The Science of Everything Podcast - Episode 148: Control of Gene Expression

Episode Date: September 30, 2024

An introduction to the processes by which cells control which genes are expressed. We begin with an overview of why genetic regulation is necessary and the key stages where such regulation occurs, including key concepts such as transcription factors and DNA binding domains. We then discuss prokaryotic gene regulation, focusing on the lac operon in E. coli. We then expand the discussion to cover the various mechanisms of eukaryotic gene regulation, including chromatic remodelling, transcriptional regulation, post-transcriptional regulation, RNA editing, and micro RNAs. Recommended pre-listening is Episodes 34-35: DNA Structure and Function, and Episode 118: Cell Signalling. If you enjoyed the podcast please consider supporting the show by making a PayPal donation or becoming a Patreon supporter. https://www.patreon.com/jamesfodor https://www.paypal.me/ScienceofEverything

you're listening to The Science of Everything podcast, episode 148. Control of Gene Expression. I'm the host, James Fodor. So, in this episode, we are going to take a look at the control or regulation of gene expression and discuss the need for gene regulation and the key stages of control of gene regulation. We'll start by talking about genetic regulation in prokaryotes, so talking about operons and specifically the lack operon. and then we'll move on to talking about the processes in eukaryers,

which are much more complicated and involved, including chromatin remodeling, various aspects of transcriptional regulation, post-transcriptional regulation, and concluding with a look at translational regulation. Recommended pre-listening for this episode is episodes 34 and 35 on DNA structure and function, which will provide a lot of the background necessary

for understanding the content that we go through today. episode 68 on protein structure and function will also be helpful. So with that out of the way, let's jump in and begin with an introduction about what is genetic regulation and why do we need it, or what role does it serve? So regulation of gene expression includes a wide range of mechanisms used by cells to change the production of specific genes, gene products, so proteins. Gene regulation effectively involves either increasing or decreasing the production of specific protein products from particular genes at particular times. So, as I mentioned in the introduction, any step of along the pathway and gene expression

may be modulated right from the transcription of messenger RNA from the DNA itself, right through to post-translational modifications of the protein to affect its function. Every somatic cell in the body has the same set of DNA, barring a few ad hoc mutations. This is called your genome, right? it's the set of DNA that every somatic cell has.

However, expression of the proteins differs substantially between different cells in different tissues and different organs. That's what differentiates different parts of your body and different tissues, is the fact that the proteins expressed in different cells are different to each other. And the differentiation of cells begins early on in the development process and then continues and resulting in different types of cells becoming more and more different from one another. This differentiation is necessary to have the specialized tissue that we need for various specific functions in complex organisms. There's different requirements, obviously, for cells in the digestive system versus in the liver versus in the brain. Now, in addition to the developmental differentiation of tissues and cell types, there's also a need to respond to environmental stimuli, as well as endogenous stimuli produced from various metabolic signals within the body.

So both external and internal signals that can change over time in response to all sorts of factors, those also potentially can give rise to the need for different protein expressions. As a very simple example, if you ingest a poison, there's a need to produce the enzymes that can break down that poison to render it harmless. Those might not normally be produced because they're not normally needed, right? So that stimulus requires an alteration of gene expression in order to adapt to the circumstance or respond to the change in the circumstances. So anything that affects the internal metabolic environment of the body can potentially lead to the need to change the proteins that are expressed in particular cells at a particular time.

Hence the need for gene regulation. This is very important to understand because as we'll see throughout this episode and as we've discussed in previous episode, your genome is not just a static blueprint that says how to produce each gene. It's also part of a complex interplay of mechanisms that actually gives rise to those gene products in the right numbers and right ratios at the right times in the right place. So it's not just having the instructions there, it's also about how they're implemented or how we go from the DNA to specific proteins expressed in the right amounts, in the right places, at the right times. All of that is what gene regulation or gene control is about the mechanisms that control which genes are expressed

