Key Transcription Factors

Why This Matters

Transcription factors are the master switches of gene expression—they determine which genes get turned on, when, and in what cells. In molecular biology, you're being tested on how cells regulate the flow of genetic information from DNA to protein. Understanding transcription factors means understanding signal-responsive gene control, tissue-specific expression, and the molecular logic of development. These concepts appear repeatedly in questions about gene regulation, cell differentiation, and disease mechanisms.

Don't just memorize a list of protein names. Know why each type of transcription factor exists, how its structural domains enable function, and what happens when regulation goes wrong. The exam will ask you to connect structure to function, compare regulatory mechanisms, and explain how combinatorial control creates cellular diversity from a single genome.

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Structural Domains: How Transcription Factors Recognize DNA

Every transcription factor needs to find its target sequence among billions of base pairs. The DNA-binding domain is the molecular "address reader" that makes sequence-specific recognition possible.

Zinc Finger Motifs

• Zinc ions stabilize the protein fold—each "finger" coordinates a $Zn^{2+}$ ion using cysteine and histidine residues, creating a compact structure that fits into the major groove
• Modular and versatile—multiple zinc fingers can be linked together, with each finger recognizing 3 base pairs, allowing recognition of longer sequences
• Found in large transcription factor families—including steroid receptors and the Sp1 family, making this one of the most common DNA-binding motifs in eukaryotes

Helix-Turn-Helix Domains

• Two alpha helices connected by a short turn—the "recognition helix" inserts into the major groove and makes sequence-specific contacts with DNA bases
• One of the oldest DNA-binding motifs—found in both prokaryotic repressors (like lac repressor) and eukaryotic homeodomain proteins
• Recognition helix determines specificity—amino acid side chains in this helix form hydrogen bonds with specific base pairs

Leucine Zipper Motifs

• Leucine residues every seven amino acids—create a hydrophobic interface that allows two protein monomers to "zip" together through coiled-coil interactions
• Dimerization enables DNA binding—the basic region adjacent to the zipper contacts DNA; the factor only binds as a dimer
• Homo- and heterodimer combinations—different partner choices (like Jun/Fos forming AP-1) expand the regulatory possibilities from a limited set of proteins

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Functional Domains: Turning Genes On or Off

Binding DNA is only half the job. Activation and repression domains communicate with the transcriptional machinery to determine whether a gene gets expressed.

Activation Domains

• Recruit coactivators and basal machinery—acidic, glutamine-rich, or proline-rich regions interact with mediator complex and general transcription factors
• No conserved sequence or structure—activation domains are defined by function rather than fold, often appearing "disordered" in structural studies
• Strength varies by context—the same activation domain can have different potency depending on promoter architecture and cellular environment

Repression Domains

• Block transcriptional machinery assembly—some repression domains compete with activators for binding sites or mask activation domains
• Recruit chromatin-modifying enzymes—many repressors bring in histone deacetylases (HDACs) or methyltransferases to create repressive chromatin states
• Active repression vs. passive blocking—active repression involves recruiting silencing machinery; passive repression simply prevents activator binding

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General Transcription Factors: The Core Machinery

Before any gene-specific regulation matters, the basal transcription apparatus must assemble. General transcription factors (GTFs) are required at virtually every RNA polymerase II promoter.

TFIID (TBP + TAFs)

• TATA-binding protein (TBP) recognizes the TATA box—bends DNA dramatically (~80°) to create a platform for preinitiation complex assembly
• TAFs (TBP-associated factors) expand promoter recognition—allow TFIID to function at TATA-less promoters by recognizing other core promoter elements
• First factor to bind in ordered assembly—TFIID binding is typically the committed step in transcription initiation

TFIIB

• Bridges TFIID and RNA polymerase II—positions the polymerase correctly over the transcription start site
• Determines start site selection—mutations in TFIIB cause aberrant initiation at incorrect positions
• Contains a reader domain for BRE—the TFIIB recognition element upstream of TATA provides additional specificity

TFIIH

• Dual function: helicase and kinase—unwinds DNA at the promoter to form the open complex and phosphorylates the RNA polymerase II CTD
• CTD phosphorylation triggers elongation—the transition from initiation to productive elongation requires TFIIH kinase activity
• Also functions in DNA repair—mutations cause xeroderma pigmentosum, linking transcription machinery to genome maintenance

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Signal-Responsive Factors: Connecting Environment to Expression

Cells must adjust gene expression in response to hormones, stress, and developmental cues. Inducible transcription factors translate extracellular signals into transcriptional changes.

