10.4: Eukaryotic Gene Regulation - Biology

What you’ll learn to do: Discuss different components and types of epigenetic gene regulation

Your amazing body contains hundreds of different cell types, from immune cells to skin cells to neurons. Almost all of your cells contain the same set of DNA instructions: so why do they look so different, and do such different jobs? The answer: different gene regulation!

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes – despite the fact that almost all the cells of your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell type uniquely specialized to do its job.

Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated.

Learning Objectives

  • Explain the process of epigenetic regulation
  • Discuss the role of transcription factors in gene regulation
  • Understand RNA splicing and explain its role in regulating gene expression
  • Describe the importance of RNA stability in gene regulation

Eukaryotic Epigenetic Gene Regulation

The human genome encodes over 20,000 genes; each of the 23 pairs of human chromosomes encodes thousands of genes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type.

The first level of organization, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions (Figure 1a). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string (Figure 1b). These beads (histone proteins) can move along the string (DNA) and change the structure of the molecule.

If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription (Figure 2). Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner.

Practice Question

In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing?

[practice-area rows=”2″][/practice-area]
[reveal-answer q=”670204″]Show Answer[/reveal-answer]
[hidden-answer a=”670204″]The nucleosomes would pack more tightly together.[/hidden-answer]

This type of gene regulation is called epigenetic regulation. Epigenetic means “around genetics.” The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA.

View this video that describes how epigenetic regulation controls gene expression.

A link to an interactive elements can be found at the bottom of this page.

Learning Objectives

In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.

Eukaryotic Transcription Gene Regulation

Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. Transcription factors are proteins that bind to the promoter sequence and other regulatory sequences to control the transcription of the target gene. RNA polymerase by itself cannot initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established.

View the process of transcription—the making of RNA from a DNA template:

A YouTube element has been excluded from this version of the text. You can view it online here:

The Promoter and the Transcription Machinery

Genes are organized to make the control of gene expression easier. The promoter region is immediately upstream of the coding sequence. The purpose of the promoter is to bind transcription factors that control the initiation of transcription.

Enhancers and Transcription

In some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called enhancers, are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away. Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes (Figure 3). This shape change allows for the interaction of the activators bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase.

Turning Genes Off: Transcriptional Repressors

Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors.

Learning Objectives

To start transcription, transcription factors, must first bind to the promoter and recruit RNA polymerase to that location. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.

Practice Questions

The binding of ________ is required for transcription to start.

  1. a protein
  2. DNA polymerase
  3. RNA polymerase
  4. a transcription factor

[reveal-answer q=”670222″]Show Answer[/reveal-answer]
[hidden-answer a=”670222″]Answer c. The binding of RNA polymerase is required for transcription to start.


What will result from the binding of a transcription factor to an enhancer region?

  1. decreased transcription of an adjacent gene
  2. increased transcription of a distant gene
  3. alteration of the translation of an adjacent gene
  4. initiation of the recruitment of RNA polymerase

[reveal-answer q=”829037″]Show Answer[/reveal-answer]
[hidden-answer a=”829037″]Answer b. Increased transcription of a distant gene will result from the binding of a transcription factor to an enhancer region.


A mutation within the promoter region can alter transcription of a gene. Describe how this can happen.

[practice-area rows=”2″][/practice-area]
[reveal-answer q=”332179″]Show Answer[/reveal-answer]
[hidden-answer a=”332179″]A mutation in the promoter region can change the binding site for a transcription factor that normally binds to increase transcription. The mutation could either decrease the ability of the transcription factor to bind, thereby decreasing transcription, or it can increase the ability of the transcription factor to bind, thus increasing transcription.


What could happen if a cell had too much of an activating transcription factor present?

[practice-area rows=”2″][/practice-area]
[reveal-answer q=”162780″]Show Answer[/reveal-answer]
[hidden-answer a=”162780″]If too much of an activating transcription factor were present, then transcription would be increased in the cell. This could lead to dramatic alterations in cell function. [/hidden-answer]

Post-Transcriptional Control of Gene Expression

RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized.

RNA splicing, the first stage of post-transcriptional control

In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons (Figure 4). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing.

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 (Figure 5).

This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation.

Visualize how mRNA splicing happens by watching the process in action in this video:

A YouTube element has been excluded from this version of the text. You can view it online here:

Control of RNA Stability

Before the mRNA leaves the nucleus, it is given two protective “caps” that prevent the end of the strand from degrading during its journey. The 5′ cap, which is placed on the 5′ end of the mRNA and poly-A tail, which is attached to the 3′ end. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate. This rate of decay is referred to as the RNA stability. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm.

