Transcription Factors, DNA Binding, and Chromatin Regulation in Eukaryotic Gene Expression

Transcription factors

Proteins that bind specific DNA sequences to regulate transcription by recruiting or blocking the transcriptional machinery.

Activation domain

The region of a transcription factor that interacts with coactivators, Mediator, or general transcription machinery to increase transcription.

Modularity of transcription factors

Principle that transcription factors have separable domains (DNA-binding, activation/repression, dimerization) that can be mixed and matched.

Dimerization domain

Protein domain that allows transcription factors to form dimers (e.g., leucine zipper), enabling cooperative DNA binding.

Zinc finger motif

A common DNA-binding motif where zinc stabilizes a small fold that contacts base pairs in the major groove.

Homeodomain

60-amino-acid DNA-binding domain common in developmental regulators that recognizes specific DNA sequences.

Leucine zipper motif

Protein dimerization motif that mediates DNA binding in basic-region leucine zipper (bZIP) transcription factors.

Helix-turn-helix motif

Structural motif in DNA-binding proteins where two α-helices are joined by a short turn, one helix contacts the DNA.

Basic region DNA-binding domain

Positively charged region (basic) in some TFs that binds DNA, often in bZIP and bHLH proteins.

Sequence-specific DNA binding

Recognition of short DNA motifs by transcription factors, enabling targeted gene regulation.

Combinatorial control

Regulation of gene expression by different combinations of transcription factors binding to the same regulatory region to produce cell-type specific outputs.

Proximal promoter

Regulatory DNA region within ~100 bp of the transcription start site containing core promoter elements like the TATA box.

Core promoter

Minimal DNA sequence necessary to recruit the preinitiation complex and position RNA polymerase II at the start site.

TATA box

Consensus core promoter sequence (TATAAA) found in ~25% of eukaryotic promoters, bound by TBP/TFIID.

General transcription factors (GTFs)

Proteins (e.g., TFIID, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH) that assemble at core promoters to recruit and position RNA Pol II.

TFIID

A complex containing TBP and TAFs that recognizes promoter elements and nucleates PIC assembly.

TBP (TATA-binding protein)

Subunit of TFIID that directly binds the TATA box and bends DNA to facilitate PIC assembly.

Preinitiation complex (PIC)

The assembly of general transcription factors and RNA polymerase II at a promoter prior to transcription initiation.

TFIIH

A general transcription factor with helicase activity that opens the transcription bubble and a kinase that phosphorylates the Pol II CTD.

RNA polymerase II

The multisubunit enzyme that synthesizes mRNA in eukaryotes and whose CTD phosphorylation state regulates progression through transcription.

CTD phosphorylation

Phosphorylation of the Pol II C-terminal domain by TFIIH (and other kinases) that promotes promoter clearance and coordinates co-transcriptional processing.

Mediator complex

A large multiprotein coactivator that transmits signals from transcription factors to RNA polymerase II and helps recruit the PIC.

Coactivators

Proteins (e.g., CBP, Mediator, GCN5) that do not bind DNA directly but increase transcription by interacting with activators and chromatin.

Corepressors

Proteins that repress transcription by interacting with repressors and recruiting chromatin-modifying enzymes (e.g., HDACs).

Enhancer

Short DNA element bound by transcription factors that increases transcription from a distance and can function upstream, downstream, or within introns.

Proximal enhancer

Regulatory sequences located close to the promoter (part of proximal regulatory region) that enhance transcription efficiency.

Distal enhancer

Enhancer located far from the promoter that can loop to interact with promoter-bound factors and influence transcription.

UAS (upstream activating sequence)

Yeast equivalent of an enhancer; binding sites for activators like Gal4.

Enhanceosome

A tightly assembled complex of multiple transcription factors bound cooperatively to an enhancer that recruits coactivators and chromatin remodelers.

Reporter gene

An easily assayed gene (e.g., lacZ) used experimentally to monitor regulatory sequence activity.

Modular activation demonstration (LexA-Gal4 experiment)

Experiment showing that a DNA-binding protein fused to an activation domain can activate transcription, proving separable TF domains.

Gal4

Yeast transcription factor that binds UAS elements and activates GAL genes; contains separate DNA-binding and activation domains.