and give ruse to protein products when and where and how that all works. There are many stages to gene regulation as I mentioned and I'll just sort of I'll outline them in a little bit more detail and what we'll do is we'll go through them in more detail step by step throughout this episode. So in order to control gene expression, the very first thing that needs to happen, this is in eukaryotes, will come to procurates in a second. The very first thing that needs to happen is that the gene needs to be made accessible so that the polymerase and other enzymes can transcribe that gene into a protein. And the process of making the gene excessible, kind of unwinding the complex system that keeps the DNA normally wound up and bound tightly together in chromatin. It's called

chromatin remodeling. And so that's one mechanism by which gene expression is controlled. You can't even make the MRNA transcripts if the gene is not accessible. So controlling which regions of the genome and which chromosomes and which parts of the chromosomes are accessible to the enzymes within the nucleus is sort of the first stage of control of gene expression. So that's chromatin remodeling. The next step, once we've made the gene accessible, is actually reading the DNA sequence and detecting which sequence it is, like what it codes for. And this is where special enzymes called transcription factors comes in. So these are proteins which are able to read the DNA sequence, but from the outside. So they don't have to, they don't have to unwind the double helix or denature

the two strands of the DNA. They're able to read it from the outside. I'll talk a bit more about how that works in a moment and detect what the sequence is. And this is important because obviously if we're going to regulate gene expression, if we're going to say, oh, we need more of this gene, more of the product of this gene, we need to be able to find that gene in the genome and detect where it is and then have the requisite enzymes then bind to that and the RNA polymerase come in and make the MRI transcripts. So there needs to be a mechanism for reading the DNA and identifying those sequences. And that's where transcription factors come in. They can read the DNA from the outside and detect what the sequence is. We then need a mechanism for selective binding to those DNA sequences.

So it's one thing to be able to read them from the outside, but we also need to bind to them so that the RNA polymerase and other enzymes can come in. And that's where these specially evolved protein regions called DNA binding motifs come in. So they're able to bind to specific regions to then recruit all of the enzymatic machinery needed to begin the transcription process. Once we've found the right gene bound the relevant enzymes to transcribe the gene into an mRNA, the next stage is modifying those MRI transcripts as needed. And this is the stage called post-transcriptional regulation. So there's various modifications that can be made to mRNA, as well as the fact that it also needs to be transported out of the nucleus for processing

to make protein products. So all of those stages between essentially from the MRNA to actually making the protein is post-transcription regulation, and that's another point in which we can intervene to modify the number and type of protein products. One aspect of that that's only become understood relatively recently is selective degradation of unnecessary MRNA transcripts, using special types of RNA, small RNAs, called microRNAs. And we'll talk more about these in a moment, but that's a sort of aspect of post-dramed and regulation is to essentially degrade or remove unneeded mRNA transcripts after the fact. So that's another point of intervention.

And the last step, which happens after protein translation, is called post-translational regulation, which involves modifying the protein as well as sending it out to the right location. And that's another point of intervention that can affect the amount and type of protein product produced. So as you can see, there are many steps of gene regulation and many points in the pathway where signals can be integrated to determine what the outcome should be. And this is important because, as we'll see later, it's not the gene regulation because at one point or another, it's that there's an integration of information at multiple steps in a pathway, which together determines the regulation and the expression of each gene in a given cell at a given time. So that's an outline of the different stages. What we're going to do now is we'll talk first about prokaryotic gene regulation,

which is much simpler than eukaryotic gene regulation, but does exemplify and illustrate some of the core principles. So after we've gone through that, then we'll turn to eukaryotic gene regulation, where we'll spend most of the episode and go through the wider range of processes that are relevant there. But first, let's start with prokaryotes, which are simpler, and so have a simpler set of mechanisms, and also a somewhat different set of mechanisms, but again, some principles in common. So I'll try to highlight things that are the same and things that are different. Now, if you've forgotten, prokaryotes refers to bacteria and archaea. Sometimes I may say bacteria,

just sort of as a shorthand, but technically they're archaea as well, which are different. But these are relatively small, single-celled organisms, the simplest and sort of oldest forms of life that still exist, and they lack many of the more complex, more evolutionarily recent components and functions of ucarot cells. So, for example, they don't have a nucleus. They don't have much in the way of organelles, or a much simpler set of internal organelles, and the DNA is packaged very differently. They have much less DNA. I've talked about this in previous episode, so this is just a reminder of the difference between prokaryotes and eukaryotes. So even though they're much simpler, procurates still need to regulate gene expression.