Nuclear Receptors

• Ligand-activated transcription factors—bind small hydrophobic molecules (steroids, thyroid hormone, retinoic acid) that diffuse through the membrane
• Conformational change exposes activation domain—ligand binding shifts receptor structure, releasing corepressors and recruiting coactivators
• Direct repeats, inverted repeats, and spacing—different receptor dimers recognize DNA elements with characteristic arrangements, creating specificity

Heat Shock Factors (HSFs)

• Activated by protein-damaging stress—elevated temperature, oxidative stress, or toxins cause HSF trimerization and DNA binding
• Bind heat shock elements (HSEs)—recognize inverted repeats of the sequence nGAAn in promoters of chaperone genes
• Rapid, transient response—HSF activation is fast but self-limiting; restored proteostasis leads to HSF inactivation

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Tissue-Specific Factors: Creating Cellular Identity

A liver cell and a neuron contain identical genomes but express completely different gene sets. Tissue-specific transcription factors establish and maintain cell type identity.

Myogenic Factors (MyoD Family)

• Master regulators of muscle differentiation—MyoD, Myf5, myogenin, and MRF4 can convert fibroblasts into muscle cells when ectopically expressed
• Basic helix-loop-helix (bHLH) structure—dimerize with ubiquitous E proteins to bind E-box sequences (CANNTG) in muscle gene promoters
• Pioneer factor activity—can access target sites in closed chromatin, initiating the chromatin remodeling needed for differentiation

Homeodomain Proteins (Hox Genes)

• Control body plan and segment identity—mutations cause dramatic homeotic transformations (e.g., legs where antennae should be)
• Helix-turn-helix DNA binding—the 60-amino-acid homeodomain is highly conserved from flies to humans
• Collinear expression—Hox genes are arranged on chromosomes in the same order as their expression domains along the body axis

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Regulatory Logic: Combinatorial Control and Cooperativity

No transcription factor works alone. The specific combination of factors present—and how they interact—determines the transcriptional output.

Cooperative Binding

• Adjacent factors stabilize each other's binding—protein-protein interactions between nearby transcription factors increase overall DNA affinity
• Creates switch-like responses—cooperativity converts gradual changes in factor concentration into sharp on/off transcriptional responses
• Enables integration of multiple signals—a gene can require several conditions to be met before activation occurs

Enhancers and Silencers

• Enhancers boost transcription from a distance—can be located thousands of base pairs away, upstream, downstream, or within introns
• DNA looping brings enhancers to promoters—cohesin and mediator complexes facilitate physical contact between distant regulatory elements
• Silencers work through analogous mechanisms—recruit repressive factors and chromatin modifiers to shut down transcription

Post-Translational Regulation of Activity

• Phosphorylation controls localization and activity—kinase cascades (like MAPK) can activate cytoplasmic factors by triggering nuclear import
• Ligand binding induces conformational change—nuclear receptors and many other factors are held inactive until the appropriate signal arrives
• Proteolytic cleavage releases active forms—some factors (like SREBP) are membrane-bound until specific signals trigger their release

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Quick Reference Table

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Self-Check Questions

1. Which two DNA-binding domains require dimerization to function, and how does this expand regulatory possibilities?

2. Compare the roles of TFIID and TFIIH in transcription initiation—which acts first, and what distinct functions does each provide?

3. How do nuclear receptors and heat shock factors differ in their mechanisms of activation, even though both are classified as inducible transcription factors?

4. A mutation eliminates the activation domain of a transcription factor but leaves the DNA-binding domain intact. Predict the effect on target gene expression and explain why this might act as a dominant negative.

5. Explain how enhancers can regulate transcription from thousands of base pairs away. What molecular mechanism allows this "action at a distance"?