Regulation of Transcription

9.1: Principles of Transcription Regulation

●​ Overview of Transcriptional Regulation
○​ Transcriptional regulation controls when and how much a gene is expressed
○​ This process ensures that cells produce the right proteins at the right time, which
is essential for:
■​ Cell differentiation (how cells become specialized, like muscle or nerve
cells)
■​ Development (forming tissues and organs during growth)
■​ Responding to environmental signals (like stress or nutrient availability)
○​ Transcription factors are proteins that regulate gene expression by either:
■​ Activating transcription (helping RNA polymerase bind)
■​ Repressing transcription (blocking RNA polymerase)
●​ Levels of Transcriptional Regulation
○​ RNA Polymerase Holoenzyme: The enzyme responsible for transcribing DNA
into RNA
○​ Gene regulation can happen at different stages:
■​ Initiation: The most common regulatory step, where RNA polymerase is
either encouraged or blocked from starting transcription
■​ Elongation: Some genes regulate how efficiently RNA is synthesized after
transcription begins
■​ Termination: Control over when transcription stops
■​ Post-transcriptional Regulation: Some RNA molecules self-regulate how
much of a protein gets made
○​ Repressors: Proteins that decrease transcription by blocking RNA polymerase
○​ Activators: Proteins that increase transcription by making it easier for RNA
polymerase to bind
●​ Regulatory Proteins and Binding Sites
○​ Many genes are controlled by regulatory proteins that bind near the gene
○​ These regulatory sequences are short DNA segments where proteins attach to
influence transcription
○​ Regulatory sequences can be:
■​ Near the promoter (immediately upstream)
 Regulation of Transcription
■​ Far away, requiring DNA looping to bring them into contact with RNA
polymerase
○​ In Bacteria:
■​ Regulatory sequences are called operator sites
■​ These sites are usually very close to the promoter or even overlap with it
■​ If an operator is farther away, the DNA loops to bring the regulatory
protein closer to the polymerase
●​ Eukaryotic Enhancers and Distal Regulation
○​ Eukaryotic genes are more often regulated by distal (far away) sequences
○​ These distant regulatory sequences are called enhancers
○​ Enhancers can be:
■​ Upstream (before the gene)
■​ Downstream (after the gene)
○​ How do distant enhancers regulate transcription?
■​ The DNA loops, bringing the enhancer into contact with the promoter
■​ This looping is aided by architectural proteins, which help stabilize the
interaction
●​ Locus Control Regions (LCRs)
○​ LCRs are a specialized type of enhancer region found in complex eukaryotic
genes
○​ Example: The beta-globin gene (important for hemoglobin in red blood cells)
○​ LCRs contain multiple elements:
■​ Enhancers: Increase transcription
■​ Insulators: Prevent unwanted interactions with nearby genes
○​ How do LCRs work?
■​ Multiple proteins bind to the LCR
■​ This recruits additional factors that help RNA polymerase start
transcription
■​ DNA loops to bring the LCR closer to the gene's promoter
●​ DNA-Binding Proteins and Specificity
○​ For regulation to be precise, regulatory proteins must recognize the correct DNA
sequence
 Regulation of Transcription
○​ Each regulatory protein contains a DNA-binding domain, which allows it to
attach to a specific DNA sequence
○​ Regulatory proteins often have additional functional domains that:
■​ Help proteins bind together (oligomerization)
■​ Activate or repress transcription
■​ Interact with other transcription factors
○​ Eukaryotic transcription factors often recruit "helper" proteins:
■​ Co-activators: Increase transcription but do not bind DNA directly
■​ Co-repressors: Decrease transcription but also do not bind DNA directly
●​ Regulation by Allosteric Effectors
○​ Gene regulation can change in response to environmental conditions
○​ Allosteric effectors are small molecules that bind to regulatory proteins and
change their shape
■​ Estrogen is an allosteric effector that binds to the estrogen receptor and
influences gene transcription
○​ Other modifications can also change regulatory protein activity:
■​ Phosphorylation (adding a phosphate group)
■​ Other covalent modifications like methylation or acetylation
○​ These modifications help fine-tune gene expression by controlling:
■​ Where the regulator is located in the cell
■​ How strongly it interacts with DNA
■​ Whether it activates or represses transcription
●​ Chromatin and Transcriptional Regulation
○​ In eukaryotes, DNA is wrapped around histone proteins to form chromatin
○​ Chromatin structure affects gene accessibility:
■​ Open chromatin (euchromatin): Genes are accessible and can be
transcribed
■​ Closed chromatin (heterochromatin): Genes are tightly packed and
transcription is blocked
○​ Histone modifications regulate chromatin structure:
■​ Acetylation: Loosens chromatin → activates transcription
■​ Deacetylation: Compacts chromatin → represses transcription
○​ Histone acetyltransferases (HATs) add acetyl groups, promoting gene expression
 Regulation of Transcription
○​ Histone deacetylases (HDACs) remove acetyl groups, repressing transcription
●​ The Histone Code Hypothesis
○​ Histones can also be modified by:
■​ Acetylation
■​ Methylation
■​ Phosphorylation
■​ Ubiquitination
○​ These modifications form a "histone code" that determines gene activity
○​ Scientists are still studying how different combinations of modifications
influence transcription

