Lecture 3 controlling gene expression

Question 1

learning objectives

Answer 1

What we will cover:
1.Comparison between Eukaryotic and Prokaryotic control: basic structures and their effects.
2.Basic principles of Eukaryotic gene expression in the form of transcriptional control:
➢What elements are important and why
➢Types of promoters
➢What effect these have on recruitment of initiation factors & RNA polymerase
➢Examples of activators, mediators and chromatin modifying enzymes as transcriptional control factors.
➢Types of transcription factors with named examples.
➢Principles of epigenetics focussing on chromatin modification.
➢Example effects on transcription and relationships with genetic disease.

➢Explain the principles governing interactions between DNA and protein that take place at the promoter or enhancer.
➢Describe the differences between DNA binding domains, using an example protein of each to help you explain their functional differences.
➢Explain the effect of multicomponent complexes on DNA binding, including those recruited to the mediator complex.

Question 2

Anatomy of a gene
Complete the labels for prokaryotic genes

Answer 2

Question 3

Complete the labels for Eukaryotic genes

Answer 3

Question 4

Genomes of prokaryotes vs eukaryotes

coding vs non-coding DNA

Answer 4

Question 5

What is meant by “control” of gene expression

Answer 5

Levels of protein controlled by:
➢Rate of transcription
➢Rate of mRNA degradation
➢Rate of protein synthesis
➢Rate of protein degradation

Question 6

In Eukaryotes what proteins control gene expression?

Answer 6

In eukaryotes, gene expression is controlled by a variety of proteins that regulate transcription, translation, and post-transcriptional modifications. These proteins include:

1. Transcription Factors (TFs):General Transcription Factors: Required for the assembly of the transcription machinery at the core promoter (e.g., TFIID, which binds to the TATA box).Specific Transcription Factors: Bind to enhancers, silencers, or other regulatory elements to activate or repress gene expression. Examples include activators and repressors.
2. DNA-binding Proteins:Activators: Bind to enhancers to increase the rate of transcription. They often work by recruiting co-activators or stabilizing the binding of the transcription machinery.Repressors: Bind to silencers or other negative regulatory regions to inhibit transcription.
3. Co-regulators:Co-activators: Help activators initiate transcription by recruiting the transcription machinery or modifying chromatin structure (e.g., CBP/p300).Co-repressors: Assist repressors in silencing gene expression, often by modifying chromatin to a more compact state (e.g., histone deacetylases).
4. Chromatin Remodeling Proteins:Histone Modifying Enzymes:Histone Acetyltransferases (HATs): Add acetyl groups to histones, loosening chromatin and promoting gene expression.Histone Deacetylases (HDACs): Remove acetyl groups, leading to chromatin condensation and gene repression.Histone Methyltransferases (HMTs): Add methyl groups to histones, which can either activate or repress transcription depending on the context.ATP-dependent Chromatin Remodeling Complexes: These proteins reposition or evict nucleosomes, making DNA more or less accessible to transcription machinery (e.g., SWI/SNF complex).
5. Mediator Complex:A multi-protein complex that bridges transcription factors and RNA polymerase II, helping to facilitate the assembly and activation of the transcription machinery.
6. RNA-binding Proteins:Regulate post-transcriptional processes such as splicing, polyadenylation, RNA stability, and transport.Splicing factors: Control alternative splicing, leading to different mRNA isoforms.Polyadenylation factors: Help process the 3’ end of mRNA.RNA interference (RNAi) machinery: Proteins like Dicer and Argonaute that are involved in RNA-induced silencing complexes (RISC), leading to gene silencing via microRNAs or small interfering RNAs (siRNAs).
7. Epigenetic Regulators:DNA Methyltransferases (DNMTs): Add methyl groups to cytosine residues in DNA, typically resulting in gene silencing.Methyl-binding Proteins (e.g., MeCP2): Bind to methylated DNA and recruit other repressors or chromatin remodelers to silence gene expression.

These proteins work together in a highly regulated manner to ensure that genes are expressed in the right place, at the right time, and in the appropriate amount.4o

Question 7

What is in the promoter?

Answer 7

Non-coding part of the gene that controls where transcription starts, which direction and on what strand it occurs from.

