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How gene expression is regulated? - Module 4 Reading / Watching

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Course: An introduction to Gene Regulation and Gene Expression
Book: How gene expression is regulated? - Module 4 Reading / Watching
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Date: Sunday, 20 July 2025, 1:24 AM

Table of contents

1. How gene expression is regulated ?

In this book you will see an overview of the topics of Module Four and reference links.

2. Learning Objectives

By the end of this chapter, readers will be able to

  • Define Operons
  • Explain the roles of Lac I, Lac Z, and Lac Y of the lactose Operon
  • Predict the effects on lactose metabolism when the concentration of lactose is changed.
  • Explain about the Trp Operon
  • Define attenuation
  • Explain molecular mechanisms that control Eukaryotic gene regulation
  • Define Epigenetics
  • Discuss the role of epigenetics in gene expression and regulation


    • 2.1. Regulation of Gene expression in Prokaryotes

    Prokaryotic Gene regulation

    The process of turning on a gene to produce RNA and protein is called gene expression. For a cell to function properly appropriate  proteins must be synthesized at the appropriate  time. Whether in a simple unicellular organism  or a complex multi-cellular organism, each cell controls  when and how its genes are expressed.

    Prokaryotic organisms are single-celled organisms that lack a defined nucleus; therefore, their DNA floats freely within the cell cytoplasm. To synthesize a protein, the processes of transcription (DNA to RNA) and translation (RNA to protein) occur almost simultaneously. The expression of a gene is a highly regulated process and ensures that a cell’s resources are not wasted making proteins that the cell does not need at that time.

    Prokaryotic transcription and translation occur simultaneously in the cytoplasm, and regulation occurs at the transcriptional level.

     Regulation of Gene expression  in Prokaryotes
    Operons

    In prokaryotes , genes with  related functions for example  the genes that encode the enzymes of a single biochemical pathway— are found next to each other on the DNA  or clustered together and  regulated together  . Such gene clusters  shares same promoter and a regulatory sequence  that controls the transcription of the entire unit. The organization of genes in this manner is called an  This arrangement enables the prokaryote to rapidly adapt to changes in the environment.

    Prokaryotic  mRNAs are   , meaning they contain the information to make more than one protein. The promoter has simultaneous control over the regulation of the transcription of these structural genes.

    The operon includes two main components namely

    • Structural genes – genes that encode proteins used in metabolism or biosynthesis or that play a structural role in the cell and 
    • Regulatory elements-  includes the promoter and the region surrounding the promoter and the genes that code for the regulatory proteins

    In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons namely ;

    •  Repressors– are proteins that suppress transcription of a gene in response to an external stimulus,
    • Activators – are proteins that increase the transcription of a gene in response to an external stimulus and
    • Inducers – are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate.

     


    2.2. Prokaryotic gene regulation- Lac Operon

    Francois Jacob & Jacques Monod. studied the mechanisms of transcriptional regulation in E. coli.   

    The lac operon consists of  two main components  namely  the regulatory genes and  structural genes .

    The structural genes

    The structural genes are lax Z, lac Y and lac A. These encode the three enzymes involved in lactose metabolism ; These are  lac Z encodes an enzyme calledβ-galactosidase, which digests lactose into its two constituent sugars namely  glucose and galactose.  lac Y encodes the enzyme called  permease that helps to transfer lactose into the cell and lac A  encodes  trans-acetylase; the relevance of which in lactose metabolism is not clearly understood.

    The regulatory genes 

    In addition to the three protein-coding genes, the lac operon contains short DNA sequences that do not encode proteins,  These sequences are called P (promoter), O (operator), and CBS (CAP-binding site) . These are  binding sites for proteins involved in transcriptional regulation of the operon.

     These sequences are called cis-elements as they are located on the DNA of  the genes they regulate. On the other hand, the proteins that bind to these cis-elements are called trans-regulators . These are diffusible molecules and are not necessarily need to be encoded on the same piece of DNA as the genes they regulate.

    One of the major trans-regulators of the lac operon is encoded by lacI. which codes for the lac I protein. Four identical molecules of lacI proteins assemble together to form a homotetramer called a repressor.

    Negative regulation of the Lac Operon 

    In the absence of Lactose and when glucose is available in the medium , the repressor binds to two operator sequences adjacent to the promoter of the lac operon. Binding of the repressor prevents RNA polymerase from binding to the promoter . Therefore, the operon will not be transcribed when the operator is occupied by a repressor. This is called negative regulation.

     

    Positive Regulation 

    When  the level of glucose in the medium is   very low or non-existent and when lactose is available in the medium, the lac operon is induced to express the genes i.e., Only when glucose is absent and lactose is present will the lac operon be transcribed .When lactose is present, its metabolite, allolactose, binds to the lac repressor and changes its shape so that it cannot bind to the lac operator to prevent transcription.  This is referred to as positive regulation

     It should be mentioned that the lac operon is transcribed at a very low rate even when glucose is present and lactose absent.