9.2: DNA-binding Domains in Proteins that Regulate Transcription

●​ DNA-Binding Motifs
○​ DNA-binding motifs are specific structural patterns in proteins that allow them
to interact with DNA
○​ Some motifs are found in all organisms, while others are specific to eukaryotes or
metazoans (multicellular animals)
○​ Why are these motifs important?
■​ They enable transcription factors to read and bind specific DNA
sequences
■​ They help regulate gene activation and repression by recruiting RNA
polymerase or blocking it
●​ Helix-Turn-Helix Motif
○​ The Helix-Turn-Helix (HTH) motif is a common DNA-binding structure
○​ Found in many protein families, including bacterial repressors and homeodomain
proteins in eukaryotes
○​ Structure:
■​ It consists of two α-helices connected by a short turn
■​ The second helix (recognition helix) fits into the major groove of DNA to
make sequence-specific contacts
○​ Key Features:
■​ Often found in dimeric proteins, meaning two copies of the protein bind
to DNA together
 Regulation of Transcription
■​ The two recognition helices are spaced 3.4 nm apart, allowing them to
bind in neighboring DNA grooves
○​ Example
■​ The lac repressor in E. coli, which controls lactose metabolism, uses an
HTH motif to bind DNA
●​ The Homeodomain – A Specialized Helix-Turn-Helix
○​ A homeodomain is a monomeric version of the HTH motif found in many
eukaryotic transcription factors
○​ It plays a major role in developmental gene regulation
○​ Structure:
■​ Three α-helices, with Helix 3 (red) inserting into the major groove of DNA
■​ The N-terminal arm interacts with the minor groove for extra stability
○​ Example:
■​ Homeobox (Hox) genes, which are crucial for body plan development in
animals
●​ Zinc Finger Motifs
○​ Zinc fingers are one of the most versatile and common DNA-binding domains in
eukaryotes
○​ Structure:
■​ A short α-helix and two β-strands wrapped around a central zinc ion (Zn²⁺)
■​ The zinc ion stabilizes the structure, allowing it to bind DNA
○​ Key Features:
■​ Zinc fingers interact with the minor groove of DNA
■​ Many proteins contain multiple zinc fingers, each recognizing a different
DNA sequence
■​ The most common type is the Cys2His2 zinc finger, where the zinc ion is
coordinated by two cysteine and two histidine residues
○​ Example:
■​ The TFIIIA transcription factor in Xenopus laevis (a frog species) uses
zinc fingers to bind and regulate ribosomal RNA genes
●​ Coiled-Coil DNA Binding Motifs
○​ Coiled-coils are alpha-helices that wrap around each other, forming a stable
structure
 Regulation of Transcription
○​ These motifs are found in leucine zipper and helix-loop-helix proteins
○​ Types:
■​ Basic region-leucine zipper (bZIP) proteins:
●​ Consist of two long α-helices (~60 amino acids long)
●​ These helices have hydrophobic leucine residues that interact,
forming a "zipper”
●​ The N-terminal ends of the helices separate and sit in the major
groove of DNA
●​ Example: CREB (cAMP response element-binding protein)
■​ Basic region-helix-loop-helix (bHLH) proteins:
●​ Similar to bZIP but contain a loop between two helices
●​ Only become structured when bound to DNA
●​ Example: MyoD, a muscle-specific transcription factor
●​ Beta-Sheet DNA Recognition
○​ While α-helices are the most common DNA-binding structures, beta-sheets and
loops can also bind DNA
○​ Example 1: MetJ Repressor
■​ Binds DNA using two β-strands instead of helices
○​ Example 2: Nuclear Factor kappa B (NF-κB)
■​ A mammalian transcription factor important in immune response
■​ Uses beta sheets to interact with DNA
○​ Example 3: Immunoglobulin Transcription Factors
■​ Some antibody-related transcription factors use entirely beta-sheet
structures to recognize DNA