RNA Stability and microRNAs

The microRNAs, or miRNAs, are short single-stranded RNA molecules that are only 21–24 nucleotides in length. Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA to degrade the target mRNA. They rapidly destroy the RNA molecule.

Learning Objectives

Post-transcriptional regulation can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. RNA stability is controlled by microRNAs (miRNAs). These miRNAs bind to the 5′ CAP or the 3′ Tail of the RNA to decrease RNA stability and promote decay.

Practice Questions

Which of the following are involved in post-transcriptional control?

  1. control of RNA splicing
  2. control of RNA shuttling
  3. control of RNA stability
  4. all of the above

[reveal-answer q=”681081″]Show Answer[/reveal-answer]
[hidden-answer a=”681081″]Answer d. All of the above (control of RNA splicing, RNA shuttling, and RNA stability) are involved in post-transcriptional control.


Binding of a miRNAs will ________ the stability of the RNA molecule.

  1. increase
  2. decrease
  3. neither increase nor decrease
  4. either increase or decrease

[reveal-answer q=”464261″]Show Answer[/reveal-answer]
[hidden-answer a=”464261″]Answer b. Binding of a miRNAs will decrease the stability of the RNA molecule.


Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.

Markov State Models of gene regulatory networks

Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking.


The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models. Application of transition path theory to the constructed Markov State Model decomposes global dynamics into a set of dominant transition paths and associated relative probabilities for stochastic state-switching.


In this proof-of-concept study, we found that the Markov State Model provides a general framework for analyzing and visualizing stochastic multistability and state-transitions in gene networks. Our results suggest that this framework—adopted from the field of atomistic Molecular Dynamics—can be a useful tool for quantitative Systems Biology at the network scale.


The clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune systems are widely distributed among almost all archaea and a large number of bacteria, protecting microbes against invasion by foreign DNAs, such as viruses [1]. The CRISPR-associated protein Cas9, which belongs to class 2 type II CRISPR-Cas system, has been extensively developed as a powerful tool for genome editing in both prokaryotes and eukaryotes [2,3,4,5]. With catalytically dead Cas9 (dCas9), the CRISPR/dCas9 system can be repurposed for targeting genomic DNA without introducing a double-stranded break [6]. dCas9 was first demonstrated for gene regulation in Escherichia coli, and the technology was named as CRIPSR interference (CRISPRi). A CRISPRi system consists of dCas9 and a single guide RNA (sgRNA) and the guide sequences in the sgRNA are responsible for specific recognition of target gene. As CRISPRi is of much convenience and high efficiency, it has been widely applied for efficient gene regulation [7,8,9,10,11,12,13,14,15] and epigenetic studies [16,17,18,19,] in both prokaryotes and eukaryotes.

In most cases, CRISPRi is designed for one target, which can be achieved by coexpression of a single sgRNA and dCas9. However, for multiplex gene regulation or epigenetic modifications, multiple sgRNAs may need to be independently expressed [20], and the construction procedure is time-consuming. As the studied gene networks become more and more complicated, it would be very useful to develop a convenient multiplex targeting system.

Besides of Cas9, another CRISPR-Cas protein Cpf1, which belongs to the class 2 type V-A CRISPR-Cas system, is also widely applied for genome editing in many organisms [21,22,23,24,25,26, 27,28]. Similar to Cas9, Cpf1 also cleaves double-stranded DNA and introduces double-stranded breaks at the recognition site. However, unlike Cas9, only the crRNA is required by Cpf1. Besides, Cpf1 also possesses the RNase activity and processes its own precursor crRNA [29]. Therefore, Cpf1 is so far the most minimalistic CRISPR-Cas systems with dual DNase and RNase activities [29]. Recently, its dual activities have been employed to process a single customized CRISPR array with its RNase activity and then cut target DNAs with its DNase activity, allowing for multiplex genome editing in both mammalian cells and rice [30, 31]. Because multiple mature crRNA can be conveniently obtained, the system can thus be applied for convenient multiplex genome editing.

