14  Gene Expression and Regulation

14.1 Turning Genes On and Off

14.1.1 The Light Switch Analogy

Imagine your house has 20,000 light switches (genes), but you don’t need all lights on all the time!

  • Kitchen lights ON during cooking

  • Bedroom lights ON at night

  • Bathroom lights ON when needed

  • Most lights OFF most of the time

Your cells do the same with genes! They turn genes ON or OFF depending on what’s needed.

14.2 Why Gene Regulation Matters

14.2.1 The Big Problem to Solve

Every cell in your body has the SAME DNA (all 20,000-25,000 genes).

But:

  • Brain cells act completely different from muscle cells

  • Liver cells do different jobs than skin cells

  • Eye cells need different proteins than stomach cells

How? Gene regulation!

14.2.2 What Is Gene Regulation?

Gene regulation = Controlling which genes are turned ON (expressed) or OFF (silenced)

Think of it like:

  • A conductor directing an orchestra (which instruments play when)

  • A traffic controller (which cars go when)

  • A restaurant manager (which dishes to make when)

14.3 Levels of Gene Regulation

Gene expression can be controlled at many different steps!

14.3.1 Level 1: Transcriptional Control (Before mRNA)

Control whether DNA is transcribed into RNA

Methods:

1. Transcription Factors

  • Proteins that bind to DNA

  • Can turn genes ON or OFF

  • Like keys that unlock or lock genes

Example - Heat Shock:

  • Cell gets hot (stress!)

  • Heat shock transcription factors activated

  • Turn ON heat shock protein genes

  • Proteins protect cell from heat damage

2. Chromatin Remodeling

  • Tight chromatin = gene OFF (inaccessible)

  • Loose chromatin = gene ON (accessible)

  • Chromatin remodeling complexes move nucleosomes

3. DNA Methylation

  • Adding methyl groups to DNA

  • Usually silences genes

  • Epigenetic control!

4. Enhancers and Silencers

  • DNA sequences far from genes

  • Enhancers boost gene expression

  • Silencers reduce gene expression

  • Can be thousands of base pairs away!

14.4 Cis vs Trans Regulatory Elements

Understanding the difference between cis and trans regulation is crucial!

14.4.1 Cis-Regulatory Elements

Definition: DNA sequences located on the same DNA molecule as the gene they regulate

Characteristics:

  • Position dependent (must be near gene)

  • Orientation dependent (usually must be in correct direction)

  • Work in cis (on same chromosome)

  • Cannot regulate genes on other chromosomes

Examples:

  1. Promoters

    • Immediately upstream of gene

    • Absolutely required for transcription

    • Contains TATA box, CAAT box, etc.

    • RNA polymerase binding site

  2. Operators (in prokaryotes)

    • Part of the lac operon system

    • Repressor proteins bind here

    • Control access to promoter

Key point: Cis elements are like addresses - they specify WHERE regulation happens

14.4.2 Trans-Regulatory Elements

Definition: DNA sequences that can regulate genes located anywhere in the genome (even on different chromosomes)

Characteristics:

  • Position independent (can be far away or on different chromosome!)

  • Orientation independent (can work in either direction)

  • Work through DNA looping

  • Can regulate multiple genes

Examples:

  1. Enhancers

    • Boost gene transcription

    • Can be thousands of base pairs away

    • Can be upstream, downstream, or even in introns!

    • Work by DNA looping to bring them near promoter

    • Bind activator transcription factors

  2. Silencers

    • Decrease gene transcription

    • Also work via DNA looping

    • Bind repressor transcription factors

    • Can be far from target gene

  3. Super-Enhancers

    • Clusters of multiple enhancers

    • Very strong activation

    • Control cell identity genes

    • Important in development and disease

    • Found near master regulator genes

How trans elements work:

DNA: =====[Enhancer]===========[Gene with Promoter]=====

     DNA loops to bring enhancer close to promoter:

          [Enhancer]
             ∩
DNA: ========╯╰==========[Gene]======

```

Key point: Trans elements work through diffusible factors (proteins) that can act at a distance

14.4.3 Long Non-Coding RNAs (lncRNAs)

What are they?

  • RNA molecules longer than 200 nucleotides

  • Do NOT code for proteins

  • Act as regulatory molecules

  • Relatively recently discovered!

How many?

  • Humans have ~20,000 protein-coding genes

  • But ~50,000+ lncRNAs!

  • Many still being discovered

Functions:

  1. Scaffold: Bring proteins together

  2. Guide: Direct proteins to specific DNA locations

  3. Decoy: Bind proteins to prevent them acting elsewhere

  4. Enhancer: Activate gene expression

Famous example - XIST:

  • Long non-coding RNA

  • Inactivates one X chromosome in females

  • Coats entire chromosome

  • Silences thousands of genes!

  • Essential for dosage compensation

Why they matter:

  • Vastly expand regulatory complexity

  • Many diseases involve lncRNA dysregulation

  • Potential therapeutic targets

  • Change our understanding of genome function

14.4.4 Level 2: Post-Transcriptional Control (After mRNA Made)

Control what happens to mRNA after transcription

Methods:

1. Alternative Splicing

  • Different exon combinations

  • One gene → multiple proteins

  • We covered this in Chapter 12!

2. mRNA Stability

  • Some mRNAs last hours

  • Others degrade in minutes

  • Controlled by sequences in mRNA

  • microRNAs can destabilize mRNA

3. mRNA Localization

  • Some mRNAs transported to specific cell locations

  • Proteins made where they’re needed

  • Like delivering mail to the right address!

14.4.5 Level 3: Translational Control (During Protein Synthesis)

Control whether mRNA is translated into protein

Methods:

1. Regulatory Proteins

  • Can block ribosome binding

  • Prevent translation

  • Like putting a “Closed” sign on mRNA

2. microRNAs (miRNAs)

  • Bind to mRNA

  • Block translation OR

  • Cause mRNA degradation

3. Ribosome Availability

  • If ribosomes are busy, translation slows

  • Cell can control ribosome numbers

14.4.6 Level 4: Post-Translational Control (After Protein Made)

Control what happens to proteins after they’re made

Methods:

1. Protein Modifications

  • Phosphorylation (activate or deactivate)

  • Ubiquitination (mark for degradation)

  • We covered PTMs in Chapter 13!

2. Protein Localization

  • Signal sequences direct proteins to destinations

  • Nucleus, mitochondria, membrane, etc.

3. Protein Degradation

  • Proteasome destroys tagged proteins

  • Controls protein lifespan

14.5 Transcription Factors: The Master Controllers

14.5.1 What Are Transcription Factors?

Transcription factors (TFs) = Proteins that control gene transcription

How they work:

  1. TF binds to specific DNA sequence

  2. Recruits RNA polymerase OR blocks it

  3. Gene is turned ON or OFF

Think of TFs like:

  • Boss giving orders (which work to do)

  • DJ choosing which songs to play

  • Chef deciding which recipes to make

14.5.2 Types of Transcription Factors

Activators:

  • Turn genes ON

  • Help RNA polymerase bind

  • Increase transcription

Repressors:

  • Turn genes OFF

  • Block RNA polymerase

  • Decrease transcription

14.5.3 Transcription Factor Domains

Most TFs have two parts:

DNA-Binding Domain:

  • Recognizes specific DNA sequences

  • Like a lock and key

  • Determines which genes it controls

Activation Domain:

  • Interacts with other proteins

  • Recruits RNA polymerase

  • Actually does the regulating

14.5.4 Master Regulators

Some TFs control many genes:

Example - MyoD (Muscle Development):

  • ONE transcription factor

  • Turns ON hundreds of muscle genes

  • Can convert skin cells into muscle cells!

  • Master regulator of muscle identity

Example - Oct4/Sox2/Nanog (Stem Cells):

  • Three TFs working together

  • Keep cells in stem cell state

  • Turn OFF = cells differentiate

14.6 Combinatorial Control

14.6.1 Many Regulators Work Together

Combinatorial control = Multiple TFs work together to control genes

Why it’s powerful:

  • 10 TFs can create thousands of combinations

  • Fine-tuned control

  • Cell-type specific expression

Example:

  • Gene needs TF-A AND TF-B AND TF-C to turn ON

  • Like needing three keys to open a vault

  • Very specific control!

Liver cells:

  • Have TF-Liver1, TF-Liver2, TF-Liver3

  • Together they activate liver genes

  • Don’t have muscle TFs

  • So muscle genes stay OFF

14.7 Signal Transduction and Gene Regulation

14.7.1 How Cells Respond to Signals

Signal transduction = Converting external signals into gene expression changes

The pathway:

  1. Signal arrives (hormone, growth factor, stress)

  2. Receptor on cell surface detects signal