9.3: Mechanisms for Regulating Transcription Initiation in Bacteria

●​ Transcription regulation in bacteria is primarily controlled at initiation, meaning the
decision to start transcription is tightly controlled.
●​ Key mechanisms include:
○​ Preventing RNA polymerase from binding to the promoter (negative regulation)
○​ Enhancing RNA polymerase’s ability to bind and initiate transcription (positive
regulation)
○​ Using small molecules that act as signals to regulate transcription factors
 Regulation of Transcription
●​ Trp Operon – Negative Regulation
○​ negative transcriptional regulation
○​ helix-turn-helix protein that binds to the operator when tryptophan is abundant,
blocking transcription
○​ When tryptophan levels are low, the repressor cannot bind to the operator,
allowing transcription to occur so the cell can synthesize more tryptophan
○​ This feedback inhibition prevents unnecessary gene expression and conserves
energy
●​ CAP and Positive Transcription Regulation
○​ Catabolite Activator Protein (CAP), also called the cAMP receptor protein (CRP),
activates transcription in response to low glucose levels
○​ How it works:
■​ When glucose is low, cAMP levels increase
■​ cAMP binds to CAP, changing its shape and allowing it to bind upstream
of promoters
■​ CAP recruits RNA polymerase, enhancing transcription of genes needed
to metabolize alternative sugars (like lactose)
○​ CAP regulates over 100 E. coli promoters
●​ Lac Operon and Dual Regulation
○​ Lac operon is regulated by both negative and positive control:
■​ Negative regulation (Lac repressor, LacI):
●​ When lactose is absent, the Lac repressor binds to the operator,
blocking transcription
●​ When lactose is present, it binds to the repressor, causing it to
dissociate from the DNA, allowing transcription
■​ Positive regulation (CAP):
●​ When glucose is low, CAP binds to its operator site, enhancing
transcription
●​ When glucose is high, CAP is inactive, leading to weak
transcription even if lactose is present
●​ MerR Proteins and Promoter Architecture
○​ The spacing between the -10 and -35 promoter elements is important for RNA
polymerase binding
 Regulation of Transcription
○​ If the spacing is too large, polymerase cannot bind effectively
○​ MerR family regulators solve this issue by binding to the DNA and twisting it,
changing the spacing to optimize transcription
○​ This structural modification ensures genes are transcribed efficiently
●​ ATP-Dependent Transcription Activation
○​ Some transcription factors need ATP hydrolysis to activate transcription
○​ NtrC (nitrogen regulatory protein C) is an example:
■​ It binds enhancer elements far from the promoter
■​ Phosphorylation triggers NtrC to oligomerize (form a complex)
■​ It interacts with RNA polymerase, hydrolyzing ATP to open the promoter
and initiate transcription
●​ Two-Component Regulatory Systems
○​ Bacteria often sense external signals and regulate transcription accordingly
○​ Two-component systems involve:
■​ Sensor kinase: A membrane protein that detects environmental changes
■​ Response regulator: Gets phosphorylated and binds DNA to activate or
repress transcription
●​ Ex: OmpR-EnvZ system in E. coli controls osmotic stress response