They don't have cellular differentiation, so there's not really a developmental cycle, but the cell, the bacteria, still needs to be able to respond to changes in the environment. And a good example of a change in the environment is changes in the, essentially, food that's available. It doesn't make sense for a bacteria to be producing enzymes, allowing it to digest nutrients that aren't present in the environment. That's a waste of resources. save those resources and spend them on, you know, dividing more quickly, right? So that's going to be evolutionary advantageous. So that selects for mechanisms that allow you to be selective about what

enzymes you produce, only those that you actually need. Anything else is wasteful. And an example of this in the bacteria E. coli is metabolism of lactose. Lactose is a disaccharide, so it's a sugar consisting of two monosaccharide subunits. And in order to be broken into those two components, an enzyme is required called beta galactidase. Now this enzyme, as I said, will only be produced by the bacteria when it actually needs it. That is, when there's lactose present in its environment. Otherwise, there's no need for it. In order to utilize the lactose, you obviously need the enzyme that breaks it down,

and there's another enzyme that's needed, which helps the lactose enter into the cell. So one that sort of helps to bring it into the cell, and then another that breaks it down. There's actually a third enzyme that's involved, which I'm not sure if the function is entirely. known. The point here is that there are a set of three enzymes or proteins, probably just call them proteins, that E. coli needs in order to metabolize lactose, and it only needs them for this purpose. They're often called for short, Lack Z, Lack Wine, Lack A, in case you look at other resources for this. But I might just call them our three lactose enzymes, right? Now by default, as I said, transcription of these genes is off because they're normally not needed

if there's no lactose present. If you add lactose to the media, so now E. E. coli has access to, it, what will happen is you'll see that these genes begin to be expressed and the E. coli produces the relevant protein products and it's able to metabolize lactose. Now the question is, how is this regulated? How does the bacteria sort of know that lactose is present and it now needs these genes to be active? Well, here's how it works, right? There's sort of two processes that actually occur in combination, positive regulation and negative regulation. That actually both work in this case. I'll explain them each in turn.

Now, one key concept that we need before getting into this is that of an operon. So, prokaryotes regulate many of their genes in operons. An operon essentially is a single functioning unit of genomic DNA found in prokaryotes, which involves a cluster of genes, usually like a handful, a small number of related genes, which are under the control of a single promoter. A promoter is the region of DNA that the RNA polymerase binds to in order to begin. transcription. So you always have to have a promoter upstream of the genes. In eukaryotes, typically each gene has its own promoter, but in prokaryotes, they kind of combine them together. They

bunch them up so that one promoter will control multiple genes. And usually these genes are related. So, I mean, it makes sense, right? Because they share the same promoter, there's no way to transcribe one of them, but not the other. It's sort of one or sort of all or none, right? So it wouldn't really makes sense to put unrelated genes under the control of the same promoter because then you always have to get them together and if they're unrelated why would you always want them together? So the point is that in an operon, which has a single promoter, typically you get related genes involving, which are involved in related functions. In the case of the lac operon, you've got genes under the control of a single promoter. You've got the three genes required for the enzymes needed

to process lactose, right? So that makes sense. They're needed for lactose and so you control them all together, There's one promoter for them. So that's what an operon is. Now, how do we control the operation of this lack operon, right? Because we want it to be on when lactose is present and off otherwise. What happens is that there is, in addition to the promoter, remember, that's the region where the RNA preliminaries binds. There's another region of DNA called the operator. And this is a segment of DNA whose purpose is to bind, or to be bound to, really, by a special enzyme called a repressor.

So this protein comes in and it binds to the operator and blocks the promoter. The operator is between the promoter and the gene products. So if you think about it, if the repressor is present, it binds to the operator. That means that when the RNA preliminaries comes in, binds the promoter, it then tries to move downstream along the DNA so that it can begin transcribing. But then it gets stuck because the repressor is in the way. The repressor physically blocks the RNA preliminase from moving downstream from the promoter to actually transcribe the DNA.