Different from Cas9, which contains the RuvC and HNH domains for cleavage of the non-target strand and target strand, respectively [32], Cpf1 lacks HNH domain but contains a newly found Nuc domain [33, 34]. As mutation of the RvuC domain would result in the loss of cleavage activity against both strands of target DNA, the RuvC-mutated Francisella tularensis Cpf1 (FnCpf1) has previously been employed for protospacer-adjacent motif (PAM)-screen achieved by NOT-gate repression (SCANR) in E. coli [35], indicating the possibility of employing Cpf1 in gene regulation. As distinct domains have been characterized for the DNase and the RNase activities, inactivation of the DNase activity has no influence on its RNase activity [29]. Therefore, the DNase-dead Cpf1 (namely ddCpf1) in theory can be employed to process its precursor crRNA as well as a customized CRISPR array. And in this study, we employed the ddCpf1, which remained the RNase activity, to process a precursor CRISPR array, simply generating multiple mature crRNAs for convenient multiplex gene regulation.

10.4: Eukaryotic Gene Regulation - Biology

Regulation of Gene Expression in Eukaryotes

Gene expression in eukaryotes is more complicated than in prokaryotes. The nuclear envelop makes it necessary for mRNA to be exported into cytoplasmic compartment, the gene regulation can occur at multiple levels: transcription, exportation, translation and post-translation.

Eukaryotic genes
Eukaryotic genes usually contain three basic regulatory components: enhancers, which are short regions of DNA that can be bound with proteins to promote expression of a distal or a proximal gene. Promoters which are proximal DNA sequences that binds to RNA polymerase for regulating gene expression. And TATA Box, which Binds to transcription factor for regulating gene expression, usually within 30bp of the transcription start site. Transcriptional control is all about how these elements interact with transcriptional machinery, transcriptional factors and co-factors.

Transcriptional control
Transcriptional control is regulated by basal transcription factors and regulatory transcription factors. Basal transcription factors bind to DNA and form basal transcription machinery including TFIIA, B, D, F and RNA polymerase II, they are required for transcription. Modulatory transcription factors regulate time/space differential expression. This includes 4 types: activator, co-activator, repressor and co-repressor.

Post-transcriptional control
Post-transcriptional control includes mainly splicing, 5’ capping, 3’ polyadenylation. In addition, mRNA sequestration and exportation also play roles in some genes. mRNA stability is known to be different for different genes, more and more evidence indicate that a large collection of small RNA molecules can regulate the mRNA stability in cells.

Control at protein level
This includes both translational control (i.e, when and where a protein is synthesized and how fast it is synthesized) and post-translational control (where the protein is going in or out of cell, what kind of modification it is required for activation/inactivation, etc). Translational control is largely achieved at translation initiation involving both cap-dependent and –independent mechanisms. Post-translational control includes modification such as phosphorylation, acetylation, methylation, protein folding and sorting.

Regulation of gene expression in eukaryotes is very complicated, involving essentially every step from initiation of mRNA synthesis to the end protein products. First regulation is on mRNA transcription, which involves both cis-acting elements such as promoter and TATA box, and trans-acting elements such as enhancers and transcription factors. Basal transcription factors are required for basic transcription activity while modulatory transcription factors regulate time/space differential expression. Post-transcriptional control includes mainly splicing, 5’ capping, 3’ polyadenylation. In addition, mRNA stability, sequestration and exportation also play roles in some genes. Control at protein level includes both translational control and post-translational control.

  • Basic concept map for gene regulation in eukaryotes is given.
  • Summary diagrams in gene regulation starting from transcription to protein end product.
  • Animated schemes to describe transcriptional control on the promoter
  • Detailed chemical reaction for splicing
  • Detailed step-by-step diagrams and pictures to show translational control
  • Concise key concept sheets to keep the concept easy to memorize

Gene expression in eukaryotes

  • Gene organization
  • Overview
  • Basal transcription factors
  • Transcription initiation
  • Intron splicing and alternative splicing
  • 5’ capping
  • 3’ polyadenylation
  • mRNA sequestration and exportation
  • mRNA stability and availability
  • Overview
  • Translation initiation
  • Cap-independent initiation
  • 5’ UTR and uORF
  • Leaking scanning
  • miRNA and siRNA
  • 3’ UTR and poly A
  • Post-translational modification
  • Protein folding and complex formation
  • Protein sorting

See all 24 lessons in Genetics, including concept tutorials, problem drills and cheat sheets:
Teach Yourself Genetics Visually in 24 Hours

84 Eukaryotic Translational and Post-translational Gene Regulation

By the end of this section, you will be able to do the following:

  • Understand the process of translation and discuss its key factors
  • Describe how the initiation complex controls translation
  • Explain the different ways in which the post-translational control of gene expression takes place

After RNA has been transported to the cytoplasm, it is translated into protein. Control of this process is largely dependent on the RNA molecule. As previously discussed, the stability of the RNA will have a large impact on its translation into a protein. As the stability changes, the amount of time that it is available for translation also changes.