9.4: Competition Between cl and Cro and Control of the Fate of Bacteriophage Lambda
●​ Bacteriophage lambda is a virus that infects E. coli
●​ It injects its DNA into the bacterium and must choose between:
○​ Lysogeny (dormant phase) – the viral DNA integrates into the bacterial genome
and is replicated with the host
○​ Lytic growth – the virus actively replicates, leading to cell destruction and release
of new viral particles
●​ The choice between these two fates depends on the competition between two key
proteins:
○​ cI (lambda repressor) – promotes lysogeny
○​ Cro – promotes lytic growth
●​ Role of cI, Cro, and cII in Decision-Making
○​ When bacteriophage lambda infects a bacterial cell, it produces both cI and Cro
proteins
 Regulation of Transcription
○​ The outcome depends on the concentration of another protein: cII
■​ cII stimulates transcription of cI, leading to high levels of cI protein
■​ If cI levels are high, it represses genes needed for the lytic cycle and
maintains lysogeny
■​ If cII is degraded (by host proteases), cI is not produced, and Cro
accumulates, leading to lytic growth
●​ Transcriptional Control at Four Promoters
○​ The competition between cI and Cro occurs at four key promoters on the phage
DNA:
■​ PR (Right Promoter)
■​ PL (Left Promoter)
■​ PRE (Promoter for Repressor Establishment)
■​ PRM (Promoter for Repressor Maintenance)
○​ PR and PL drive the expression of lytic genes
○​ PRE and PRM control the production of cI
○​ Key interactions:
■​ If cII is present, it activates PRE, producing cI
■​ If cI accumulates, it activates PRM, keeping its own production ON while
repressing PR and PL
■​ If cII is degraded, Cro is made from PR, and it represses PRM, preventing
cI expression
●​ How cI Promotes and Maintains Lysogeny
○​ cI is a transcriptional repressor that binds to operator sites in the lambda genome
○​ It has two functions:
■​ Repressing lytic genes: cI binds to PR and PL to block transcription of
genes needed for lysis
■​ Activating its own production: cI binds to PRM, ensuring that more cI is
made
○​ How does this maintain lysogeny?
■​ High cI levels prevent Cro from being expressed
■​ cI ensures the virus remains integrated into the bacterial genome as a
prophage
●​ How Cro Promotes Lytic Growth
 Regulation of Transcription
○​ If cII fails to accumulate (due to host cell proteases degrading it), cI is never
produced, and Cro takes control
○​ Cro binds to PRM, preventing transcription of cI
○​ This ensures lytic genes are expressed from PR and PL
○​ The virus replicates, assembles, and lyses the host cell
●​ Binding Affinity and Operator Sites
○​ The lambda genome contains six operator binding sites where cI and Cro
compete:
■​ OR1, OR2, OR3 (Right operator region)
■​ OL1, OL2, OL3 (Left operator region)
○​ cI binds first to OR1 and OL1 (high affinity).
■​ This recruits more cI to OR2 and OL2, forming a DNA loop that enhances
repression of PR and PL
○​ At high levels, cI binds OR3 and OL3, turning off its own production (negative
feedback)
○​ Cro binds in the reverse order:
■​ It binds OR3 first, shutting down PRM (stopping cI production)
■​ Then it binds OR2 and OR1, ensuring lytic genes are transcribed
●​ SOS Response and Switching from Lysogeny to Lysis
○​ Lysogeny must be reversible – if the host cell is under stress, the virus must
switch to lytic growth
○​ The SOS response (DNA damage response) is triggered when the bacterial cell is
in distress
○​ The bacterial RecA protein becomes activated and cleaves cI, causing it to
dissociate from DNA
○​ With cI gone, PR and PL are no longer repressed, and the virus enters the lytic
cycle
●​ The fate of lambda phage is controlled by competition between cI and Cro:
○​ If cI dominates → Lysogeny (viral DNA integrates into host genome)
○​ If Cro dominates → Lytic growth (virus replicates and destroys the host)
●​ Factors:
○​ cII levels (if high → lysogeny, if low → lysis)
○​ Host conditions (healthy cells favor lysogeny, stressed cells favor lysis)
 Regulation of Transcription
○​ SOS response (triggers lysis if the host is damaged)