Contains -10 and -35 consensus sequences, transcription start site and other sequences that recruit proteins able to assist in the control of initiation of transcription

A promoter is a region of DNA just before a gene that controls when and how that gene gets turned on. Here’s a simpler breakdown of what’s in a promoter:
1. TATA Box:A short DNA sequence (TATAAA) that acts like a landing pad for proteins to help start gene copying (transcription). It’s usually found close to the start of the gene.

2. Transcription Start Site (TSS):This is where the gene actually begins. The first base of the gene is called the +1 position.
3. CAAT and GC Boxes:These are special sequences where proteins that control gene activity bind. They help make sure the gene gets copied at the right time.CAAT Box helps turn on genes more often.GC Box is found in genes that are always active in many cells (like those needed for basic cell functions).
4. Enhancers and Silencers:These are sequences that can be far away from the gene, but they help control it. Enhancers boost gene activity, and silencers can turn it down or off.
5. Response Elements:These are parts of the promoter that respond to signals, like stress or hormones. They help the gene react to changes in the environment.
6. CpG Islands:These are regions with a lot of “C” and “G” letters in the DNA. If they stay unmethylated (a chemical change), the gene is active. If methylated, the gene might get silenced.In short, a promoter is like a control panel that has switches and buttons (like the TATA box and CAAT box) that tell the gene when to turn on or off and how much to be active.

Question 8

The differences between prokaryotic and eukaryotic mechanisms of regulating gene expression.

Answer 8

The regulation of gene expression in prokaryotes and eukaryotes is quite different due to the structural and functional distinctions between these two types of organisms. Below are the key differences:

1. Location of Transcription and Translation:Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm because there is no nucleus. As soon as an mRNA is made, ribosomes can attach to it and begin translating it into protein.Eukaryotes: Transcription happens in the nucleus, and the mRNA is then processed and transported to the cytoplasm for translation. The separation of transcription and translation allows for more complex regulation of gene expression.
2. Gene Organization:Prokaryotes: Genes are often organized in operons, where multiple genes are controlled by a single promoter and are transcribed together as a single mRNA. For example, the lac operon controls genes involved in lactose metabolism.Eukaryotes: Genes are usually individually regulated, each with its own promoter. There are no operons, and genes are transcribed one at a time.
3. Promoters:Prokaryotes: Promoters are relatively simple, with core elements like the -10 (Pribnow box) and -35 regions that RNA polymerase binds to directly.Eukaryotes: Promoters are more complex, often containing a TATA box and other regulatory sequences like enhancers and silencers. These require multiple transcription factors and co-regulators to help RNA polymerase bind and initiate transcription.
4. Regulation by Transcription Factors:Prokaryotes: Gene regulation mainly involves repressors and activators that either block or enhance the binding of RNA polymerase to the promoter. These regulators often respond to environmental signals (like nutrient availability).Eukaryotes: Regulation involves a more complex set of transcription factors that can be specific to each gene. These transcription factors interact with enhancers and silencers to either promote or inhibit transcription. Eukaryotic gene expression is often regulated by a combination of many factors.
5. RNA Processing:Prokaryotes: There is no RNA processing. The mRNA made during transcription is immediately used for translation.Eukaryotes: Eukaryotic mRNA undergoes several processing steps before translation:5’ capping: A special cap is added to the beginning of the mRNA.Poly-A tail: A string of adenine (A) nucleotides is added to the end.Splicing: Introns (non-coding regions) are removed, and exons (coding regions) are spliced together. Alternative splicing can produce different proteins from the same gene.
6. Chromatin Structure and Epigenetics:Prokaryotes: Their DNA is relatively simple and not wrapped around histones. Thus, chromatin structure does not play a role in gene regulation.Eukaryotes: DNA is tightly packed into chromatin, which can be modified to regulate gene expression. Histone modifications (like acetylation and methylation) and DNA methylation can either condense the chromatin to silence genes or loosen it to allow transcription.
7. Operon Model:Prokaryotes: The operon model is a common way genes are regulated, where multiple related genes are controlled by a single promoter and operator. Repressors and activators control the operon.Eukaryotes: There are no operons. Instead, each gene has its own promoter, and regulation happens independently for each gene, often involving a wide array of enhancers, silencers, and transcription factors.
8. Post-transcriptional Regulation:Prokaryotes: Little to no post-transcriptional regulation. Once mRNA is made, it is immediately translated or degraded.Eukaryotes: Regulation can happen after transcription through mRNA stability, RNA interference (e.g., miRNAs and siRNAs), alternative splicing, and other mechanisms that control how and when an mRNA is translated into protein.
9. Post-translational Modifications:Prokaryotes: Fewer types of post-translational modifications (PTMs) of proteins. Proteins are often functional as soon as they are made.Eukaryotes: Extensive post-translational modifications, like phosphorylation, ubiquitination, glycosylation, etc., that regulate protein activity, localization, and degradation

Question 9

What affects the binding of proteins to DNA?