  3. Signaling cascade inside cell

  4. Transcription factors activated

  5. Genes turned ON or OFF

  6. Proteins made

  7. Cell response

14.7.2 Example: Hormone Signaling

Scenario: You’re scared, adrenaline released

What happens:

  1. Adrenaline binds to receptors on cells

  2. Activates signaling proteins inside

  3. Transcription factors activated

  4. Genes for stress response turned ON

  5. Proteins made (more glucose, faster heart)

  6. You’re ready to run!

All in seconds to minutes!

14.8 Feedback Loops

14.8.1 Self-Regulating Systems

Positive Feedback:

  • Product enhances its own production

  • Like a snowball rolling downhill

  • Amplifies signals

  • Used for rapid responses

Example: Blood clotting

  • Clotting factor activates more clotting factors

  • Rapid cascade

  • Stops bleeding quickly

Negative Feedback:

  • Product inhibits its own production

  • Like a thermostat

  • Maintains steady levels

  • Most common type

Example: Thyroid hormone

  • High levels inhibit release of more hormone

  • Keeps levels stable

14.9 Development and Gene Regulation

14.9.1 How One Cell Becomes Many Cell Types

The amazing fact: All cells start with same DNA!

How specialization happens:

1. Maternal Factors:

  • Egg has proteins distributed unevenly

  • Different parts of embryo get different proteins

  • Sets up initial patterns

2. Morphogens:

  • Signaling molecules that form gradients

  • High concentration → one cell fate

  • Low concentration → different cell fate

  • Like a map with coordinates!

3. Transcription Factor Cascades:

  • First TFs activate second TFs

  • Second TFs activate third TFs

  • Complex patterns emerge

4. Cell-Cell Signaling:

  • Cells communicate with neighbors

  • Refine boundaries

  • Create sharp borders between cell types

14.9.2 The Hox Genes

Hox genes = Master regulators of body plan

What they do:

  • Control head-to-tail pattern

  • Determine where body parts go

  • Highly conserved across animals

Amazing fact: Fly Hox genes work in mice!

  • Shows deep evolutionary conservation

  • All animals use similar developmental programs

14.10 Gene Regulation in Prokaryotes vs Eukaryotes

14.10.1 Prokaryotic Gene Regulation (Simpler)

Characteristics:

  • Mainly transcriptional control

  • Operons (groups of genes controlled together)

  • Fast response to environment

  • Less complex

The lac operon (we covered in Chapter 8):

  • Classic example

  • Genes for lactose digestion

  • Turned ON when lactose present

  • Turned OFF when lactose absent

14.10.2 Eukaryotic Gene Regulation (Complex)

Characteristics:

  • Multiple levels of control

  • Chromatin structure important

  • Individual genes (not operons)

  • Long-distance regulation (enhancers)

  • More complex, more flexible

Why more complex?

  • Multicellular organisms

  • Cell differentiation needed

  • Developmental programs

  • Sophisticated responses

14.11 Diseases of Gene Regulation

14.11.1 When Regulation Goes Wrong

Cancer:

  • Tumor suppressor genes turned OFF (should be ON)

  • Oncogenes turned ON (should be OFF)

  • Loss of normal growth control

Developmental Disorders:

  • Hox gene mutations → body parts in wrong places

  • Transcription factor mutations → missing structures

Metabolic Diseases:

  • Insulin signaling disrupted (diabetes)

  • Cholesterol regulation abnormal (heart disease)

14.12 RNA Interference (RNAi)

14.12.1 Using RNA to Regulate Genes

RNA interference = Using small RNAs to silence genes

How it works:

  1. Small RNAs (21-23 nucleotides) made

  2. They bind to complementary mRNA

  3. Either block translation OR degrade mRNA

  4. Gene silenced!

Types:

  • miRNAs (microRNAs): Natural gene regulators

  • siRNAs (small interfering RNAs): Used in research/medicine

Applications:

  • Research tool (turn OFF genes to study function)

  • Potential therapies (silence disease genes)

  • Already FDA-approved for some diseases!

14.13 Key Takeaways

  • Gene regulation controls which genes are ON or OFF

  • Multiple levels: Transcriptional, post-transcriptional, translational, post-translational

  • Transcription factors are master controllers

  • Combinatorial control creates complexity from simple parts

  • Signal transduction connects external signals to gene expression

  • Feedback loops maintain stability or amplify signals

  • Development uses gene regulation to create specialized cells

  • Prokaryotes use simple regulation (operons)

  • Eukaryotes use complex, multi-layered regulation

  • Diseases often involve regulatory failures

  • RNAi is a powerful regulatory mechanism and research tool

Sources: Information adapted from molecular biology textbooks, Nature Education, Khan Academy, and gene regulation research literature.