9.5: Regulation of Transcription Termination in Bacteria

●​ Transcription termination is a critical regulatory step in bacteria
●​ There are two main types of termination:
○​ Intrinsic (Rho-independent) termination – relies on RNA forming a stem-loop
structure
○​ Rho-dependent termination – requires the Rho protein to disrupt transcription
●​ Some genes override termination using special regulatory mechanisms
●​ Anti-Termination in Bacteriophage Lambda
○​ Some bacteriophage (virus) genes only get transcribed when termination is
prevented, called anti-termination
○​ How it works:
■​ The N protein is produced early in infection
■​ RNA polymerase starts transcription but encounters termination sites (tL
and tR)
■​ Without intervention, transcription stops at these sites
■​ When N protein accumulates, it binds to nut sites in the transcribed RNA
■​ This recruits other proteins that modify RNA polymerase, allowing it to
bypass termination sites
●​ Role of Q Protein in Lambda Phage
○​ Another antitermination protein, Q protein, regulates late-stage lytic genes in
lambda phage
○​ How Q protein works:
■​ Q binds at the Q binding element (QBE), located between the -35 and -10
promoter regions
■​ Normally, transcription terminates early, right after the promoter
■​ Q protein interacts with the sigma factor (σ70) of RNA polymerase
■​ This interaction modifies the elongation complex, allowing RNA
polymerase to bypass termination sites and continue transcribing late
lytic genes
●​ Attenuation as a Mechanism of Transcriptional Control
 Regulation of Transcription
○​ Attenuation is a termination mechanism used to regulate amino acid
biosynthesis genes in bacteria
○​ This mechanism is dependent on RNA secondary structure
○​ Example: The trp Operon
■​ The trp operon is regulated based on tryptophan levels
■​ RNA leader sequences can fold into two alternative structures:
●​ Stem-loop structure with a terminator (high tryptophan) → Stops
transcription.
●​ Stem-loop structure without a terminator (low tryptophan) →
Allows transcription to continue
■​ This regulation allows bacteria to fine-tune tryptophan synthesis based
on availability
●​ How the trp Operon Leader Sequence Works
○​ The leader sequence of the trp mRNA contains:
■​ A short peptide-coding region
■​ A series of tryptophan codons
■​ Four RNA blocks (1, 2, 3, and 4) that can form different secondary
structures
○​ Regulation is based on ribosome behavior:
■​ Low tryptophan → Ribosome stalls at tryptophan codons → Regions 2 and
3 pair → No terminator → Transcription continues
■​ High tryptophan → Ribosome moves fast → Regions 3 and 4 pair →
Terminator forms → Transcription stops
●​ Riboswitches – RNA-Based Gene Regulation
○​ Riboswitches are RNA structures that directly bind small molecules to control
gene expression
○​ Structure of riboswitches:
■​ Aptamer region – Binds to the metabolite
■​ Expression platform – Controls whether transcription continues or
terminates
○​ Example: The Adenine Riboswitch in Bacillus subtilis
■​ Low adenine → RNA forms an anti-terminator → Transcription continues
■​ High adenine → RNA forms a terminator → Transcription stops
 Regulation of Transcription
○​ Riboswitches provide rapid regulation without needing proteins