Answer 9

The binding of proteins to DNA is influenced by several factors, which together determine how well a protein can recognize and attach to specific DNA sequences. These factors include:

1. DNA Sequence Specificity:
   Recognition Sequences: Many proteins bind to specific DNA sequences, known as motifs or recognition sequences. For example, transcription factors often recognize and bind to specific sequences (like TATA boxes, enhancers, or response elements). The more the DNA sequence matches the protein’s preferred binding site, the stronger the binding.
   Base Pair Interactions: Proteins recognize DNA through interactions with the edges of the base pairs, which are exposed in the major and minor grooves of the DNA helix. The shape and chemical properties of these grooves influence binding.
2. DNA Structure:
   DNA Conformation: DNA can adopt different shapes beyond the typical double helix (e.g., Z-DNA, bent DNA, or DNA loops). Some proteins prefer binding to certain shapes or bends in the DNA, which can enhance or reduce binding affinity.
   DNA Flexibility: DNA is not rigid, and its flexibility or stiffness can affect how well a protein can interact with it. Proteins that bend or twist DNA (like transcription factors or nucleases) may require the DNA to be in a certain flexible state to bind effectively.
3. Protein Structure and Domains:
   DNA-binding Domains: Proteins have specific regions called DNA-binding domains (DBDs) that determine how the protein interacts with DNA. Common DNA-binding domains include:
   Helix-turn-helix (HTH): Common in prokaryotic repressors.
   Zinc finger motifs: Found in many eukaryotic transcription factors.
   Leucine zippers: Found in transcription factors that bind as dimers.
   Homeodomains: Found in proteins that regulate development.
   These domains dictate how the protein recognizes and interacts with the DNA sequence and structure.
4. Chromatin Structure (in Eukaryotes):
   Histone Modifications: In eukaryotes, DNA is wrapped around histone proteins to form chromatin. Post-translational modifications of histones (like acetylation, methylation, phosphorylation) can either loosen or tighten the DNA-histone interactions. Loosely packed chromatin (euchromatin) is more accessible to DNA-binding proteins, while tightly packed chromatin (heterochromatin) can prevent protein binding.
   Nucleosome Positioning: The placement of nucleosomes (DNA wrapped around histones) can block or expose DNA binding sites. Chromatin remodeling proteins can shift nucleosomes to make certain regions of DNA more accessible.
5. Epigenetic Modifications:
   DNA Methylation: The addition of methyl groups to cytosine residues (usually in CpG islands) can block proteins from binding to DNA. Methylation typically leads to gene silencing by preventing the binding of transcription factors or by recruiting methyl-binding proteins that compact chromatin.
   Other Modifications: Non-methyl modifications, like hydroxymethylation, can also influence protein binding, although they may act in more complex or context-specific ways.
6. Protein-Protein Interactions:
   Cooperative Binding: Sometimes, one protein helps another protein bind to DNA. For example, transcription factors often work in pairs or larger complexes, where one protein helps recruit or stabilize another protein’s binding. The cooperative effect can enhance binding affinity and specificity.
   Competition: Conversely, proteins can compete for the same binding site on the DNA. This competition can prevent a particular protein from binding if another protein has a higher affinity for the same site.
7. Environmental Factors:
   Ionic Strength: DNA and proteins carry charges, and the binding involves electrostatic interactions. Changes in ionic strength (e.g., salt concentrations) in the cell can influence the strength of these interactions. Higher salt concentrations can weaken DNA-protein binding by disrupting electrostatic forces.
   pH: The pH of the environment can affect the charge of amino acids in the DNA-binding protein and the DNA itself, altering binding affinity.
   Temperature: Higher temperatures can cause protein denaturation or affect the flexibility of both the DNA and the protein, which can either enhance or weaken binding.
8. Post-translational Modifications (PTMs) of the Protein:
   Phosphorylation: The addition of phosphate groups to a protein can change its shape, charge, or binding ability. For example, phosphorylation of transcription factors can activate or inactivate their ability to bind to DNA.
   Acetylation, Methylation, and Ubiquitination: These other modifications can also regulate whether a protein binds to DNA, alters its activity, or determines how long it remains bound.
9. Small Molecules and Ligands:
   Some proteins, especially those involved in gene regulation, require small molecules or ligands to bind DNA. For instance:
   Hormone receptors (like estrogen receptors) only bind DNA after binding a hormone.
   Metabolite sensors: Certain bacterial repressors or activators only bind DNA in the presence or absence of specific nutrients or metabolites.
10. ATP and Energy-Dependent Remodeling:
    Some DNA-binding proteins, like chromatin remodelers, require ATP to change DNA structure or modify the chromatin landscape. Without ATP, these proteins cannot bind effectively or function properly.
    Summary:
    In short, DNA-protein binding is influenced by a combination of:

The specific DNA sequence and its structure.
The shape and domains of the protein involved in binding.
Chromatin structure and modifications (in eukaryotes).
Environmental conditions like ionic strength, pH, and temperature.
Post-translational modifications of the protein and protein-protein interactions.
These factors together determine whether a protein can bind to DNA and how strongly it does so, thereby regulating key cellular processes like gene expression.

Question 10

Types of DNA binding domains

Answer 10

Question 11

How transcription factors are activated

Answer 11

Transcription factors (TFs) are proteins that regulate gene expression by binding to specific DNA sequences. For them to carry out their role in gene regulation, they need to be activated. The activation of transcription factors is a tightly controlled process, influenced by both internal cellular signals and external environmental factors. Here are the main ways transcription factors can be activated:

1. Ligand Binding:
   Some transcription factors require the binding of small molecules, known as ligands, to become active. The ligand binding causes a conformational change in the transcription factor, allowing it to bind to DNA and regulate gene expression. Examples include:

Nuclear hormone receptors: These are transcription factors activated by steroid hormones, such as estrogen, cortisol, and thyroid hormones. The hormone (ligand) binds to the receptor, allowing it to move into the nucleus and regulate target genes.
Example: Estrogen receptor binds to estrogen, then moves to the nucleus to control gene expression.

2. Post-translational Modifications (PTMs):
   Transcription factors often require chemical modifications after they are made to become fully active. Common post-translational modifications include:

Phosphorylation: The addition of a phosphate group, usually by a kinase, can activate transcription factors by changing their shape or allowing them to bind DNA.
Example: The transcription factor CREB (cAMP response element-binding protein) is activated by phosphorylation via protein kinase A (PKA) in response to increased cAMP levels.
Acetylation: The addition of acetyl groups can increase the activity of some transcription factors by loosening chromatin or altering the TF’s structure.
Example: The transcription factor p53 can be acetylated, which enhances its ability to activate genes involved in cell cycle arrest and DNA repair.
Ubiquitination: While ubiquitination often marks proteins for degradation, in some cases, it can activate transcription factors by triggering their release from inhibitors or activating specific pathways.

3. Dimerization:
   Many transcription factors are only active when they form dimers or higher-order complexes with other proteins. Dimerization can happen between two identical proteins (homodimerization) or two different proteins (heterodimerization). This protein-protein interaction can be triggered by external signals and allows transcription factors to bind DNA and regulate gene expression.

Example: Basic leucine zipper (bZIP) transcription factors, such as AP-1, form dimers to become functional and regulate gene expression in response to stress and growth signals.

4. Release from Inhibitors:
   Some transcription factors are held inactive in the cytoplasm or bound to inhibitory proteins until a specific signal releases them, allowing them to enter the nucleus and bind DNA.

Example: NF-κB is held in the cytoplasm by an inhibitory protein called IκB. When a cell receives a signal (like inflammation), IκB is degraded, and NF-κB can move into the nucleus to regulate genes involved in immune responses.

5. Nuclear Translocation:
   Many transcription factors are inactive while located in the cytoplasm and only become active after moving into the nucleus, where they can interact with DNA.

Signal-triggered translocation: External signals can cause the translocation of transcription factors from the cytoplasm to the nucleus.
Example: The STAT proteins (Signal Transducers and Activators of Transcription) are located in the cytoplasm but move to the nucleus when activated by the JAK-STAT pathway (often triggered by cytokines).

6. Proteolytic Cleavage:
   In some cases, transcription factors are synthesized as inactive precursors that need to be cleaved to become active.

