Transcriptional Regulators: Study with Video Lessons, Practice Problems & Examples

Transcriptional regulators control gene expression by activating or repressing transcription. Activators bind to promoter regions, facilitating RNA polymerase attachment, while repressors inhibit transcription by blocking these sites. Key DNA binding motifs include helix-turn-helix, zinc fingers, leucine zippers, and helix-loop-helix. In prokaryotes, operons like the lac and trp operons regulate gene expression based on environmental conditions, utilizing repressors and activators to respond to nutrient availability. Enhancers and silencers, located far from genes, also play crucial roles in transcription regulation through DNA looping and insulators that maintain specificity.

Transcription Regulators Action

Hi. In this video, we're going to be talking about transcriptional regulators of gene expression. So, transcriptional regulators are exactly what they sound like. They are things that regulate transcription. But, how do they work? Transcriptional regulators control gene expression by either activating or repressing the transcription of genes. Transcriptional repressors turn off genes, and therefore inhibit transcription. How they do this is they usually have some type of protein-protein interaction with either activators that compete with them for binding, or other proteins that stimulate transcription in order to block it. Now, transcriptional activators turn genes on and, therefore, activate transcription. Generally, how transcriptional activators work is they work with promoters in order to make them fully functional, so that RNA polymerase can bind and then transcribe the gene. Now, activators and repressors often don't work alone. They can work with coactivators or corepressors, which also help to control transcription, and they do this by a lot of different ways. Facilitating transcription through interacting with RNA polymerase or altering chromatin structure or activating other regulatory proteins. They just can help the activator protein stimulate transcription or inhibit it. And then there's a special type of protein called a mediator, which is a big protein complex, and it interacts between the regulatory proteins and RNA polymerase to facilitate whatever is going to happen, whether that's activation or inhibition. So if we're going to look at this, let me back out of the way, you can see that we have genes here in red, and then these promoter regions here. And you have an activator bind, and that causes transcription. And if you have a repressor bind, that blocks transcription, and therefore, that doesn't happen. Now, in this image, I've shown them working by themselves. So here's one activator and one repressor. But, in the cell, rarely do they ever work alone, and require interactions and other proteins to be fully functional. So, some of the factors are things like transcription factors, which can be recruited to the area to regulate gene expression. There are two types of transcription factors that I really want to talk about. These are the general transcription factors, and these are the transcription factors, and these are the ones binding to the core promoter site. So, if you go back to some of our earlier lessons where we talked about transcription, These general transcription factors are found in every transcribed gene. Things like TFIIA, TFIIB. You remember back to the video what these do. But then there's also sequence-specific factors, and these also bind to regulatory sites. But, generally, the proteins that are sequence-specific only bind to specific sequences, which makes sense. So you have the general transcription factors which are present anytime a gene is transcribed, and you have specific ones that are recruited only to certain genes because each gene is regulated differently. So if we were to look at what this looks like yeah. You guys can still see this image. So we have all these different factors that we've talked about, enhancers, which can be really far away, promoters. We have RNA polymerase, which is going to transcribe the gene. And this here, this blue thing here is the gene. And you have all these different transcription factors, activator proteins, and a variety of different things that activate the transcription of this gene, so they're all working together in combination to promote this activation, not just a single factor. So now let's move on.

DNA Binding Motifs

So in this video, we're going to talk about the DNA binding motifs of transcriptional regulators that allow them to bind to the DNA. In order to exert their function, transcriptional regulators must be able to interact with DNA. There are four common DNA binding motifs or regions on these proteins that allow them to interact with the domain. Let's go through each one of these, and then I'll show you an example of helix-turn-helix. This means that one helix makes contact with the DNA, while the other helix stabilizes the interaction. An example of these that you may read about in your book are things called homeodomains, which are found on these very crucial developmental genes called Hox genes. They interact with DNA through helix-turn-helix. These are commonly found in these crucial developmental Hox genes.