    2.3. Prokaryotic gene regulation- Trp Operon

    Bacteria such as E. coli need amino acids  like tryptophan to survive, which they can ingest from the environment.

     E. coli can also synthesize tryptophan using enzymes that are encoded by five genes in the tryptophan (trp) operon .

    If tryptophan is available in the environment, then there is no necessity for   E. coli does  to synthesize it and the trp operon is switched off. However, when tryptophan availability is low,  the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized.

    Like lac operon , trp operon also consists of structural genes and regulatory genes

    The regulatory genes include

    P/O genes :  Promoter sequence and the operator sequence which is found in the promoter region.

    trp L : Leader sequence : attenuator (A) sequence is found in the leader

    The structural genes are

    The trp operon is a repressible systems because  the binding of the effector molecule to the repressor greatly increases the affinity of repressor for the operator . The repressor binds to the operator  and stops transcription. Thus if tryptophan  (effector) is  available in the medium   the repressors binds at the operator and repress the trp operon.

    2.4. Attenuation of the trp Operon

    • The leader sequence (L) of the trp Operon lies before the trpE gene at its 5′ end . This sequence about 160 bp is size and controls the expression of the operon through a process called attentuation.
    • This sequence has four domains (1-4). Domain 3 (nucleotides 108-121) of the mRNA can base pair with either domain 2 (nucleotides 74-94) or domain 4 (nucleotides 126-134).
    •  At high levels of tryptophan in the medium :  domain 3 pairs with domain 4, a stem and loop structure forms on the mRNA and transcription stops.
    • At low levels of tryptophan in the medium :     domain 3 pairs with domain 2, then the stem and loop structure does not form and transcription continues through the operon, and all of the enzymes required for tryptophan biosynthesis are produced.
    • Attenuators: Domain 4 is called the attenuator because its presence is required to reduce (attenuate) mRNA transcription in the presence of high levels of tryptophan.
    • Domain 1 is also an important component of the attenuation process. The section of the leader sequence encodes a 14 amino acid peptide that has two tryptophan residues.

    trp Operon Transcription Under High Levels of Tryptophan

    • When the cellular levels of tryptophan are high, the levels of the tryptophan tRNA are also high.
    • Immediately after transcription, the mRNA moves quickly through the ribosome complex translating the leader peptide .
    • Translation is quick because of the high levels of tryptophan tRNA.
    • Domain 2 becomes associated with the ribosome complex.
    • As result the domain 3 binds with domain 4, and
    • transcription is attenuated because of the stem and loop formation.

    trp Operon Transcription Under Low Levels of Tryptophan

    • Under low cellular levels of tryptophan, the translation of the peptide on domain 1 is slow.
    • Domain 2 does not become associated with the ribosome.
    • Rather domain 2 associates with domain 3.
    • This structure permits the continued transcription of the operon.
    • Then the trpE-A genes are translated, and the biosynthesis of tryptophan occurs.


    2.5. Eukaryotic Transcription gene regulation

    Transcriptional Regulation in Eukaryotes

    There are three classes of control elements in eukaryotes:

    •The RNA polymerase II binding region (the core promoter)
    • cis-acting binding sequences that bind to proteins with RNA polymerase affinity, which in turn help bind RNA polymerase to a promoter.
    •A trans-acting DNA element
    cis-acting DNA element
    •These are short DNA sequences that acts as a binding site for a protein that has an affinity for that specific sequence.
    include short consensus sequences
    • These elements  are usually located within 200 bp upstream of the transcription initiation site
    •They can be included in a promoter or an enhancer
    • They have an affinity for a specific protein that binds to it, serving as a regulator
    •The term “cis acting” means that the bound protein acts only upon DNA sequences on the same DNA molecule as the cis-acting sequence.
    •These are also found in prokaryotes example ; the operator of the lac operon.
    cis-acting DNA elements- enhancers and silencers

    •An enhancer DNA sequence (or positive regulatory element) turns a gene ON.

    •When the activator is bound to the enhancer, RNA polymerase is more highly attracted to the gene.

    •enhancers are located upstream or downstream of the promoter region,

    •Multiple regulatory proteins bound to binding sites in an enhancer can form a large, complex enhancesosome that has varying affinity for RNA polymerase, depending on its size and exact composition.

    •The enhanceosome can both recruit additional co-activators and facilitate chromatin remodeling.

    •A silencer DNA sequence (or negative regulatory element) turns a gene OFF or reduces its rate of transcription.

    •When the repressor is bound to the silencer, RNA polymerase cannot attach and transcribe the gene.

    •silencers are located downstream of a promoter.

    Trans-acting DNA element
    •A trans-acting DNA element is a DNA sequence that codes for a protein (a trans-acting factor) that controls the expression of a gene at a separate location by binding to its cis-acting element.