Gal80

Repressor that binds Gal4's activation domain to prevent activation in the absence of galactose.

Gal3

Galactose sensor/inducer that binds galactose and ATP and interacts with Gal80 to relieve repression of Gal4.

Regulation by protein-protein interaction

Mode where TF activity is controlled by interactions (e.g., release of an activator from an inhibitor) rather than direct DNA binding changes.

Cell-type specific expression

Result of combinations of TFs and chromatin states that produce unique gene expression patterns across cell types.

Yeast GAL pathway constituents

GAL1,GAL2,GAL7,GAL10 encode metabolic enzymes; GAL3, GAL4, GAL80 regulate expression.

Recruitment model of activation

Model where activators stimulate transcription by recruiting coactivators, Mediator, and components of PIC to the promoter.

Transcriptional synergy

Phenomenon where multiple activators bound to an enhancer produce a combined effect greater than the sum of individual effects.

RNA Pol II pausing

Regulatory step where Pol II initiates and pauses near the promoter; release from pausing can control gene expression timing.

Chromatin

Complex of DNA and histone proteins that packages eukaryotic genomes and regulates access to DNA.

Nucleosome

Basic repeating unit of chromatin: ~147 bp of DNA wrapped ~1.65 turns around a histone octamer.

Histone octamer

Core of nucleosome made of two copies each of H2A, H2B, H3, and H4.

Histone H1

Linker histone that binds DNA between nucleosomes and helps compact chromatin into higher-order structures.

Nucleosome spacing

Average of ~200 bp between nucleosome centers (including linker DNA); nucleosomes can be repositioned by remodelers.

Euchromatin

Less compact chromatin associated with active transcription and accessible regulatory regions.

Heterochromatin

Highly compact chromatin associated with silenced genes, repeats, centromeres, and telomeres.

Constitutive heterochromatin

Regions that remain condensed across cell types and cell cycle (e.g., centromeres, telomeres).

Chromatin fiber (30-nm)

Higher-order folding of nucleosome arrays into a thicker fiber aided by H1 and histone tail interactions.

Nucleosome-free region (NFR)

Short regions at active promoters and enhancers where nucleosomes are excluded to allow TF and PIC binding.

Topologically associating domain (TAD)

Self-interacting genomic region where enhancers and promoters are more likely to physically contact each other.

CTCF

Insulator-binding protein that helps form TAD boundaries and mediates enhancer-promoter specificity.

Insulator

Regulatory DNA element that blocks enhancer action when placed between enhancer and promoter or acts as a barrier to heterochromatin spread.

Enhancer-promoter looping

Physical interaction where an enhancer bound by TFs contacts the promoter to stimulate transcription.

Chromatin modification

Chemical covalent changes to histone tails or DNA (e.g., acetylation, methylation) that influence chromatin structure and TF binding.

Histone tail acetylation

Addition of acetyl groups to lysines by HATs, neutralizing positive charge and loosening histone-DNA interactions to promote transcription.

HAT (histone acetyltransferase)

Enzyme that acetylates histone lysines (e.g., GCN5, CBP), associated with activation.

HDAC (histone deacetylase)

Enzyme that removes acetyl groups, increasing chromatin compaction and repressing transcription.

Histone methylation

Covalent addition of methyl groups to lysine or arginine residues; can correlate with activation or repression depending on site and degree.

H3K4me3

Trimethylation of histone H3 at lysine 4 associated with active promoters and transcription start sites.

H3K9 methylation

Methylation of H3 lysine 9 associated with heterochromatin and recruitment of HP1.

Histone code hypothesis

Idea that combinations of histone modifications constitute a regulatory code read by proteins to specify transcriptional outcomes.

Writers

Enzymes that add chromatin marks (e.g., HATs, HMTases for methylation, DNMTs for DNA methylation).

Erasers

Enzymes that remove chromatin marks (e.g., HDACs, demethylases).

Readers

Proteins that recognize specific chromatin marks and mediate downstream effects (e.g., bromodomains bind acetyl-lysine).

Bromodomain

Protein domain that recognizes acetylated lysine residues on histones.

Chromodomain

Protein domain that recognizes methylated lysines (e.g., HP1 binds H3K9me).