The second one is called zinc fingers, and this one has repeats of cytosine and histidine that bind zinc and fold into a finger-like structure to bind DNA. I'll show you exactly what this looks like in a second. The third one is going to be the Leucine zipper. This actually has two alpha helices that dimerize and bind DNA. Then, we have the helix-loop-helix, which is again two alpha helices that are connected by a loop that can bind DNA.

The transcriptional regulators all have one of these four DNA binding motifs that allow them to interact with the DNA. It is important to understand what these DNA motifs are, what they look like, and how they differ from each other.

Now, transcriptional regulators bind to DNA sequences, but how long are those? They can vary quite considerably, from 10 to 10000 nucleotides in length. These regulators don't necessarily bind to a single sequence; they can bind to a bunch of different similar sequences, meaning that they are degenerate. They don't need an exact sequence; they just need something similar. It's also important to realize that when binding the DNA, that means they can bind to the nucleotides themselves, but they don't have to. They can also bind to the backbone or the helix itself, not just the nucleotides.

Here's what the four binding motifs look like: you have your helix-turn-helix, your zinc finger, your leucine zipper, and your helix-loop-helix. These are the four DNA binding motifs that are really important for transcriptional regulators.

Now, prokaryotic cells use different ways to regulate and bind to DNA in order to regulate transcription. Prokaryotic cells use interchangeable RNA polymerase subunits. Remember, RNA polymerase is what is driving transcription, and it controls how it's going to transcribe and which genes it's going to activate by changing out some of the parts of the RNA polymerase. The part that it changes out is called the sigma subunit, and the sigma subunit is what recognizes a promoter. There are many types of sigma subunits, each recognizing a different set of promoters. If you need to block transcription of something, you just remove the sigma subunit that recognizes that promoter and put something else in. This is how prokaryotic cells control gene expression by replacing the sigma subunits of RNA polymerase.

If we're to look at what this might look like, we have our RNA polymerase here, and we have three different sigma factors or subunits. The blue one, the green one, and the purple one. Let's say that the blue one activates promoters 1 through 3, the green one does 4 through 6, and the purple one does 7 through 10. If you want to activate gene number 5 or promoter number 5, then you use this subunit. If you want to activate promoter number 10, you use this subunit. Prokaryotes just interchange these parts in order to activate some genes and not others. Now let's move on.

Types of Transcriptional Regulators

So in this video, I'm going to talk about 2 different kinds of transcriptional regulators, and those regulators, the 2 different kinds depend on transcriptional regulators that bind to sequences located near or far. So, those are the two kinds, if they're binding near to the gene or far away from the gene. So the ones that bind near, they bind to a region called promoter proximal elements, that lie very near the promoter site. And the promoter, in case you need a refresher, is where the RNA polymerase binds and orients it, so that it can transcribe the gene. So regulatory factors are all recruited to these nearby regions, to the promoter proximal elements or the promoter itself to initiate transcription. So if we are looking at what this looks like, you would have here your promoter or your promoter proximal elements, and your gene and RNA polymerase. And so, activators, so your RNA polymerase is going to go here eventually, and some other activators will bind to this promoter or the promoter proximal elements in order to transcribe the gene.

Now there are another elements, and these are regulators that bind to DNA sequences that are far from the gene. So, we've gone over a couple of these, but I just want to hit them again and maybe add a little bit more information. So, enhancers is one of these. And, so, to enhancers, gene activators bind enhancers. They can be upstream or downstream, but, generally, the sort of common thing between enhancers is that they lie thousands of nucleotides away from the gene. And how they actually impact the gene is the enhancer causes the DNA to loop between the enhancer and the promoter, so that the promoter enhancer actually sort of loop around and come in very close contact with each other in order to activate the gene.