9.6: Regulation of Transcription Initiation and Elongation in Eukaryotes

●​ Eukaryotic transcription is regulated primarily by DNA-binding proteins that recruit
co-activators or co-repressors
●​ These factors do not work alone but interact with other proteins to either promote or
inhibit RNA polymerase II transcription
●​ Example: ELK1
○​ ELK1 is a transcription factor that recruits Mediator, which is needed for RNA
polymerase II activity
○​ Mitogens (extracellular signals) activate kinases that phosphorylate ELK1,
leading to recruitment of Mediator and activation of transcription
●​ Regulation of Galactose Metabolism in Yeast
○​ The Gal4 transcriptional activator regulates galactose metabolism genes
○​ Key proteins involved:
■​ Gal4: Binds to UASG (Upstream Activating Sequence for Galactose) to
activate transcription
■​ Gal80: Inhibits Gal4 in the absence of galactose
■​ Gal3: Senses galactose presence and removes Gal80 inhibition, allowing
Gal4 to activate transcription
○​ Process:
■​ Without galactose → Gal80 binds Gal4 and blocks activation
■​ With galactose → Gal3 binds Gal80, removing repression and allowing
Gal4 to recruit SAGA and Mediator, activating transcription
●​ Repression of Transcription by Ume6 in Yeast
○​ Ume6 is a transcriptional regulator that can act as both a repressor and activator
based on cellular conditions
○​ Repression (in presence of nutrients like nitrogen and carbon):
■​ Ume6 binds DNA and recruits co-repressors Sin3, Rpd3, and Isw2
■​ Rpd3 (histone deacetylase) removes acetyl groups from histones →
chromatin compacts → transcription is repressed
■​ Isw2 (nucleosome remodeling enzyme) helps form a repressive chromatin
structure
 Regulation of Transcription
○​ Activation (in absence of nutrients):
■​ Ume6 is phosphorylated, causing Sin3 and Rpd3 to dissociate
■​ A co-activator Ime1 is recruited, allowing transcription to proceed
●​ Regulation of Transcription Elongation in Drosophila Hsp70 Gene
○​ RNA polymerase can pause after initiating transcription. This pausing is a
regulatory mechanism
○​ Example: Drosophila Hsp70 (Heat-Shock Protein 70) gene:
■​ Hsp70 protects cells from heat stress
■​ Without heat shock, GAGA factor recruits NURF, keeping the promoter
open
■​ Transcription starts but then pauses because RNA polymerase is not
sufficiently phosphorylated
■​ Heat shock causes the Heat Shock Factor (Hsf) to trimerize and bind to
heat shock elements (HSEs)
■​ Hsf recruits Mediator and a kinase phosphorylates RNA polymerase II,
allowing elongation to continue
●​ HIV Transcription and Anti-Termination
○​ HIV uses an anti-termination mechanism to regulate viral transcription
○​ Key elements:
■​ TAR element (a stem-loop RNA structure) acts as a termination signal
■​ The Tat protein (HIV regulatory protein) binds to TAR
■​ Tat recruits pTEFb kinase (Cdk9-CyclinT), which phosphorylates RNA
polymerase II CTD
■​ This phosphorylation prevents premature termination, allowing
full-length viral RNA synthesis

