Post-Transcriptional Regulators - Online Tutor, Practice Problems & Exam Prep

Post-transcriptional regulation of gene expression involves RNA processing, translation, and degradation. Key processes include splicing, export, and editing of mRNA, which must be properly processed to be translated. Translation can be inhibited by factors like EIFs and translational repressors. Additionally, mRNA degradation rates vary, influenced by poly(A) tail length and mechanisms such as exosomes and nonsense-mediated decay. RNA interference, through siRNAs and microRNAs, further regulates gene expression by targeting mRNAs for degradation, highlighting the complexity of gene regulation beyond transcription.

RNA Regulation

Hi. In this video, we're going to be talking about post-transcriptional regulation. So we've talked about all these different kinds of gene regulation, but these videos are going to focus on what controls gene expression after the transcript has been transcribed. So the first thing that is really responsible for controlling gene transcription is going to be RNA processing, translation, and degradation. So how the cell handles the RNA. Regulation of mRNA after transcription is a major way to control gene expression. These are things that we've already gone over for the most part. These are like RNA processing events like splicing, export, or editing, because improperly processed RNAs actually remain in the nucleus and are not exported or translated. For RNA translation, that can also be controlled. If you remember these proteins called eukaryotic initiation factors (EIFs), which are factors involved and necessary for translation, they can also act to inhibit translation. And so, for instance, if they become phosphorylated, they can no longer hydrolyze GDP in exchange for GTP, and therefore, they cannot promote translation. This is another form of regulation. If they can't be translated, then, of course, it's not going to be expressed. Also, there are things called translational repressors, and these are proteins that control the translation of an RNA, at a variety of different factors, but all these things are impacting translation and, therefore, impacting gene expression.

Now, another thing to consider is actually the rates of degradation of mRNA. mRNA degradation rates actually vary between transcripts and are another way to control gene expression. For instance, mRNAs with shorter poly A tails are less stable and so, they get degraded more quickly than those with longer tails. There are a few ways that mRNAs get degraded and each of these ways is regulated in its own fashion. One way is exosomes, and these are complexes that degrade mRNA from 3' to 5' using exonucleases. You have P bodies, and these are actually nuclear mRNA processing bodies. These are regions of the nucleus that also degrade mRNA. And then you also have nonsense-mediated decay, and so this decay or degradation is focused on improperly spliced mRNA. For instance, if the stop codon gets put in the wrong place due to some kind of mutation, then the splice is wrong and nonsense-mediated decay recognizes that and controls gene expression by degrading that RNA.

This is just an example of all the different ways, or all the different steps that RNA can be regulated. We have our DNA up here, it gets transcribed, but we are really focused on everything that happens after that. That ensures having the mature mRNA. If it's not properly processed, it doesn't ever properly become mature. It won't get exported, but if it is mature and it does get exported, but we can control it at translation, by a variety of different translation factors. Another mRNA that doesn't need to be expressed, for some reason, can also be degraded in a variety of ways. So now let's turn the page.

RNA Interference

So, in this video, we're going to be talking about another way of post-transcriptionally controlling gene expression, and that's through RNA interference. RNA interference is just using regulatory RNAs to control gene expression. One of these types of RNAs that can control gene expression are called small interfering RNAs or siRNAs, and this is actually a way that has evolved to use RNAs to protect cells from viruses. This is because viruses typically do not want their genes expressed, and so this is the way the body has evolved to handle those. siRNA are double-stranded RNAs that enter cells. Once inside the cell, they interact with an enzyme called dicer, which cleaves the siRNAs into really small fragments. These fragments then bind to what's known as the RISC complex, and this is a double-stranded RNA that degrades into one strand, and then that single strand can bind complementary mRNA and then be degraded by RISC. The component of RISC responsible for this degradation is called argonaut. Let’s look at what this looks like. We have this double-stranded RNA that's usually come from some kind of virus or bacteria, and it enters cells. When it ends in the cells, dicer comes in and cleaves it into various fragments. Remember this is double-stranded still. It's then loaded onto the RISC complex, which you can see here, and this eventually degrades one of the strands, which sort of goes off and does whatever, and you have RISC bound to one of the strands of sRNA. This can then go back and bind to mRNA that the virus has tried to create in the cell. When it's bound here, it actually gets degraded. This is one way that gene expression from foreign objects or foreign molecules gets degraded by the cells. But there is another way that RNA interference works, and that’s through microRNAs. MicroRNAs differ because they are actually encoded in the genome. How this works is that mRNAs actually begin as single-stranded RNAs, created through transcription, so normal transcription of the genome. After transcription, the microRNAs form these structures called hairpins or loops. These just fold onto each other and create these secondary complex structures. Then, drosha recognizes these structures and comes in, cleaves them off, and the free microRNA can then associate with RISC. Remember, this is the same as the siRNA. When it's associated with RISC, the single-stranded microRNA can then bind to the 3' untranslated region (UTR) of an mRNA and inhibit expression because it gets degraded by RISC. This is a significant way that the cell regulates gene expression because each microRNA can regulate around 200 mRNAs by controlling their degradation. Let's go through these steps here. We have our gene or our microRNA in the genome. It gets transcribed. Now, it's transcribed and it forms into these structures here. And remember, they have hairpins or loops, but they are these complex structures, hairpins. Then drosha comes in and cleaves off different regions of the microRNA to fully process it. This gets exported into the cytosol. All of this has happened in the nucleus. When the pre microRNAs are in the cytosol, they interact with dicer. Dicer again comes and helps cleave them to make sure that they are single-stranded RNA. When it is a single-stranded RNA, it can bind to the RISC complex, and this RISC complex goes on and binds the 3' UTR of mRNAs for degradation. You can imagine this controls a lot of different genes because if the mRNAs get degraded, they can't be expressed. These are siRNAs and microRNAs, which are extremely important in genetics and cell biology, but there are also a couple more that I haven't really talked about, but I just want to mention briefly. These are lesser-known ones but still essential to realize. Gene expression can be regulated by other RNAs, including piwi-interacting RNAs that suppress the movement of transposons, and also long non-coding RNAs, which are greater than 200 nucleotides in length but also act in their own mechanisms to regulate gene expression. RNA interference is a major way that genes are regulated, generally, by those RNAs interacting with an mRNA and then causing that mRNA to become degraded. So now, let’s move on.