Now there's this other type called a silencer, and this is going to be where gene repressors bind, and it acts very similar to an enhancer. Thousands of nucleotides away, upstream or downstream, and it also loops to sort of prevent gene expression. Now, if the DNA can just sort of loop in whatever direction it wants to, then enhancers could essentially regulate any gene on a chromosome. But we don't necessarily want that to happen. It needs to be more specific than that. So, there are these regions called an insulator. You may also see these as barrier elements. And insulators divide chromosomes into regions. So they say, okay. You are an enhancer, then you can regulate genes that are within this region. But once you get an insulator once you reach an insulator, you're not going to be able to enhance the transcription of other regions of the chromosome, and that provides specificity to enhancers, which would otherwise just be able to loop wherever they wanted. So we don't really want that. So insulators prevent distant elements, things like enhancers, from acting on promoters on a different segment, things that they shouldn't be activating.

Now, we've talked about a lot of things, both near and far, but, the term that describes the entire DNA sequence involved in regulating the gene is called a gene control region. So that's going to include the promoter, promoter proximal elements, insulators, silencers, enhancers, this entire region that's responsible for regulating the gene, the transcription of the gene is called the gene control region. So, the gene control region for this gene that we're looking at, which if you remember from the colors above is going to be here. You have your promoter, and you have your enhancer. So this is going to be the entire gene control region for this gene, And, there can be proteins that, you know, recruit to the enhancer, result in DNA folding that brings the enhancer close to the nearby genes, and then all of the proteins involved, including RNA polymerase, are attached on correctly.

Transcriptional Operons

So in this video, I'm going to talk about the tryptophan repressor and the lac operon. These are two examples of transcriptional regulation in prokaryotes, but I think it's really important, and you're going to read a lot about it in your textbook. I really just want to take a second to briefly go over what these are, so when you're reading about it or hear about it in class, you're not confused. Tryptophan, when the amino acid tryptophan acts as a major regulator of gene expression. Tryptophan has the ability to bind to operons, which are prokaryotic stretches of many related genes. Genes that can all do or have a similar function or work in the same pathway are called an operon. Tryptophan can actually bind to different operons and inhibit transcription. For instance, how this works is that tryptophan directly binds a transcriptional repressor and activates the repressor, and then that activated repressor binds to regulatory sequences to inhibit the genes involved in tryptophan creation. So, if there's a lot of tryptophan in the environment, tryptophan is going to bind to a repressor that represses the genes responsible for tryptophan creation. Right? Because there's so much tryptophan in the environment, the cell doesn't need to create tryptophan, so it wants to repress those genes. So, like I said, it allows gene expression to be controlled by environmental levels of tryptophan. In high levels of tryptophan these genes are going to be repressed. So, you have this tryptophan repressor, and you have tryptophan itself. When tryptophan is present, it binds to the repressor, and that binds to this operon here, which has a bunch of different genes responsible for tryptophan creation. And so because the tryptophan repressor is binding here, it blocks transcription so that the cell doesn't waste that energy making tryptophan when it's already available. Now, the second one you are going to read about is the lac operon, which is a little more complicated. Essentially, the lac operon is a bunch of genes that control or regulate lactose in E. Coli. There can be, like the tryptophan, a response of this activation or repressing going to depend on, you know, how much lactose is in the environment. So, when there's no lactose available, the lac repressor, something that's going to repress this, halts transcription of the lac operon. Now if there's glucose available, this is a different type of sugar, but glucose can be used to make lactose, what happens is there's this activator protein called the cap protein, but it remains inactive. Right. But there's no direct repression of the lac operon. So, the lac operon is not being inhibited, but it's also not being activated. So, it's just kind of existing and there might be low levels of transcription, but nothing too big. But, when lactose is available, the activator cap binds upstream and actively activates the lac operon. So, here we have our lac operon, and we have the cap binding site. So, this is going to be the activator site. And then there are 3 conditions here. If there is lactose available, the cap protein binds, and this results in strong expression. If lactose is unavailable, then the cap protein doesn't bind, and therefore, RNA polymerase doesn't bind, and so these lac genes are not expressed. But you have this third option here, whereas if lactose is low, but there is a high amount of glucose. What happens is the cap protein is activated, but it doesn't really do anything. So you don't get RNA polymerase, it's not really binding here, and so what you get is just very low levels of gene expression of this operon. So that is how the lac operon and the tryptophan repressor work. Hopefully, that was clear. Feel free to rewatch these videos if you need to. But now, let's turn the page.