Example: SREBP (Sterol Regulatory Element-Binding Protein) is anchored to the endoplasmic reticulum membrane in an inactive form. When cholesterol levels are low, a protease cleaves SREBP, allowing the active fragment to enter the nucleus and activate genes involved in cholesterol synthesis.

7. Signal Transduction Pathways:
   Many transcription factors are activated as a final step in a signal transduction pathway. These pathways often involve multiple steps, starting with a signal (like a hormone, growth factor, or stress) that activates a series of enzymes or proteins, ultimately leading to the activation of the transcription factor.

MAPK/ERK pathway: A common pathway where external growth signals activate a kinase cascade that leads to the phosphorylation and activation of transcription factors like ELK1 or FOS.
Wnt/β-catenin pathway: In the absence of Wnt signaling, β-catenin is degraded. When the Wnt signal is present, β-catenin stabilizes, accumulates, and enters the nucleus to activate transcription factors that control cell proliferation.

8. Response to Environmental Stimuli:
   Transcription factors can be activated in response to changes in the environment, such as temperature, nutrient levels, oxidative stress, or hypoxia (low oxygen).

Example: HIF-1α (Hypoxia-Inducible Factor) is activated in low oxygen conditions. Normally, it is degraded quickly in the presence of oxygen, but under hypoxic conditions, it stabilizes and moves to the nucleus to regulate genes involved in the adaptation to low oxygen, like those controlling blood vessel formation.

9. Co-factor Binding:
   Some transcription factors need to bind to co-factors (other proteins) to become active or enhance their activity. These co-factors can either help the transcription factor bind to DNA more efficiently or recruit other machinery required for transcription.

Example: p300/CBP co-activators are often recruited by transcription factors to modify chromatin, making the DNA more accessible and promoting transcription.

10. Regulation by Small RNAs:
    In some cases, the activation or inhibition of transcription factors is influenced by small RNA molecules, such as microRNAs (miRNAs), which can regulate the stability of the mRNA that encodes transcription factors. This form of regulation does not directly affect the transcription factor protein but influences whether the TF can be synthesized in the first place.

Question 12

Types of DNA Binding domains

Answer 12

Question 13

Effects of multi-protein complexes

Answer 13

Multi-protein complexes play essential roles in nearly all biological processes, including gene expression, DNA repair, cell signaling, and metabolic pathways. These complexes often consist of several proteins working together to perform tasks that would not be possible by individual proteins alone. Their assembly, stability, and interactions can have significant biological effects. Below are key effects of multi-protein complexes:

1. Increased Efficiency and Specificity
   Function: Multi-protein complexes can coordinate multiple steps of a biological process simultaneously, ensuring that reactions happen efficiently and at the right location within the cell.
   Example:
   RNA polymerase II transcription complex: Transcription in eukaryotes involves several proteins forming a complex that includes RNA polymerase II, general transcription factors, and mediator complexes. This assembly ensures that transcription occurs with the right initiation, elongation, and termination steps.
2. Regulation of Gene Expression
   Function: Many multi-protein complexes act to regulate the expression of genes by controlling transcription, translation, or chromatin structure.
   Example:
   Chromatin remodeling complexes: Complexes such as SWI/SNF alter the structure of chromatin, making DNA more or less accessible to transcription factors, thus regulating gene expression.
   Enhanceosome: A highly cooperative multi-protein complex that binds enhancers to activate transcription. The interferon enhanceosome (which regulates immune response genes) consists of various transcription factors (like NF-κB, IRF, and AP-1) bound together to precisely regulate gene expression in response to pathogens.
3. Signal Transduction Pathways
   Function: In signaling pathways, multi-protein complexes ensure that signals from receptors on the cell surface are efficiently transmitted to their targets within the cell, often via a cascade of protein interactions.
   Example:
   MAPK/ERK pathway: This pathway involves a sequence of protein kinases that form a complex to transmit signals from the cell surface to the nucleus, leading to changes in gene expression and cell behavior (like growth and differentiation).
4. Enhanced Stability and Activity
   Function: Forming a multi-protein complex can increase the stability of individual proteins, making them less prone to degradation. It can also enhance the catalytic activity of enzymes or protein functions through cooperative interactions.
   Example:
   Proteasome complex: The proteasome is a large multi-protein complex that degrades damaged or misfolded proteins. The complex’s organization ensures highly efficient and specific degradation, preventing the accumulation of unwanted proteins.
5. Coordination of Complex Biological Processes
   Function: Multi-protein complexes help synchronize complicated biological processes by bringing together the necessary components. This coordination ensures that each step happens in the correct order and location.
   Example:
   Spliceosome: The spliceosome is a multi-protein complex responsible for the removal of introns from pre-mRNA in eukaryotes. It consists of small nuclear RNAs (snRNAs) and proteins that assemble at the correct RNA splice sites and execute splicing in a highly regulated manner.
6. Dynamic Assembly and Disassembly
   Function: Many multi-protein complexes assemble only when needed and disassemble when their task is complete, allowing the cell to tightly regulate their activity. This is often controlled by post-translational modifications like phosphorylation.
   Example:
   Cyclin-CDK complexes: These complexes control the progression of cells through the cell cycle. Cyclins bind to cyclin-dependent kinases (CDKs), forming an active complex that drives the cell cycle forward. After completing their role, cyclins are degraded, and the complex disassembles to prevent unnecessary cell division.
7. DNA Repair and Genome Integrity
   Function: Multi-protein complexes play critical roles in recognizing DNA damage, recruiting repair machinery, and fixing the damage to maintain genome integrity.
   Example:
   Nucleotide excision repair (NER): The NER pathway involves multiple proteins, such as XPA, RPA, and TFIIH, that form a complex to recognize and repair bulky DNA lesions (like those caused by UV radiation).
   MRN complex (MRE11, RAD50, NBS1): Involved in detecting DNA double-strand breaks and initiating DNA repair pathways.
8. Allosteric Regulation
   Function: Multi-protein complexes often exhibit allosteric regulation, where the binding of one protein or ligand affects the function of another protein in the complex, enhancing or inhibiting its activity.
   Example:
   Hemoglobin: Though not a transcription factor, hemoglobin is a classic example of allosteric regulation in multi-protein complexes. The binding of oxygen to one subunit affects the affinity of the other subunits for oxygen.
9. Metabolic Channeling
   Function: In metabolic pathways, multi-enzyme complexes ensure that intermediate products are efficiently passed from one enzyme to another without diffusing away, a process known as metabolic channeling.
   Example:
   Pyruvate dehydrogenase complex: This complex catalyzes the conversion of pyruvate to acetyl-CoA, with multiple enzyme subunits working together to shuttle intermediates from one enzyme to the next, increasing the efficiency of the reaction.
10. Spatial and Temporal Regulation
    Function: Multi-protein complexes can be spatially or temporally regulated to ensure their function occurs at the right time and place within the cell. This is often controlled by compartmentalization within organelles or specific post-translational modifications.
    Example:
    Nuclear pore complex (NPC): Regulates the transport of proteins and RNA between the nucleus and the cytoplasm. The NPC is a large, multi-protein structure that selectively allows the passage of molecules into and out of the nucleus.
11. Formation of Macromolecular Machines
    Function: Multi-protein complexes can form massive, intricate structures that carry out complex cellular tasks, such as protein synthesis, DNA replication, and chromosome segregation.
    Example:
    Ribosome: The ribosome is a multi-protein complex consisting of rRNAs and proteins that synthesizes proteins from mRNA templates. The complex ensures accurate translation and proper folding of newly synthesized proteins.
    DNA polymerase complex: A large multi-protein machine responsible for DNA replication during cell division, involving DNA polymerase, helicase, primase, and other factors to ensure accurate replication.
12. Response to Cellular Stress
    Function: In response to stress (e.g., oxidative stress, heat shock, or DNA damage), multi-protein complexes are often activated to protect the cell or repair damage.
    Example:
    Heat shock proteins (HSPs): These chaperone proteins form complexes that help refold misfolded proteins during heat shock or other stress conditions. They prevent aggregation and ensure proper protein function.
13. Epigenetic Regulation
    Function: Some multi-protein complexes regulate gene expression at the epigenetic level by modifying histones or altering chromatin structure.
    Example:
    Polycomb Repressive Complexes (PRC1 and PRC2): These complexes modify histones to maintain the repressive state of specific genes during development and differentiation.

Conclusion
Multi-protein complexes are essential for coordinating biological functions with high specificity, efficiency, and regulation. They allow for sophisticated control mechanisms over gene expression, cell signaling, metabolism, and DNA repair, ensuring that the right processes happen in the right place and time. Their ability to integrate multiple signals and execute complex tasks makes them critical for maintaining cellular homeostasis and responding to environmental changes