Key RNA Transcription Factors

Why This Matters

Transcription is the gateway to gene expression—and understanding how it's regulated is fundamental to nearly everything in biochemistry, from metabolism to disease. You're being tested on more than just a list of protein names; exams want you to understand how the transcription machinery assembles, what each factor contributes to that process, and how cells fine-tune gene expression through activators, repressors, and chromatin modifications. These concepts connect directly to topics like signal transduction, epigenetics, and cancer biology.

Don't just memorize that TFIIH has helicase activity—know why DNA unwinding is essential for transcription initiation and how CTD phosphorylation triggers the shift to elongation. The factors below are organized by their functional roles in the transcription process: core machinery, assembly factors, regulatory proteins, and chromatin modifiers. Master the logic of each category, and you'll be able to tackle any FRQ that asks you to explain how a mutation in one factor would affect gene expression.

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The Core Transcription Engine

These are the central players that directly carry out transcription. RNA Polymerase II synthesizes mRNA, while TFIID positions the machinery at the correct start site.

RNA Polymerase II

• Synthesizes mRNA from DNA templates—the enzyme that actually performs transcription of protein-coding genes
• Requires general transcription factors (GTFs) for promoter recognition and initiation; cannot bind DNA alone
• C-terminal domain (CTD) serves as a regulatory platform whose phosphorylation state controls the transition from initiation to elongation

TFIID (Including TBP)

• Recognizes and binds the TATA box—this is the first step in assembling the pre-initiation complex (PIC)
• TBP (TATA-binding protein) bends DNA sharply upon binding, creating a structural landmark for other factors
• TAFs (TBP-associated factors) recognize other promoter elements and integrate regulatory signals from activators

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Pre-Initiation Complex Assembly Factors

These GTFs assemble sequentially to build the pre-initiation complex. Each factor recruits or stabilizes the next, creating an ordered pathway from promoter recognition to transcription initiation.

TFIIA

• Stabilizes TFIID-promoter binding—strengthens the interaction between TBP and the TATA box
• Blocks repressor binding by preventing inhibitory factors from displacing TFIID
• Enhances activator function by facilitating communication between upstream activators and the core machinery

TFIIB

• Bridges TFIID and RNA Polymerase II—physically connects promoter-bound factors to the enzyme
• Recognizes the BRE (TFIIB recognition element)—provides additional promoter specificity beyond the TATA box
• Positions the transcription start site by orienting Pol II correctly for accurate initiation

TFIIF

• Associates directly with RNA Polymerase II—escorts Pol II to the promoter as a complex
• Stabilizes Pol II-promoter interaction and suppresses nonspecific DNA binding
• Facilitates the transition to elongation by helping Pol II escape the promoter region

TFIIE

• Recruits TFIIH to the complex—essential for bringing in helicase and kinase activities
• Regulates initiation-to-elongation transition by modulating TFIIH function
• Stabilizes the open complex once DNA strands begin to separate

TFIIH

• Contains helicase activity (XPB and XPD subunits)—unwinds DNA at the transcription start site to form the open complex
• Phosphorylates the Pol II CTD at Ser5 residues via its kinase subunit (CDK7), triggering promoter escape
• Functions in nucleotide excision repair (NER)—mutations cause diseases like xeroderma pigmentosum and Cockayne syndrome

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Signal Integration: The Mediator Complex

The Mediator serves as the central hub connecting regulatory signals to the transcription machinery. It translates information from activators and repressors into changes in Pol II activity.

Mediator Complex

• Bridges activators/repressors to RNA Polymerase II—a massive multi-subunit complex (~30 subunits in humans)
• Integrates multiple regulatory signals simultaneously, allowing combinatorial control of gene expression
• Stimulates CTD phosphorylation and PIC assembly in response to activator binding

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Transcriptional Activators and Their Partners

Activators and coactivators work together to increase transcription above basal levels in response to cellular signals. They typically function by recruiting the transcription machinery or modifying chromatin structure.

Activators (e.g., NF-κB, AP-1)

• Bind enhancer sequences that can be located thousands of base pairs from the promoter
• Recruit coactivators and Mediator to stimulate PIC assembly and Pol II activity
• Respond to signaling pathways—NF-κB activates inflammatory genes; AP-1 responds to growth factors and stress

Coactivators (e.g., p300/CBP)

• Possess histone acetyltransferase (HAT) activity—acetylate histones to open chromatin structure
• Serve as scaffolds connecting DNA-bound activators to the general transcription machinery
• Acetylate non-histone proteins including transcription factors themselves, modulating their activity

Enhancer-Binding Proteins

• Bind distal enhancer elements—can act over distances of 100 kb or more
• Function through DNA looping—physical contact between enhancer and promoter regions, often visualized by chromosome conformation capture
• Provide tissue-specific and developmental regulation by integrating multiple binding sites for different factors

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Transcriptional Repressors and Their Partners

Repressors and corepressors work to silence gene expression, often by recruiting chromatin-modifying enzymes that compact DNA structure.

Repressors (e.g., NRSF/REST)

• Bind silencer elements to block transcription of target genes
• Compete with activators for DNA binding or recruit factors that block activator function
• Maintain tissue-specific expression—REST silences neuronal genes in non-neuronal tissues

Corepressors (e.g., NCoR, SMRT)

• Recruit histone deacetylases (HDACs)—remove acetyl groups to compact chromatin and block transcription
• Interact with nuclear hormone receptors in the absence of ligand, keeping target genes silent
• Form large repressive complexes that spread silencing marks across chromatin domains

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Chromatin Remodeling Factors

These complexes physically restructure nucleosomes to control DNA accessibility. Unlike histone-modifying enzymes, they use ATP hydrolysis to move or evict nucleosomes.

Chromatin Remodeling Complexes (e.g., SWI/SNF)

• Use ATP hydrolysis to slide, eject, or restructure nucleosomes—distinct from covalent histone modifications
• Create accessible DNA regions by exposing promoter and enhancer sequences to transcription factors
• Function as tumor suppressors—SWI/SNF subunit mutations are found in ~20% of human cancers

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General Transcription Factors: The Complete Set

The GTFs work as a coordinated unit to assemble the pre-initiation complex. Understanding their assembly order is key to predicting what happens when individual factors are disrupted.

General Transcription Factors (GTFs)

• Include TFIID, TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH—required for all Pol II transcription
• Assemble in a defined order: TFIID → TFIIA/TFIIB → Pol II-TFIIF → TFIIE → TFIIH
• Establish basal transcription levels—activators and repressors modulate this baseline up or down

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Quick Reference Table

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Self-Check Questions

1. Which two GTFs are most directly responsible for the transition from transcription initiation to elongation, and what specific activities do they contribute?

2. Compare the mechanisms by which SWI/SNF and p300/CBP promote transcription. Why might a cell need both types of chromatin regulation?

3. If a mutation eliminated TFIIB function, at what step would PIC assembly be blocked? Which factors would still be present at the promoter?

4. Explain how the same gene could be activated in one cell type and repressed in another, using specific examples of activators, repressors, and coregulators.

5. An FRQ describes a patient with mutations in TFIIH. Predict two distinct cellular processes that would be affected, and explain why TFIIH is required for each.