9.7: Combinatorial Regulation of Eukaryotic Transcription

●​ Combinatorial regulation refers to the control of gene expression by multiple
transcription factors and signals
●​ A single gene can be activated or repressed depending on the combination of factors
present
 Regulation of Transcription
●​ This system allows for fine-tuned gene expression and enables complex cell
differentiation and responses to environmental signals
●​ Example: Yeast Mating Types
○​ Yeast cells exist as haploid a, haploid α, or diploid a/α cells
○​ The expression of mating-type genes is controlled by a set of transcriptional
regulators
●​ Regulation of Yeast Mating-Type Genes
○​ The three cell types (a, α, and a/α) have distinct gene expression patterns
controlled by four key regulators:
■​ a1
■​ α1
■​ α2
■​ MCM1 (a general transcription factor)
○​ Mating-type determination:
■​ a cells express a-specific genes regulated by MCM1
■​ α cells express α-specific genes activated by α1 and repressed by α2
■​ a/α diploid cells suppress mating genes and can undergo meiosis under
starvation conditions
●​ Combinatorial Regulation in a/α Diploid Cells
○​ In a/α diploid cells, the combination of a1 and α2 proteins forms a heterodimer
○​ This heterodimer binds to DNA and represses genes required for mating
○​ Key outcomes:
■​ The α1 gene is turned off → No α-specific genes are expressed
■​ RME1 (a repressor of meiosis genes) is also turned off → Allows meiosis
when nutrients are low
○​ This combinatorial regulation ensures diploid cells do not attempt to mate, but
instead prepare for meiosis when conditions worsen

●​ Combinatorial Control in Higher Eukaryotes – Interferon-β Enhanceosome

○​ In mammals, combinatorial control is seen in the regulation of immune response
genes.
○​ Example: Interferon-β (IFN-β) gene
■​ The IFN-β gene is activated in response to viral infections
 Regulation of Transcription
■​ Multiple transcription factors bind to an enhancer sequence, forming an
enhanceosome
■​ An important architectural DNA-binding protein, HMG-I(Y), bends the
DNA to help other transcription factors bind
■​ Once the enhanceosome is fully assembled, the IFN-β gene is transcribed,
triggering an immune response
●​ Full Summary:
○​ Combinatorial regulation allows precise control over gene expression
■​ Yeast mating-type regulation shows how different combinations of
transcription factors determine cell fate
■​ Diploid cells use combinatorial repression to prevent mating and allow
for meiosis when necessary
■​ In humans, interferon-β activation relies on multiple transcription factors
and DNA bending
○​ This regulatory strategy enables eukaryotic cells to integrate multiple signals and
respond appropriately

9.8: The Role of Signaling Cascades in the Regulation of Transcription

●​ Cells constantly adjust gene expression in response to:
○​ Developmental signals
○​ Environmental changes
○​ Hormones and metabolic changes
○​ Pathogen infections
●​ Many of these responses are mediated by signaling cascades, where a series of molecular
interactions lead to transcriptional changes
●​ Example: Nuclear receptor proteins
○​ These directly regulate gene expression in response to small molecules like
hormones
○​ Nuclear receptors have two domains:
■​ DNA-binding domain (recognizes specific genes)
■​ Ligand-binding domain (responds to signals like hormones)
●​ Nuclear Receptors and Ligand-Dependent Gene Activation
○​ Nuclear receptors regulate transcription based on ligand binding
 Regulation of Transcription
○​ How it works:
■​ Without a ligand (e.g., estrogen), the receptor is bound to a co-repressor,
keeping transcription OFF
■​ When a ligand binds, it induces a conformational change, releasing
co-repressors
■​ The receptor recruits co-activators, leading to gene activation
○​ Example: Estrogen Receptor (ER)
■​ Estrogen binds to ER, which then activates genes related to cell growth
and development
■​ This mechanism is critical in breast cancer, where estrogen-responsive
genes can promote tumor growth
●​ Nuclear Receptors Can Also Regulate Nuclear Localization
○​ Some nuclear receptors are not always inside the nucleus
○​ Example: Glucocorticoid Receptor (GR)
■​ In the absence of glucocorticoids, GR remains in the cytoplasm
■​ When a glucocorticoid hormone binds, GR undergoes a conformational
change, exposing its nuclear localization signal (NLS)
■​ This allows GR to enter the nucleus and activate transcription
●​ NF-κB and Inflammatory Signaling
○​ NF-κB (Nuclear Factor Kappa B) is a key transcription factor in immune
responses
○​ In unstimulated cells, NF-κB is kept inactive in the cytoplasm by I-κB (Inhibitor
of NF-κB)
○​ How NF-κB is activated:
■​ Infection or stress triggers a signaling cascade
■​ I-κB kinase (IKK) phosphorylates I-κB, marking it for degradation
■​ Once I-κB is degraded, NF-κB’s nuclear localization signal (NLS) is
exposed, allowing it to enter the nucleus
■​ NF-κB activates genes related to inflammation, immune response, and
cell survival

