Name: eukaryotic promoter motifs and gene control
Uploaded: 2020-11-23T11:47:37.000Z
Duration: 2 min 40 s
Channel: JoVE

The promoter is a major regulator of gene expression that contains binding sites for RNA polymerase, the enzyme responsible for transcription, and transcription factors, that facilitate or inhibit the binding of RNA polymerase.&#160;
The promoter region is mostly located upstream of the gene it regulates. It has distinct structural features, such as a curved structure with the ability to bend when transcriptional regulators bind and low thermodynamic stability due to the presence of AT-rich regions.&#160;&#160;
In eukaryotes, this transcriptional control region is more complex than in prokaryotes. In addition to the core promoter, eukaryotic genes have many additional cis-regulatory sequences that transcription factors can bind.
Prokaryotic RNA polymerase requires a sigma factor to bind to the promoter, whereas eukaryotic RNA polymerases require several such regulators.&#160;
Additionally, the three different RNA polymerases in eukaryotes that bind to distinct promoters, require different transcriptional regulators.&#160;
The core eukaryotic promoter contains several signature motifs that work together in various combinations to allow RNA polymerase to bind.&#160;
The TATA box is highly conserved across organisms. TATA boxes are usually present in genes that show high levels of cell-specific expression, such as proteins involved in cell differentiation.
Initiator and downstream promoter elements consist of degenerate sequences that follow a specific pattern of nucleotides, though their exact sequence varies.&#160;&#160;
The initiator element is the most common promoter motif. It can either help to maintain basal levels of transcription or work together with the TATA box to improve the binding of transcription factors.&#160;
The downstream promoter element is located downstream of the transcription start site and was initially found in promoters lacking a TATA box.&#160; The DPE often works in conjunction with the initiator element to regulate transcription.
CpG islands consist of sections of DNA where a cytosine is followed by a guanine. CpG islands usually regulate housekeeping genes, which are continuously expressed in small amounts and do not require high levels of transcription.

the eukaryotic promoter region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.&#160; The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are cis-regulatory sequences, thousands of base pairs away from a gene. The length of a promoter region can vary significantly from gene to gene.
The core promoter contains characteristic motifs where general transcription factors can bind and recruit RNA polymerase.&#160; The TATA box is a motif located 25-30 base pairs upstream from the transcription start site. It is more flexible and less thermodynamically stable than other promoter motifs due to its high A-T content, allowing the efficient binding of the transcription machinery. It is found in genes that require high levels of expression under specific conditions, such as those genes involved in cell differentiation. The TATA box is often flanked by a set of short nucleotide motifs, known as B-recognition elements.&#160; Transcription Factor II B,&#160; an important component involved in the assembly of the transcription machinery at the TATA box, binds to these B-elements.
The initiator element, composed of the degenerate sequence YYANWYY*, contains the transcription start site.&#160; Downstream of the initiator element is another characteristic motif, known as the downstream promoter element (DPE), made up of the degenerate sequence RGWYVT. The TATA box and the DPE regulate similar types of genes, and a eukaryotic promoter can have either a TATA box or a DPE. The initiator element can function synergistically either with a TATA box or DPE to regulate transcription.
The CpG islands are another type of core promoter motif that regulates the expression of other types of genes,&#160; like housekeeping genes, that require constant expression in small amounts. They are called CpG islands because they contain sequences that are high in cytosine followed by guanine. The &#8220;p&#8221; represents the phosphodiester bond that links C to G. CpG islands are also known to occur in distal promoter regions.
*R codes for either A or G; W codes for either A or T; Y codes for C or T; V codes for A or G or C;&#160; and N codes for any of the four bases.

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and ...

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Gene Expression

KEY TERMS AND CONCEPTS

eukaryotic promoter motifs and gene control

The eukaryotic promoter region is a stretch of DNA located upstream of a gene. It includes an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. These DNA signals help control when transcription begins.

The promoter can be divided into proximal and distal regions. The proximal promoter lies close to the gene and includes cis-regulatory sequences and the core promoter. The core promoter is the RNA polymerase binding site, and it is usually found between -35 and +35 nucleotides from the transcription start site. Distal promoter regions are cis-regulatory sequences that can sit thousands of base pairs away from a gene. Promoter length can vary a lot from one gene to another.