Key point: Trans elements work through diffusible factors (proteins) that can act at a distance

14.13.1 Long Non-Coding RNAs (lncRNAs)

What are they?

  • RNA molecules longer than 200 nucleotides

  • Do NOT code for proteins

  • Act as regulatory molecules

  • Relatively recently discovered!

How many?

  • Humans have ~20,000 protein-coding genes

  • But ~50,000+ lncRNAs!

  • Many still being discovered

Functions:

  1. Scaffold: Bring proteins together

  2. Guide: Direct proteins to specific DNA locations

  3. Decoy: Bind proteins to prevent them acting elsewhere

  4. Enhancer: Activate gene expression

Famous example - XIST:

  • Long non-coding RNA

  • Inactivates one X chromosome in females

  • Coats entire chromosome

  • Silences thousands of genes!

  • Essential for dosage compensation

Why they matter:

  • Vastly expand regulatory complexity

  • Many diseases involve lncRNA dysregulation

  • Potential therapeutic targets

  • Change our understanding of genome function

14.13.2 Level 2: Post-Transcriptional Control (After mRNA Made)

Control what happens to mRNA after transcription

Methods:

1. Alternative Splicing

  • Different exon combinations

  • One gene → multiple proteins

  • We covered this in Chapter 12!

2. mRNA Stability

  • Some mRNAs last hours

  • Others degrade in minutes

  • Controlled by sequences in mRNA

  • microRNAs can destabilize mRNA

3. mRNA Localization

  • Some mRNAs transported to specific cell locations

  • Proteins made where they’re needed

  • Like delivering mail to the right address!

14.13.3 Level 3: Translational Control (During Protein Synthesis)

Control whether mRNA is translated into protein

Methods:

1. Regulatory Proteins

  • Can block ribosome binding

  • Prevent translation

  • Like putting a “Closed” sign on mRNA

2. microRNAs (miRNAs)

  • Bind to mRNA

  • Block translation OR

  • Cause mRNA degradation

3. Ribosome Availability

  • If ribosomes are busy, translation slows

  • Cell can control ribosome numbers

14.13.4 Level 4: Post-Translational Control (After Protein Made)

Control what happens to proteins after they’re made

Methods:

1. Protein Modifications

  • Phosphorylation (activate or deactivate)

  • Ubiquitination (mark for degradation)

  • We covered PTMs in Chapter 13!

2. Protein Localization

  • Signal sequences direct proteins to destinations

  • Nucleus, mitochondria, membrane, etc.

3. Protein Degradation

  • Proteasome destroys tagged proteins

  • Controls protein lifespan

14.14 Transcription Factors: The Master Controllers

14.14.1 What Are Transcription Factors?

Transcription factors (TFs) = Proteins that control gene transcription

How they work:

  1. TF binds to specific DNA sequence

  2. Recruits RNA polymerase OR blocks it

  3. Gene is turned ON or OFF

Think of TFs like:

  • Boss giving orders (which work to do)

  • DJ choosing which songs to play

  • Chef deciding which recipes to make

14.14.2 Types of Transcription Factors

Activators:

  • Turn genes ON

  • Help RNA polymerase bind

  • Increase transcription

Repressors:

  • Turn genes OFF

  • Block RNA polymerase

  • Decrease transcription

14.14.3 Transcription Factor Domains

Most TFs have two parts:

DNA-Binding Domain:

  • Recognizes specific DNA sequences

  • Like a lock and key

  • Determines which genes it controls

Activation Domain:

  • Interacts with other proteins

  • Recruits RNA polymerase

  • Actually does the regulating

14.14.4 Master Regulators

Some TFs control many genes:

Example - MyoD (Muscle Development):

  • ONE transcription factor

  • Turns ON hundreds of muscle genes

  • Can convert skin cells into muscle cells!

  • Master regulator of muscle identity

Example - Oct4/Sox2/Nanog (Stem Cells):

  • Three TFs working together

  • Keep cells in stem cell state

  • Turn OFF = cells differentiate

14.15 Combinatorial Control

14.15.1 Many Regulators Work Together

Combinatorial control = Multiple TFs work together to control genes

Why it’s powerful:

  • 10 TFs can create thousands of combinations

  • Fine-tuned control

  • Cell-type specific expression

Example:

  • Gene needs TF-A AND TF-B AND TF-C to turn ON

  • Like needing three keys to open a vault

  • Very specific control!

Liver cells:

  • Have TF-Liver1, TF-Liver2, TF-Liver3

  • Together they activate liver genes

  • Don’t have muscle TFs

  • So muscle genes stay OFF

14.16 Signal Transduction and Gene Regulation

14.16.1 How Cells Respond to Signals

Signal transduction = Converting external signals into gene expression changes

The pathway:

  1. Signal arrives (hormone, growth factor, stress)

  2. Receptor on cell surface detects signal

  3. Signaling cascade inside cell