9.9: Gene Silencing

 Regulation of Transcription
●​ Gene silencing refers to the long-term inactivation of specific genes, often over multiple
cell divisions (epigenetic inheritance)
●​ It is primarily caused by changes in chromatin structure:
○​ Euchromatin: Open and transcriptionally active
○​ Heterochromatin: Condensed and transcriptionally silent
●​ Example: Yeast Mating Locus
○​ The yeast MAT locus controls mating type (a or α cells)
○​ Extra copies of mating genes exist on chromosome III but are silenced
○​ HMRa and HMLα regions are inactive due to chromatin modifications
●​ Silencing of HMLα and HMRa by Sir Proteins
○​ Silencing Information Regulator (Sir) proteins maintain heterochromatin in yeast
○​ Key players:
■​ Sir2: A histone deacetylase that removes acetyl groups, leading to
chromatin compaction
■​ Sir3 & Sir4: Spread heterochromatin along the chromosome
■​ Abf1, Rap1, Orc1: Help recruit Sir proteins to the silencing regions
○​ Effect:
■​ Silencing spreads along the chromatin, blocking transcription
■​ Telomere-adjacent genes are also silenced in a similar manner
●​ DNA Methylation and Imprinting
○​ DNA methylation is a major mechanism of transcriptional silencing
○​ Example: IGF2 and H19 Genes (Genomic Imprinting)
■​ IGF2: A growth factor gene expressed only from the paternal
chromosome
■​ H19: A non-coding RNA gene expressed only from the maternal
chromosome
○​ Mechanism:
■​ A region called the Insulator Control Region (ICR) controls which gene is
active
■​ CTCF protein binds to ICR when it is unmethylated (maternal
chromosome), blocking IGF2 and allowing H19 expression
■​ On the paternal chromosome, ICR is methylated, preventing CTCF
binding → IGF2 is transcribed, and H19 is silenced
 Regulation of Transcription
○​ Failure of imprinting can cause diseases like Beckwith-Wiedemann syndrome,
where excessive IGF2 leads to overgrowth and cancer risk
●​ MeCP2 and Human Gene Silencing
○​ MeCP2 is a protein that binds methylated DNA and recruits co-repressors
(Sin3A) and histone deacetylases (HDACs)
○​ MeCP2 mutations cause Rett Syndrome, a severe neurological disorder in girls.
■​ Since MeCP2 is on the X chromosome, males with mutations rarely
survive
■​ Rett Syndrome leads to intellectual disability, movement disorders, and
autism-like symptoms
●​ RNA Interference (RNAi) and Chromatin Silencing
○​ RNA interference (RNAi) helps establish heterochromatin and silence
transcription
○​ Example: Fission Yeast (S. pombe)
■​ Small RNA molecules target centromeric regions near mating-type loci
■​ These RNAs base pair to form double-stranded RNA (dsRNA)
■​ The dsRNA is processed into small interfering RNAs (siRNAs)
■​ RITS (RNA-Induced Transcriptional Silencing) Complex:
●​ siRNAs guide the RITS complex to heterochromatin
●​ RITS recruits histone deacetylases (HDACs) and histone
methyltransferases (HMTs)
●​ Histone hypoacetylation and methylation (H3K9) promote
chromatin compaction, reinforcing long-term gene silencing