DNA methylation (5mC)

Addition of a methyl group to cytosine in CpG dinucleotides, commonly associated with transcriptional repression in vertebrates.

CpG island

Regions (~200-4000 bp) with high CpG density often found at promoters and typically unmethylated in active genes.

DNA methyltransferase (DNMT)

Enzyme that catalyzes the addition of methyl groups to cytosine residues, establishing 5mC.

CpG methylation effect

Methylated CpGs recruit methyl-binding proteins and corepressors, promoting chromatin compaction and silencing.

Organisms lacking DNA methylation

Drosophila, C. elegans, and S. cerevisiae have little or no genomic CpG methylation.

Chromatin remodeling complexes

ATP-dependent multisubunit complexes (e.g., SWI/SNF) that reposition or evict nucleosomes to alter DNA accessibility.

SWI/SNF complex

An ATP-dependent chromatin remodeler that slides or ejects nucleosomes to expose promoter elements (contains SWI2/SNF2 ATPase).

Discovery of SWI/SNF

Identified in genetic screens for sugar non-fermenting (snf) and switching defects (swi) in yeast; same locus impacts both phenotypes.

Mechanisms of remodeling

Slide nucleosomes, eject histone octamers, or exchange histone variants, using ATP hydrolysis.

Histone variants

Noncanonical histones (e.g., H2A.Z, H3.3) that can replace canonical histones and alter nucleosome stability/function.

H2A.Z role

Variant often incorporated near promoters and enhancers associated with transcriptional responsiveness.

Chromatin remodeling exposes regulatory sequences

Removal or repositioning of nucleosomes allows TFs and PIC to bind previously occluded DNA.

Enhanceosome function

Ordered assembly of TFs and coactivators at enhancers that recruits HATs and remodelers to activate transcription.

GCN5

Histone acetyltransferase that acetylates lysines like H3K9 and H4K8 during activation.

CBP (CREB-binding protein)

A coactivator with HAT activity that bridges TFs and transcriptional machinery.

β-interferon enhanceosome

Well-studied example where several TFs assemble cooperatively at an enhancer to trigger high-level IFN-β transcription during viral infection.

Mediator recruits Pol II

Mediator subunit interactions bridge enhancer-bound activators and general transcription factors to recruit RNA Pol II.

Tup1 corepressor

Yeast corepressor that is recruited by sequence-specific repressors (e.g., Mig1) and interacts with HDACs to repress transcription.

Mig1 repressor

Yeast repressor that recruits Tup1 to repress GAL1 in presence of glucose via histone deacetylation.

Short-term gene activation in chromatin

Rapid transcriptional upregulation achieved by multiple TFs binding enhancer clusters and recruiting coactivators & remodelers.

Chromatin remodeling energy source

ATP hydrolysis by remodeler ATPase subunits provides energy for nucleosome repositioning.

Enhancer-blocking insulator

Element that blocks enhancer action on promoters when positioned between them, maintaining regulatory specificity.

Barrier insulator

Element that prevents heterochromatin spreading by creating a local environment unfavorable to silencing.

Topological organization and TADs

TADs compartmentalize chromosomes so enhancers interact preferentially with promoters within the same domain.

Long-term gene inactivation

Stable silencing of genes achieved by repressive chromatin marks and DNA methylation maintained through cell divisions (epigenetic inheritance).

Epigenetic inheritance

Transmission of gene expression states (chromatin marks, DNA methylation) through cell divisions without changes in DNA sequence.

Position-effect variegation (PEV)

Phenomenon where gene relocation near heterochromatin causes stochastic silencing in some cells but not others, producing mosaic phenotypes.

HP1 (Heterochromatin Protein 1)

Protein that binds H3K9me and promotes heterochromatin formation and spreading.

Su(var) genes

Suppressors of variegation; mutations reduce heterochromatin spreading.

E(var) genes

Enhancers of variegation; mutations increase heterochromatin spreading.

Mechanism of heterochromatin spreading

HMTase methylates H3K9 → HP1 binds → recruits more HMTase → propagation of H3K9me and HP1 binding.

Barrier insulator function

Blocks the propagation of repressive chromatin into neighboring domains to protect gene activity.

Genomic imprinting

Parent-specific silencing of autosomal genes due to parent-specific epigenetic marks at imprinting control regions (ICRs).