The Initiation Complex and Translation Rate

Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, the complex that assembles to start the process is referred to as the translation initiation complex . In eukaryotes, translation is initiated by binding the initiating met-tRNAi to the 40S ribosome. This tRNA is brought to the 40S ribosome by a protein initiation factor, eukaryotic initiation factor-2 (eIF-2) . The eIF-2 protein binds to the high-energy molecule guanosine triphosphate (GTP) . The tRNA-eIF2-GTP complex then binds to the 40S ribosome. A second complex forms on the mRNA. Several different initiation factors recognize the 5′ cap of the mRNA and proteins bound to the poly-A tail of the same mRNA, forming the mRNA into a loop. The cap-binding protein eIF4F brings the mRNA complex together with the 40S ribosome complex. The ribosome then scans along the mRNA until it finds a start codon AUG. When the anticodon of the initiator tRNA and the start codon are aligned, the GTP is hydrolyzed, the initiation factors are released, and the large 60S ribosomal subunit binds to form the translation complex. The binding of eIF-2 to the RNA is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the initiation complex cannot form properly and translation is impeded ((Figure)). When eIF-2 remains unphosphorylated, the initiation complex can form normally and translation can proceed.

An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. What impact do you think this might have on protein synthesis?

Chemical Modifications, Protein Activity, and Longevity

Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell—for example, in the nucleus, in the cytoplasm, or attached to the plasma membrane.

Chemical modifications occur in response to external stimuli such as stress, the lack of nutrients, heat, or ultraviolet light exposure. These changes can alter epigenetic accessibility, transcription, mRNA stability, or translation—all resulting in changes in expression of various genes. This is an efficient way for the cell to rapidly change the levels of specific proteins in response to the environment. Because proteins are involved in every stage of gene regulation, the phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications).

The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin acts like a flag indicating that the protein lifespan is complete. These proteins are moved to the proteasome , an organelle that functions to remove proteins, to be degraded ((Figure)). One way to control gene expression, therefore, is to alter the longevity of the protein.

Section Summary

Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein.

Visual Connection Questions

(Figure) An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. What impact do you think this might have on protein synthesis?

(Figure) Protein synthesis would be inhibited.

Review Questions

Post-translational modifications of proteins can affect which of the following?

  1. protein function
  2. transcriptional regulation
  3. chromatin modification
  4. all of the above

A scientist mutates eIF-2 to eliminate its GTP hydrolysis capability. How would this mutated form of eIF-2 alter translation?

  1. Initiation factors would not be able to bind to mRNA.
  2. The large ribosomal subunit would not be able to interact with mRNA transcripts.
  3. tRNAi-Met would not scan mRNA transcripts for the start codon.
  4. eIF-2 would not be able to interact with the small ribosomal subunit.

Critical Thinking Questions

Protein modification can alter gene expression in many ways. Describe how phosphorylation of proteins can alter gene expression.

Because proteins are involved in every stage of gene regulation, phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering the transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications).

Alternative forms of a protein can be beneficial or harmful to a cell. What do you think would happen if too much of an alternative protein bound to the 3′ UTR of an RNA and caused it to degrade?

If the RNA degraded, then less of the protein that the RNA encodes would be translated. This could have dramatic implications for the cell.

Changes in epigenetic modifications alter the accessibility and transcription of DNA. Describe how environmental stimuli, such as ultraviolet light exposure, could modify gene expression.

Environmental stimuli, like ultraviolet light exposure, can alter the modifications to the histone proteins or DNA. Such stimuli may change an actively transcribed gene into a silenced gene by removing acetyl groups from histone proteins or by adding methyl groups to DNA.

A scientist discovers a virus encoding a Protein X that degrades a subunit of the eIF4F complex. Knowing that this virus transcribes its own mRNAs in the cytoplasm of human cells, why would Protein X be an effective virulence factor?

Degrading the eIF4F complex prevents the pre-initiation complex (eIF-2-GTP, tRNAi-Met, and 40S ribosomal subunit) from being recruited to the 5’ cap of mature mRNAs in the cell. This allows the virus to hijack the translation machinery of the human cell to translate its own (uncapped) mRNA transcripts instead.



Some transcription factors ("Enhancer-binding protein") bind to regions of DNA that are thousands of base pairs away from the gene they control. Binding increases the rate of transcription of the gene.

Enhancers can be located upstream, downstream, or even within the gene they control.

There are thousands of enhancers in the genome but which ones are active depends on the type of cell and the signals which it is receiving. Most genes, at least in Drosophila, are regulated by 2&ndash3 enhancers, but some may be controlled by 8 or more. Multiple enhancers are particularly characteristic of "housekeeping" genes.