  4. Transcription factors activated

  5. Genes turned ON or OFF

  6. Proteins made

  7. Cell response

14.16.2 Example: Hormone Signaling

Scenario: You’re scared, adrenaline released

What happens:

  1. Adrenaline binds to receptors on cells

  2. Activates signaling proteins inside

  3. Transcription factors activated

  4. Genes for stress response turned ON

  5. Proteins made (more glucose, faster heart)

  6. You’re ready to run!

All in seconds to minutes!

14.17 Feedback Loops

14.17.1 Self-Regulating Systems

Positive Feedback:

  • Product enhances its own production

  • Like a snowball rolling downhill

  • Amplifies signals

  • Used for rapid responses

Example: Blood clotting

  • Clotting factor activates more clotting factors

  • Rapid cascade

  • Stops bleeding quickly

Negative Feedback:

  • Product inhibits its own production

  • Like a thermostat

  • Maintains steady levels

  • Most common type

Example: Thyroid hormone

  • High levels inhibit release of more hormone

  • Keeps levels stable

14.18 Development and Gene Regulation

14.18.1 How One Cell Becomes Many Cell Types

The amazing fact: All cells start with same DNA!

How specialization happens:

1. Maternal Factors:

  • Egg has proteins distributed unevenly

  • Different parts of embryo get different proteins

  • Sets up initial patterns

2. Morphogens:

  • Signaling molecules that form gradients

  • High concentration → one cell fate

  • Low concentration → different cell fate

  • Like a map with coordinates!

3. Transcription Factor Cascades:

  • First TFs activate second TFs

  • Second TFs activate third TFs

  • Complex patterns emerge

4. Cell-Cell Signaling:

  • Cells communicate with neighbors

  • Refine boundaries

  • Create sharp borders between cell types

14.18.2 The Hox Genes

Hox genes = Master regulators of body plan

What they do:

  • Control head-to-tail pattern

  • Determine where body parts go

  • Highly conserved across animals

Amazing fact: Fly Hox genes work in mice!

  • Shows deep evolutionary conservation

  • All animals use similar developmental programs

14.19 Gene Regulation in Prokaryotes vs Eukaryotes

14.19.1 Prokaryotic Gene Regulation (Simpler)

Characteristics:

  • Mainly transcriptional control

  • Operons (groups of genes controlled together)

  • Fast response to environment

  • Less complex

The lac operon (we covered in Chapter 8):

  • Classic example

  • Genes for lactose digestion

  • Turned ON when lactose present

  • Turned OFF when lactose absent

14.19.2 Eukaryotic Gene Regulation (Complex)

Characteristics:

  • Multiple levels of control

  • Chromatin structure important

  • Individual genes (not operons)

  • Long-distance regulation (enhancers)

  • More complex, more flexible

Why more complex?

  • Multicellular organisms

  • Cell differentiation needed

  • Developmental programs

  • Sophisticated responses

14.20 Diseases of Gene Regulation

14.20.1 When Regulation Goes Wrong

Cancer:

  • Tumor suppressor genes turned OFF (should be ON)

  • Oncogenes turned ON (should be OFF)

  • Loss of normal growth control

Developmental Disorders:

  • Hox gene mutations → body parts in wrong places

  • Transcription factor mutations → missing structures

Metabolic Diseases:

  • Insulin signaling disrupted (diabetes)

  • Cholesterol regulation abnormal (heart disease)

14.21 RNA Interference (RNAi)

14.21.1 Using RNA to Regulate Genes

RNA interference = Using small RNAs to silence genes

How it works:

  1. Small RNAs (21-23 nucleotides) made

  2. They bind to complementary mRNA

  3. Either block translation OR degrade mRNA

  4. Gene silenced!

Types:

  • miRNAs (microRNAs): Natural gene regulators

  • siRNAs (small interfering RNAs): Used in research/medicine

Applications:

  • Research tool (turn OFF genes to study function)

  • Potential therapies (silence disease genes)

  • Already FDA-approved for some diseases!

14.22 Key Takeaways

  • Gene regulation controls which genes are ON or OFF

  • Multiple levels: Transcriptional, post-transcriptional, translational, post-translational

  • Transcription factors are master controllers

  • Combinatorial control creates complexity from simple parts

  • Signal transduction connects external signals to gene expression

  • Feedback loops maintain stability or amplify signals

  • Development uses gene regulation to create specialized cells

  • Prokaryotes use simple regulation (operons)

  • Eukaryotes use complex, multi-layered regulation

  • Diseases often involve regulatory failures

  • RNAi is a powerful regulatory mechanism and research tool

Sources: Information adapted from molecular biology textbooks, Nature Education, Khan Academy, and gene regulation research literature.