Protein Regulation

So, in this video, we are going to be focusing on protein regulation of gene expression. These are things that happen to proteins, after they have already been created, to either suppress or activate gene expression. We have already talked about this, but regulating mRNA after transcription is a major method of controlling gene expression, and that also you know controls translation, RNA editing, or various RNA interference, but protein modifications can also inhibit or activate protein function. Some modifications of proteins that we've talked about before, but I just want to bring up again as examples of ways that this could actually impact gene expression are things like protein phosphorylation, dephosphorylation, which control phosphates and activity of a protein, but also protein cleavage, and these are all modifications that can happen to regulate gene expression by regulating the protein. Another way is protein degradation, and, of course, if the protein isn't there, it's not going to be able to function, and, therefore, that's a major just a little bit related to this. Protein degradation usually occurs through labeling of ubiquitin, which targets that protein for proteasome destruction or lysosomal destruction. But then there's this other term, that we haven't talked about specifically, but this is called a degron, and that’s actually a region of the protein that controls the protein’s destruction. So for instance, this is an image looking at the presence of a degron and how it affects protein presence over time. So we have this protein, this is called the GFP protein, and this is over time. So as it is degrading, let me back away here. Here's a degron. This is just going to be some kind of protein sequence or protein structure that's on the protein that marks it for degradation, and you can see that the GFP with the degron is actually being degraded significantly over time, whereas the protein without the degron is still present in similar amounts to when it started. The degrons are just regions of a protein that control the protein's, destruction and degradation. So that's protein regulation of gene expression, so now let's move on.

Choose all of the following post-transcriptional regulators of gene expression.

a) Micro RNAs

b) siRNAs

c) RNA Polymerase Degradation

d) Exosomes

Hello, everyone. Choose all of the following post-transcriptional regulators of gene expression. Okay, so we know there are tons of regulators of gene expression, but we're specifically being asked about post-transcriptional regulators of gene expression? So, after the mRNA has already been transcribed, how can we regulate how that mRNA is going to be expressed? Okay, so choose all the following post-transcriptional regulators of gene expression. Okay, so we start off with microRNAs. What are these going to be? Well, micro RNAs are going to be a specific type of non-coding RNA. So this means that they are not like mRNA. They don't actually code for anything. They're actually going to do a function. They're not actually going to be turned into a protein like mRNA would. So these are non-coding RNAs that are going to silence mRNA by Complementary Bonding with mRNA. So, how does this actually function? Remember, microRNAs are going to be these small non-coding RNAs that are complementary to a particular mRNA, and they're going to bind to that mRNA. And now that mRNA is double-stranded, which means it cannot be translated and it cannot be turned into a protein. So, this is a regulator of gene expression because that gene is not being fully expressed if the protein is not being created. And the protein's not being created because the mRNA has been bound by this microRNA. Now, is this a post-transcriptional regulator? Yes. It is a post-transcriptional regulator because the mRNA has already been transcribed and then the microRNA binds to it. So, yes, this is a post-transcriptional regulator of gene expression. So choose all of the following: A is going to be an answer. So now, let's see if any other answers here are correct as well because we might have more than one answer. Okay, so now we have siRNAs, which remember are small interfering RNAs. Now these are also going to be non-coding RNAs, and how do they function? They're going to function a little bit differently from microRNAs, but they do RNA interference. So basically, you can think of them as interfering with the mRNA and its function. They're going to do RNA interference by degrading mRNA. So they're basically going to chop up the mRNA and, excuse me. And if the mRNA is all chopped up, it can't be translated, right? So yes, this is a regulator of gene expression. Is it a post-transcriptional regulator of gene expression? Yes, because the mRNA is already made and then the small interfering RNAs come and chop it all up. So, yes, transcription has already happened. So this is going to be another of our answers. Okay. So now we have 2 left. We have RNA polymerase degradation and Exosomes, and we're going to have to figure out if both of these are correct. Maybe this is an all of the above kind of question. Now, let's talk about Exosomes. What are those? Remember, Exosomes are also going to be very important for interference with the RNA. So they also interfere with RNA like small interfering RNAs and micro RNAs. So they interfere with RNA. But how do they do it? Remember, these are going to degrade the mRNA from the 5 prime end to the 3 prime end. You can basically just think of this as it is completely eating away the mRNA and destroying the mRNA from one end to the other. So is this a form of gene expression regulation? Yes, it is. It is destroying the mRNA which can never be translated. So is this post-transcriptional degradation? So, basically, we have here, RNA Polymerase Degradation? So, basically, they're saying that RNA Polymerase is destroyed. So, is this a form of gene expression regulation? Yes, it is entirely a form of gene expression regulation. Because if RNA polymerase is destroyed the mRNA cannot be created, so that gene is never expressed. Is this post-transcriptional? It's not post-transcriptional. This is actually pre-transcriptional. Because the mRNA can never be created if RNA polymerase is destroyed because RNA polymerase makes mRNA. So this is before transcription because the mechanism of transcription is being destroyed. Transcription because the mechanism of transcription is being destroyed. So this is not going to be one of our answers because they're specifically asking us about post-transcriptional regulators. It is a regulator of gene expression, but it's a pre-transcriptional regulator of gene expression. So choose all of the following post-transcriptional regulators of gene expression: micro RNAs, small interfering RNAs, and exosomes are all going to interfere with the mRNA and be post-transcriptional regulators of gene expression. Okay, everyone. Let's go on to our next question.

