/dL with a low C-peptide, and TSH is elevated with a low free T4. His mother's brother died in infancy after intractable diarrhea. Small-bowel biopsy shows villous atrophy with a dense lymphocytic infiltrate, and laboratory studies show impaired regulatory T-cell function. A loss-of-function mutation in which gene is most likely?
A. AIRE B. BTK C. CD40LG D. FOXP3 E. IKBKG (NEMO)
Answer: D. FOXP3 is the forkhead transcription factor that regulatory T cells need; without it, autoimmunity starts in infancy (IPEX: immune dysregulation, polyendocrinopathy, enteropathy, X-linked). Enteropathy is usually the first sign and type 1 diabetes the most common endocrine disorder; eczema and thyroid disease are common. The affected maternal uncle fits X-linked recessive inheritance.
- A: AIRE loss also causes multigland autoimmunity, but APS-1 is autosomal recessive and usually begins in childhood or adolescence with chronic mucocutaneous candidiasis, hypoparathyroidism and adrenal insufficiency, not infant enteropathy with a regulatory T-cell defect.
- B: BTK deficiency (X-linked agammaglobulinemia) blocks B-cell development: infections from absent antibodies, not autoimmunity.
- C: CD40 ligand deficiency (X-linked hyper-IgM syndrome) blocks class switching to IgG, IgA and IgE: infections, not autoimmunity.
- E: NEMO is needed to release NF-κB; its defects cause incontinentia pigmenti or anhidrotic ectodermal dysplasia with immune deficiency (abnormal skin, teeth and sweat glands), not a regulatory T-cell defect.
Key takeaways
- Transcription factors bind DNA and steer RNA polymerase; they don't make RNA themselves.
- General factors: TFIID (TBP binds the TATA box) docks first; TFIIH = helicase plus CTD kinase, shared with nucleotide excision repair (xeroderma pigmentosum).
- Specific factors act at promoter-proximal elements, enhancers (any distance, via DNA looping) and silencers, recruiting Mediator and histone acetylases.
- Motifs: zinc finger (steroid receptors), leucine zipper (CREB), helix-loop-helix (MYC), helix-turn-helix (bacterial repressors, homeodomain).
- Nuclear receptors are ligand-activated transcription factors: PPARγ = pioglitazone, PPARα = fibrates, PML-RARα = APL.
- Diseases: p53 (Li-Fraumeni), MYC (Burkitt), FOXP3 (IPEX), AIRE (APS-1), SRY (Swyer, 46,XX testicular DSD), PAX3 (Waardenburg), TBX5 (Holt-Oram).
- Rifampin blocks bacterial RNA polymerase; α-amanitin blocks RNA polymerase II.
Sources
- Eukaryotic RNA Polymerases and General Transcription Factors — The Cell: A Molecular Approach, 2nd ed., NCBI Bookshelf (2000)
- Regulation of Transcription in Eukaryotes — The Cell: A Molecular Approach, 2nd ed., NCBI Bookshelf (2000)
- 15.3 Eukaryotic Transcription — OpenStax Biology 2e
- 8.1 Introduction to Transcription — Cells: Molecules and Mechanisms (Wong), LibreTexts
- 9.2 Eukaryotic Transcriptional Regulation — Cells: Molecules and Mechanisms (Wong), LibreTexts
- 37.2 How Hormones Work — OpenStax Biology 2e
- Intracellular Control of Cell-Cycle Events — Molecular Biology of the Cell, 4th ed., NCBI Bookshelf (2002)
- TP53 Gene — MedlinePlus Genetics
- ERCC2 Gene — MedlinePlus Genetics
- Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-linked Syndrome — MedlinePlus Genetics
- AIRE: Autoimmune Regulator — UniProtKB O43918
- Amanita phalloides Mushroom Poisonings — Northern California, December 2016 — CDC MMWR (2017)
Frequently Asked Questions
What is a transcription factor?
A transcription factor is a protein that binds a specific DNA sequence, such as a promoter element or an enhancer, and helps decide whether, when and how much a gene is transcribed into RNA. It does not make RNA itself. Instead, it recruits or blocks RNA polymerase and the general transcription machinery, often together with coactivators that remodel chromatin. Examples tested on Step 1 include TFIID, p53, MYC, NF-kappa-B, FOXP3 and the steroid and thyroid hormone receptors.
What is the difference between general and specific transcription factors?
General, or basal, transcription factors such as TFIID, TFIIB, TFIIF, TFIIE and TFIIH are needed at the core promoter of essentially every gene transcribed by RNA polymerase II; they position the polymerase, open the DNA and release it into elongation. Specific transcription factors bind promoter-proximal elements, enhancers or silencers outside the core promoter and raise or lower transcription of selected genes in particular cell types or in response to signals such as hormones.
What do TFIID and TFIIH do?
TFIID is the first general transcription factor to bind the promoter: its TATA-binding protein (TBP) recognizes the TATA box about 25 to 35 base pairs upstream of the start site and distorts the DNA, starting assembly of the preinitiation complex. TFIIH joins last. Its helicase subunits unwind the DNA, and its kinase phosphorylates the C-terminal domain of RNA polymerase II so the enzyme can leave the promoter. The TFIIH helicase subunits also work in nucleotide excision repair.
What are the main DNA-binding motifs of transcription factors?
The four classic motifs are the zinc finger, in which a zinc ion held by cysteines and histidines stabilizes a fold that binds the major groove (steroid hormone receptors); the leucine zipper, a dimerization helix with leucines at every seventh position next to a basic DNA-binding region (CREB); the basic helix-loop-helix (MYC); and the helix-turn-helix, two helices joined by a short turn, classic for bacterial repressors and also the DNA-binding structure of the eukaryotic homeodomain found in HOX proteins.
Which diseases are caused by transcription factor mutations?
High-yield examples include Li-Fraumeni syndrome (germline TP53), Burkitt lymphoma (MYC translocation, usually t(8;14)), IPEX syndrome (FOXP3; X-linked infant enteropathy, type 1 diabetes and eczema), APS-1 (AIRE; mucocutaneous candidiasis, hypoparathyroidism and adrenal insufficiency), some cases of Swyer syndrome and 46,XX testicular difference of sex development (SRY), Waardenburg syndrome (PAX3), Holt-Oram syndrome (TBX5), hand-foot-genital syndrome (HOXA13) and acute promyelocytic leukemia (PML-RARA fusion).
What does alpha-amanitin inhibit?
Alpha-amanitin, the main toxin of the death cap mushroom Amanita phalloides, inhibits RNA polymerase II, the enzyme that makes messenger RNA; RNA polymerase III is only moderately sensitive and RNA polymerase I is insensitive. Liver cells stop making proteins, so after a 6- to 24-hour delay patients develop gastroenteritis, seem to recover, and then progress to fulminant liver failure around days 3 to 5. Rifampin, by contrast, inhibits bacterial RNA polymerase.