Which of the following is not a DNA binding motif?

• A. Zinc Finger
• B. Leucine Zipper
• C. Helix-loop-Helix
• D. Helix-zipper-Helix

What is the purpose of a transcriptional mediator?

• A. To mediate regulation between transcription and translation
• B. To mediate the process of transcription
• C. To mediate between regulatory proteins and RNA polymerase
• D. To mediate between RNA polymerase and DNA

Enhancers can reside downstream of the gene they regulate.

• A. True
• B. False

If lactose is present, what happens to the lac operon? 

• A. It is activated
• B. It is repressed

Here’s what students ask on this topic:

What are transcriptional regulators and how do they control gene expression?

Transcriptional regulators are proteins that control gene expression by either activating or repressing the transcription of genes. Activators bind to promoter regions, facilitating the attachment of RNA polymerase, which then transcribes the gene. Repressors, on the other hand, inhibit transcription by blocking these sites. They often interact with other proteins, such as coactivators or corepressors, to modulate their effects. Additionally, mediators, which are large protein complexes, can facilitate interactions between regulatory proteins and RNA polymerase. This intricate network ensures that genes are expressed at the right time and in the right amount, maintaining cellular function and response to environmental changes.

What are the common DNA binding motifs found in transcriptional regulators?

Transcriptional regulators often contain specific DNA binding motifs that allow them to interact with DNA. The four common motifs are:

• Helix-turn-helix: One helix makes contact with the DNA, while the other stabilizes the interaction. Found in homeodomains of Hox genes.
• Zinc fingers: Repeats of cysteine and histidine bind zinc, folding into a finger-like structure to bind DNA.
• Leucine zipper: Two alpha helices dimerize and bind DNA.
• Helix-loop-helix: Two alpha helices connected by a loop that can bind DNA.

These motifs enable transcriptional regulators to bind to specific DNA sequences, facilitating or inhibiting transcription.

How do enhancers and silencers regulate gene expression from a distance?

Enhancers and silencers are regulatory DNA sequences located far from the genes they control. Enhancers bind gene activators and can be thousands of nucleotides away from the gene. They function by causing the DNA to loop, bringing the enhancer close to the promoter region to facilitate transcription. Silencers work similarly but bind gene repressors, looping the DNA to inhibit transcription. Insulators, or barrier elements, ensure that enhancers and silencers only affect specific genes by dividing chromosomes into distinct regulatory regions, preventing unwanted interactions with other genes.

What is the role of the lac operon in gene regulation in prokaryotes?

The lac operon in E. coli is a set of genes involved in lactose metabolism. It is regulated based on the availability of lactose and glucose. When lactose is absent, the lac repressor binds to the operator, halting transcription. When lactose is present, it binds to the repressor, preventing it from binding to the operator, allowing transcription. Additionally, the presence of glucose affects the activity of the catabolite activator protein (CAP). When glucose levels are low, CAP binds to the promoter, enhancing transcription. This dual regulation ensures efficient use of available sugars.

What is the function of the tryptophan repressor in prokaryotic gene regulation?

The tryptophan repressor regulates gene expression in response to tryptophan levels in prokaryotes. When tryptophan levels are high, tryptophan binds to the repressor, activating it. The activated repressor then binds to the operator region of the trp operon, inhibiting transcription of genes involved in tryptophan synthesis. This prevents the cell from wasting energy producing tryptophan when it is already abundant. Conversely, when tryptophan levels are low, the repressor is inactive, allowing transcription of the trp operon and synthesis of tryptophan.