The core promoter contains specific motifs where general transcription factors bind and recruit RNA polymerase. One common motif is the TATA box. It sits about 25 to 30 base pairs upstream from the transcription start site. Because it has a high A-T content, it is more flexible and less thermodynamically stable than other promoter motifs. This feature helps the transcription machinery bind efficiently. TATA boxes often appear in genes that need high expression under certain conditions, such as genes involved in cell differentiation.

The TATA box is often flanked by short nucleotide motifs called B-recognition elements. Transcription Factor II B, or TFIIB, binds these B-elements and helps assemble the transcription machinery at the TATA box. Another core motif is the initiator element, which contains the transcription start site. Its degenerate sequence is YYANWYY*. Downstream of the initiator element is the downstream promoter element, or DPE. The DPE has the degenerate sequence RGWYVT. The TATA box and the DPE regulate similar types of genes, and a promoter can have either one. The initiator element can work together with either motif to support transcription.

CpG islands are another core promoter motif. They help regulate genes that need constant, low-level expression, such as housekeeping genes. These regions are named for sequences rich in cytosine followed by guanine. The &quot;p&quot; refers to the phosphodiester bond that links C to G. CpG islands can also appear in distal promoter regions.

Eukaryotic Promoter Motifs and Gene Control

eukaryotic-promoter-motifs-and-gene-control

cell specific gene expression

How Cells Switch Genes On and Off

Cells switch genes on and off to make different proteins for different jobs. In multicellular organisms, many cell types are built from the same DNA, but they do not use the same genes in the same way. This difference in gene expression helps explain why cells can look and act so differently. Liver cells are a clear example. They help detoxify blood, make bile to help digest fats, and produce proteins needed for metabolism. To do these jobs, liver cells must express a specific set of genes.

regulation of expression occurs at multiple steps

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How Cells Control Gene Expression

Cells control gene expression at several points between DNA and protein. The most common control point is transcription. At this stage, proteins bind to short regulatory DNA sequences and can either increase or reduce transcription of the linked gene. After transcription, a precursor mRNA is made. This pre-mRNA contains exons, which code for protein, and introns, which do not. It must be processed before translation, and splicing removes the introns and joins the exons. Cells can also regulate...

cis-regulatory sequences

How Cis-Regulatory DNA Controls Transcription

Cis-regulatory sequences are short, non-coding DNA segments that control gene transcription. They sit on the same chromosome as the genes they regulate and act as binding sites for transcriptional regulators. In eukaryotes, these proteins help control gene expression patterns in different cell types. These DNA sequences can be close to a gene or thousands of bases away. When they are far from the gene in the DNA sequence, they are often brought close together in space because chromosomes are...

cooperative binding of transcription regulators

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How Transcription Factors Bind DNA

Transcriptional regulators bind to cis-regulatory DNA sequences to control gene transcription. These DNA sequences are very short, usually fewer than ten nucleotide pairs long. Because they are so short, the same sequence can appear by chance in many places across the genome. Some regulators can also bind to groups of similar sequences. That raises the chance of random binding even more. To lower this risk, transcription regulators often form dimers, which are pairs of proteins that bind a DNA...

prokaryotic transcriptional activators and repressors

prokaryotic-transcriptional-activators-and-repressors

Operon Control by Activators and Repressors

Operon control in prokaryotes depends on activators and repressors. Prokaryotic genes are often arranged in groups, not one by one like in eukaryotes. Genes that help carry out the same biochemical process are placed together with their regulatory elements. This group is called an operon, and it is transcribed into a single polycistronic mRNA strand. Activators and repressors are DNA-binding proteins that control transcription in an operon. Activators bind near the promoter, which is the site...

operons

Operons in Bacterial Gene Control

Operons help bacteria control groups of genes at the same time. An operon is a set of genes that are regulated together and can be turned on or off as a unit. This shared control helps bacteria respond quickly to changes in their environment. In many operons, a promoter gives RNA polymerase a place to bind and start transcription. The operon also includes a regulatory region that helps control whether the genes are expressed. When conditions change, the cell can use this setup to manage gene...