     Trans-acting factors:

    • These are enzymes that interact with RNA polymerase
    • They bind to RNA polymerase to stabilize the initiation complex
    • They may bind to a few promoters and serve as positive regulators
    •A trans-acting factor can affect the expression of genes located on separate chromosomes.
    Post-Translational Control of Gene Expression
    • RNA is transcribed, but must be processed into a mature form before translation can begin. This processing is called post-transcriptional modification. 
    • This post-transcriptional step can also be regulated to control gene expression in the cell. 
    • In eukaryotic  RNA transcript often contains regions, called introns, that are removed prior to translation.
    • The regions of RNA that code for protein are called exons .
    • By a process called , the RNA is processed and the introns are removed and exons are ligated together.

    ALTERNATIVE RNA SPLICING
    • Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript.
    • Alternative splicing  acts as a mechanism of gene regulation,
    • The frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells or at different stages of development.
    •  70 percent of genes in humans are expressed as multiple proteins through alternative splicing.



    2.6. Eukaryotic Epigenetic Gene Regulation

    The DNA and histones that bind the DNA can undergo changes. These changes do not alter the nucleotide sequence and are not permanent, though they often persist through multiple rounds of cell division. These temporary changes can alter the chromosome structure as required. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA. This type of gene regulation is called epigenetic regulation.
    •Histone/nucleosome winding of the DNA molecule may change with the gene activity in a particular cell or tissue.
    •When a gene needs to be transcribed but is unavailable because of histone proximity, moving the histone from the DNA strand can free the promoter and associated regulatory sequences so that the sequences are exposed and the  gene can be expressed.
    •Conversely, if an active gene associated with a nucleosome must be turned off, then moving the DNA so that repressors can attach to the gene’s silencers can also be achieved by rewinding the DNA (in the next cell cycle) on the nucleosomes in a different way.
    • Histone modification is a covalent post-translational modification (PTM) to histone proteins.
    • N terminal tails of histone are modified  by
    • methylation,
    • phosphorylation,
    • acetylation,
    • ubiquitylation, and
    • sumoylation. (small ubiquitin-related modifier (SUMO) family are conjugated to proteins to regulate such cellular processes as nuclear transport, transcription, chromosome segregation and DNA repair.)
    • Histones modifications is  carried out by acetyltransferases and deacetylases, methyltransferases and demethylases.
    • The PTMs made to histones can impact gene expression by altering chromatin structure or recruiting histone modifiers.
    Histone -Lysine acetylation

    Role of Histones in gene regulation
    Histone Modifications
    • Histone -Lysine acetylation is regulated by two enzymes:
    • Histone Acetyltransferases (HATs)–use acetyl-CoA that is specifically recognized and bound by the Arg/Gln-X-X-Gly-X-Gly/Ala segment of HATs to transfer an acetyl group to the ε-amino groups on the N-terminal tails of histones .
    • Histone Deacetylases (HDACs)–reverses the above modification by HATs
    • Lysine acetylation causes a destabilization of the nucleosome and chromatin structure–effectively facilitating access to the DNA for various nuclear factors like the transcription complex.
    • Hyperacetylated histones are regarded to be a hallmark of transcriptionally active chromatin.
    • The work of HDACs increases the affinity between the nucleosome and the DNA, leading to a closed (heterochromatin-like) chromatin conformation that minimizes accessibility for the transcriptome.
    Histone methylation
    • This unique posttranslational modification is performed by a specific enzyme family known as the Protein Arginine N-Methyltransferases (PRMTs).
    • Along with serine/threonine phosphorylation, and lysine methylation and acetylation, arginine methylation is an epigenetic histone modification that regulates gene expression as part of the histone code

    2.7. Chromatin remodeling

    It is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.
    •When chromatin is tightly packed, and not actively being transcribed it is called heterochromatin.
    •When chromatin is more loosely packed, and therefore accessible for transcription it is called euchromatin.
    •Chromatin remodeling is highly implicated in epigenetics.
    •Epigenetic modifications to histone proteins such as methylation/demethylation and acetylation/deacetylation can alter the structure of chromatin resulting in transcriptional activation or repression.

    Two classes of chromatin remodeling enzymes
    a) Class I : Histone modifying enzymes
    • These do not alter nucleosome position
    •  They bring about covalent modification of histone proteins like  histone tail modifications (Ac, Me, P, Ub, etc.)
    •  Proteins recruited by these modifications include: i)transcription factors ii)ATP-dependent nucleosomal remodeling enzymes iii)histone modifying enzymes

     

    b) Class II : Chromatin remodeling factors
    •It shifts nucleosome position with respect to DNA, exposing regulatory sequences.
    •These are often referred to as Swi/Snf factors (because they were first identified as yeast mutants defective in mating type switching and in the ability to metabolize sucrose , sucrose non-fermenting).
    •Chromatin remodeling factors use energy from ATP hydrolysis to rearrange the packing of nucleosomes in higher order chromatin structures.
    •Remodeling improves access to DNA or histone binding sites recognized by transcriptional regulators or histone modifiers.
    • Some of these bind to :
      •  Activation domains and de-condense the associated chromatin.
      • Repression domains and condense the associated chromatin.