How does the binding of a protein to an enhancer regulate the transcription of a gene thousands of base pairs away?

One possibility is that enhancer-binding proteins &mdash in addition to their DNA-binding site, have sites that bind to transcription factors ("TF") assembled at a promoter of the gene.

This would draw the DNA into a loop (as shown in the figure).

  • a protein designated CTCF ("CCCTC binding factor" named for the nucleotide sequence to which it binds). The CTCF at one site on the DNA forms a dimer with the CTCF at another site on the DNA binding the two regions together. CTCF has 11 zinc fingers. [View another example of a zinc-finger protein]
  • cohesin &mdash the same protein complex that holds sister chromatids together during mitosis and meiosis. [Link]

Visual evidence

  • several (4) promoter sites for Sp1 about 300 bases from one end. Sp1 is a zinc-finger transcription factor that binds to the sequence 5' GGGCGG 3' found in the promoters of many genes, especially "housekeeping" genes.
  • several (5) enhancer sites about 800 bases from the other end. These are bound by an enhancer-binding protein designated E2.
  • 1860 base pairs of DNA between the two.

When these DNA molecules were added to a mixture of Sp1 and E2, the electron microscope showed that the DNA was drawn into loops with "tails" of approximately 300 and 800 base pairs.

At the neck of each loop were two distinguishable globs of material, one representing Sp1 (red), the other E2 (blue) molecules. (The two micrographs are identical the lower one has been labeled to show the interpretation.)

Artificial DNA molecules lacking either the promoter sites or the enhancer sites, or with mutated versions of them, failed to form loops when mixed with the two proteins.

Significance of "Looping"

Introduction to Eukaryotic Gene Regulation

  • Transcriptional control: This is control of the promoter and operator, and is very similar to what was seen with the Lac operon.
  • Enhancers and Activators: Enhancers are sequences on the DNA that are found away from the initiation site (promoter). Activators are proteins that bind to enhancer sequences and help regulate the RNA Polymerase complex. This allows for variable expression of the gene. Eliminating one enhancer does not abolish transcription, but can reduce the efficiency of transcirption.
  • Epigenome: This occurs in both prokaryotes and eukaryotes. In eukaryotes, the epigenome is noted by chemical changes to DNA and histone molecules that result in changes to the chromatin strand. These changes can "lock down" genes, preventing even the recognition of the promoter.
    • IMPORTANT: the epigenome does not represent mutations. Instead, it is a reversible chemical alteration to chromatin structure.
    • This chromatin alteration can be passed vertically to offspring.
    • Changes to the epigenome occur due to chemical signals and environmental changes (they change the organisms adaptation range).

    Epigenome Videos
    At present, I want you to concentrate on gene regulation at the promoter. This includes the concepts discussed in regards to the Lac and Trp operons, as well as enhancers and activators. Having an idea of how chromatin remodeling works will also help in regards to eukaryotic gene regulation. In subsequent semesters, these concepts will be the foundation for further exploration of gene expression.


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    10.4: Eukaryotic Gene Regulation - Biology

    Regulation of Gene Expression in Eukaryotic Cells

    Research in the lab focuses on learning how cells control gene activity so they can grow and thrive, and how cells alter gene activity when they encounter changes in the environment so they can adapt and survive. We focus on two main research areas: (1) detailing the molecular processes involved in gene activation and transcription, and (2) understanding how cells use SUMO post-translational modifications to regulate gene expression. Primarily, we use budding yeast, a popular model organism, as our biological system and our methodologies include a combination of molecular biology, biochemistry, yeast genetics, and genome-scale technologies.

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    Regulation of Eukaryotic DNA Transcription

    This animation shows how a variety of proteins interact to regulate the transcription of eukaryotic DNA into RNA.

    During transcription, DNA is copied into RNA by an enzyme called RNA polymerase. As shown in the animation, this process involves many different proteins. Some of these proteins are general transcription factors that recruit RNA polymerase to the gene. Other proteins, such as activators, repressors, and mediators, are transcription factors that regulate the action of RNA polymerase.

    Depending on students’ background, it may be helpful to pause the animation at various points to discuss different molecules or regions of DNA.


    activator, chromatin, enhancer, mediator, promoter, regulator, repressor, RNA polymerase

    The resource is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license. No rights are granted to use HHMI’s or BioInteractive’s names or logos independent from this Resource or in any derivative works.

    Watch the video: Genregulation bei Eukaryoten (December 2021).