So it gets in the way and it prevents transcription. So the name makes sense, right? Repressor because it represses the regulation of the gene. It prevents the transcription because it physically gets in the way and blocks the RNA polymerase. Okay, well, that explains how we can turn off the lack operon, but how does it get turned on? I mean, after all, the whole point is that when lactose is present, it needs to get turned on. So how does that happen? Well, the way it happens is that this repressor doesn't just always block the operator.

it blocks the operator, but only in cases where the effector is absent. So the effector is a special molecule which comes in and binds to the repressor and causes it to change shape and dissociate from the DNA. So it's like a key, essentially, that this effector comes in and unlocks the repressor so that it detaches from the operator and then allows the RNA preliminaries to go and transcribe all the genes in the lack operon. So what might this effector be, you might be wondering? Well, let's think about it.

What we want is for the Lachoporon to be working to actively transcribe MRNA when lactose is present and not otherwise. So how about if we used lactose as the effector? Because after all, when lactose is present, if lactose is the effector, it can come in and unlock the repressor, cause it to dissociate, and then allow the lack operon to work. When lactose is absent, then there won't be any effector. There'll be nothing to unlock the repressor.

The repressor will stay bound to the operator, and the RNA polymerase will be blocked, and you'll get no transcription. And this is, in fact, what happens, right? So the very molecule, the effector molecule that kind of unlocks the repressor, allows transcription from the lacopron, is lactose itself. So this makes perfect sense.

It's all very sort of logical, right? When lactose is present, it unlocks the, repression of the lac operon and allows the enzymes needed to metabolize that lactose. So this is an example of a sort of biological mechanism that kind of just makes sense, right? It seems very well designed. A lot of cases you wonder why would it work that way? Well, in this case, it kind of makes a lot of sense. So this is called negative regulation because by default the operon is turned off. It's inactive and it needs the presence of a special molecule to kind of unlock it and cause the

repressor to dissociate from the operator. Now I mentioned there's another type of regulation called positive regulation, which works essentially the same way, but opposite. So instead of having a repressor, which needs a special molecule to get it out of the way, positive regulation has an activator, which binds to a different site. It's like the operator, but it's the site for the activator, right? So the activator will have its own site, usually just upstream of the promoter, because what happens is that in order for the LACOPORON to turn on to be activated,

the activator needs to bind to the special site, and what the activator does is it helps the binding of RNA preliminaries. RNA polymerase can bind to the promoter and begin transcription without the presence of the activator. So it's not, the activator isn't strictly necessary. It's just that without the activator, the binding is very inefficient. So you'll get only a small amount of protein product without the activator, essentially because it's hard for the RNA preliminaries to bind to the promoter just by itself. When the activator is bound, however, to its special site, just upstream of the promoter, then the activator really activates.

It really sort of turbocharges the transcription of the operon by recruiting the RNA prelimin and then sort of transcribing away, producing lots of MRNA transcripts. So the activator is kind of like the repressor, but the opposite. When the activator is bound to the DNA, that leads to an increase in transcription, whereas when the repressor is bound to the DNA, it removes transcription. And the activator is also regulated by an effector molecule. It will be a different effector to the one that affects the repressor, but when that effector is present, it will bind to the activator,

causing it to change shape, and then associate to its site on the DNA. And the effector for the Lackoperon is actually a molecule called cyclic AMP. And the reason for that is because cyclic AMP is regulated by glucose, and without getting into the metabolic details, glucose is a preferred carbon source for E. coli. So if it has glucose, carbon source and an energy source, so if glucose is present, E. coli will prefer to eat that, and therefore it doesn't need the lactose. So if glucose is present, for regulatory reasons I won't explain, that means that cyclic AMP will be in low concentrations, right?

but cyclic amp is the effector for the activator for the lack operon so high glucose means low cyclic a mp which means low effectors to bind to the activator which means not much activated binding to the DNA which means not much transcription a little bit but not very much transcription of the lacoporon now conversely if there's no glucose present or very little glucose present cyclic amp is high, which means there's lots of this effector molecule, so lots of binding to the activator, lots of activator binding to the DNA, and that activator binding to the DNA, therefore, increases and activates, turbocharges the Lackopron, helps the RNA polymerase bind to the promoter, and thereby turbocharges the transcription of lots of gene product from the Lackopron.