When the siRNA interacts with RISC for the first time it is single stranded.

• A. True
• B. False

What is the name of the enzyme that cleaves the miRNA in the nucleus before it travels to the cytoplasm to exert its effects?

• A. RISC
• B. Argonaut
• C. DROSHA
• D. RNA Polymerase

What is the name of the region on a protein that controls its degradation over time?

• A. Degradation sequences
• B. Ubiquitin
• C. Ubiquitin binding site
• D. Degron

All non-coding RNAs are responsible for regulating gene expression.

• A. True
• B. False

Here’s what students ask on this topic:

What is post-transcriptional regulation and why is it important?

Post-transcriptional regulation refers to the control of gene expression after an mRNA molecule has been created during transcription. This regulation is crucial because it ensures that mRNA is properly processed, exported, translated, and degraded. Key processes include splicing, export, and editing of mRNA. If mRNA is not correctly processed, it remains in the nucleus and is not translated. Additionally, translation can be inhibited by factors like EIFs and translational repressors. mRNA degradation rates also vary, influenced by poly(A) tail length and mechanisms such as exosomes and nonsense-mediated decay. This regulation allows cells to respond quickly to changes and maintain homeostasis.

How does RNA interference (RNAi) regulate gene expression?

RNA interference (RNAi) regulates gene expression by using small regulatory RNAs, such as siRNAs and microRNAs, to target mRNAs for degradation. siRNAs are double-stranded RNAs that are cleaved by the enzyme Dicer into small fragments. These fragments bind to the RISC complex, which degrades one strand and uses the other to bind complementary mRNA, leading to its degradation. MicroRNAs, encoded in the genome, form hairpin structures that are processed by Drosha and Dicer before associating with RISC. The single-stranded microRNA then binds to the 3' UTR of target mRNAs, inhibiting their expression by promoting degradation. This mechanism is vital for controlling gene expression and protecting cells from viruses.

What role do poly(A) tails play in mRNA stability?

Poly(A) tails play a crucial role in mRNA stability by protecting the mRNA from degradation. The length of the poly(A) tail influences the stability of the mRNA; longer poly(A) tails generally make the mRNA more stable, while shorter tails lead to quicker degradation. This stability is essential for the proper translation of mRNA into proteins. Various mechanisms, such as exosomes and nonsense-mediated decay, target mRNAs with shorter poly(A) tails for degradation. By regulating the length of the poly(A) tail, cells can control the lifespan of mRNA and, consequently, the level of protein production.

What are translational repressors and how do they affect gene expression?

Translational repressors are proteins that inhibit the translation of mRNA into proteins, thereby affecting gene expression. They can bind to specific sequences or structures within the mRNA, preventing the assembly of the translation machinery or the progression of translation. For example, some translational repressors bind to the 5' UTR of mRNA, blocking the binding of ribosomes. Others may interact with EIFs, preventing their function. By inhibiting translation, these repressors ensure that certain proteins are not produced, allowing the cell to finely tune gene expression in response to various signals and conditions.

How does nonsense-mediated decay (NMD) contribute to mRNA regulation?

Nonsense-mediated decay (NMD) is a surveillance pathway that degrades mRNAs containing premature stop codons, preventing the production of truncated, potentially harmful proteins. This process is crucial for maintaining the quality of gene expression. NMD recognizes and targets mRNAs with premature stop codons, often resulting from mutations or improper splicing. The degradation of these faulty mRNAs ensures that only correctly processed and functional mRNAs are translated into proteins. By eliminating defective mRNAs, NMD contributes to the overall fidelity and efficiency of gene expression.