The eukaryotic promoter region is a stretch of DNA located upstream of a gene. It includes an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. These DNA signals help control when transcription begins. The promoter can be divided into proximal and distal regions. The proximal promoter lies close to the gene and includes cis-regulatory sequences and the core promoter. The core promoter is the RNA polymerase binding site, and it is usually found...

co-activators and co-repressors

Chromatin Control in Gene Transcription

Chromatin control plays a major role in gene transcription in eukaryotes. Gene expression is regulated by several proteins that work together at a gene regulatory site. Some of these proteins bind directly to specific DNA sequences, while co-regulators attach to those regulators but do not bind DNA on their own. Co-regulators can act as co-activators or co-repressors, depending on the complex they join. One co-regulator may even switch roles in different settings. For example, the...

eukaryotic transcription activators

How Transcription Activators Turn Genes On

Transcription activators are proteins that help turn genes on by promoting transcription from DNA to RNA. They often have two parts. One part binds to DNA, and the other part activates transcription. In some proteins, such as the glucocorticoid receptor and MyoD, one domain can do both jobs. The DNA-binding part recognizes specific regulatory sequences on the DNA. These binding domains are grouped into families based on their structure. Common examples include the leucine zipper, zinc finger,...

eukaryotic transcription inhibitors

How Eukaryotic Gene Repressors Work

Eukaryotic gene repressors help turn specific genes off when the cell needs to control growth, development, or other biochemical processes. These DNA-binding proteins regulate gene expression in eukaryotes. Their presence at the right time and place can be triggered by hormones and signals from other cells. Most transcription inhibitors have two main parts. One part binds DNA, and the other is a repressor domain, which helps shut down transcription. Repressor domains can connect with basal...

combinatorial gene control

Gene Expression by Transcription Factor Combinations

Gene expression can depend on combinations of transcription factors working together. In combinatorial gene control, several transcription factors act in a coordinated way to regulate a single gene. If one or more of these factors are missing, the level of gene expression or repression can change a lot. This kind of control helps explain how a relatively small number of transcription factors can regulate a very large number of genes. More than 30,000 genes are controlled by about 2,000 to...

induced pluripotent stem cells

Reprogramming Cells into Stem Cells

Induced pluripotent stem cells are created by reprogramming mature cells back into a stem-cell state. This process shows that specialized cells can be changed into cells with broader developmental potential. The topic is important in biology because it links cell identity, gene control, and stem cell research. These cells begin as ordinary body cells and are pushed to de-differentiate, or lose their specialized features. After reprogramming, they behave like pluripotent stem cells, which means...

master transcription regulators

MEF2C and Gene Control Cascades

MEF2C is a master transcription regulator that controls gene expression in coordinated cascades. These regulators are proteins that manage the activity of multiple genes that often work together to produce a complex outcome. When a master transcription regulator is activated, it can start a chain of transcriptional activation that supports that outcome. Master transcription regulators can act in two main ways. They may bind directly to the regulatory sequences of several genes involved in a...

epigenetic regulation

DNA Methylation and Histone Changes

Epigenetic regulation controls gene activity without changing the DNA sequence. It helps determine when genes are turned on or off in a cell. Two major epigenetic mechanisms are DNA methylation and histone modification. DNA methylation adds chemical groups to DNA, while histone changes affect how tightly DNA is packed around histone proteins. These changes can make genes easier or harder to use. In high school biology, epigenetic regulation is important for understanding how cells with the...

genomic imprinting and inheritance

Genomic Imprinting in Human Disease

Genomic imprinting affects how some inherited genes are turned on or off in human cells. Diploid organisms inherit chromosomes from both parents, and each gene usually has two alleles. In most cases, both alleles are expressed. If one allele is missing or mutated, the other can often compensate, but some genes do not work that way. In genomic imprinting, a gene or its regulatory sequence carries chemical tags, such as methyl groups, on the copy inherited from only one parent. These tags are...

key terms and concepts

Explore eukaryotic promoter motifs, including the TATA box, initiator element, DPE, and CpG islands, and how they help control transcription in genes.

Eukaryotic Promoter Motifs and Gene Control | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

Eukaryotic Promoter Motifs and Gene Control

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