Now, these, I've talked about these positive and negative regulation mechanisms as if they're separate, but in fact they both operate at the same time for the Lackoperon. In other words, if there's no lactose present, the repressor will just be bound to the operator in the Lackoporon. And that means you get essentially no MRNA product, because RNA polymerase, whether it binds to the promoter or not, it can't move anywhere. It can't get downstream. It's blocked. So if there's no lactose, you've got no chance of any significant amount of MRNA product, right? That's the negative regulation.

If lactose is present, lactose serves as the effector for the repressor, so the lactose comes in, binds to the repressor, change a shape, dissociates, repressor. has gone, now the way is clear. The path is opened up for the RNA preliminaries. However, that doesn't necessarily mean you're going to get very much in RNA products. You'll get a little bit, but you only get a significant amount if the LACOPRON is also activated. If the activator protein also binds to its site and thereby helps to recruit the RNA prelimerase to the promoter and get transcribing. When does that happen? When does the activator get into action? so to speak. Well, remember, that happens when there is no glucose present. No glucose present means high levels of cyclic AMP, and cyclic AMP is the effect of molecule which recruits the

activator and causes it to bind to the DNA. So in order to have maximal transcription of the Lackoporon, you need the presence of lactose to remove the repression, so that's the negative regulation, plus you need the absence of glucose, which means that there's lots of sick oprens, you need the lots of cyclic AMP, which brings in the activate, and that's the positive regulation. It activates the transcription of the lacoperon. So you have removal of negative regulation, and the presence of positive regulation together, maximize the transcription of the lacoperon, producing the gene products needed for the metabolism of lactose. So hopefully you get an idea of how that works.

It's all about the signal from the environment, which in this case comes in the form of the presence or absence of glucose and cyclic amp, and the presence or absence of lactose, signals from the environment then being fed into, sort of fed into information that connects to the DNA via these activator or repressor molecules which bind to the DNA and also affectors bind to the activator and repressor, which then bind to the DNA. And in turn, these activator and repressor molecules then affect the transcription of mRNA by interacting with the RNA prelimer. So either promoting, increasing the binding of RNA preliminaries to the promoter, which increased transcription, or blocking the transcription by physically inhibiting the RNA preliminaries from

moving down along the DNA. So it all kind of makes sense, right? It's the signaling molecules that relate to the signal in the environment, have an effect on proteins, which then have an effect on the DNA and affect its transcription. It's all kind of logical. Now, it will be kind of nice in a way if this is also how gene regulation worked in eukaryotes, because then I could just say, oh, well, everything I just told you about the lack operon, well, that's how other gene products are also regulated. And, you know, end of story, nice neat to explanation. Unfortunately, biology isn't so simple. So prokaryotes have many of these operons. I've told you about the lacoperon, because that's a very well studied example, but there are many others as well that have, you know,

different activators and repressors and different effector molecules and the pathways may be a bit more complicated, but fundamentally it's the same thing. There'll be, you know, signaling molecules which affect proteins, which bind to the DNA, and then affect the rate at which RNA preliminaries produces protein transcripts or blocks it or enhances it and different things like that. So that's how it works in prokaryotes. Unfortunately, or at least unfortunately for explaining it, I guess it's fortunate for sort of biological flexibility, but unfortunately for us understanding it, eukaryotes don't have operons. So this whole operon thing I've been talking about, that's not you carrots, there aren't any, or extremely few at least. However, the basic processes that I've

been talking about, where you have signaling molecules which then bind to proteins, which in turn bind to the DNA and affects the rate at which RNA preliminaries comes in and transcribes, all of that still happens. It just happens in a more complicated way, and the story is not so neat as the nice Operon example, but the underlying logic is still the same. So if you get confused as we go forward and I'll start talking about the mechanisms that are operative in eukaryotes, just think back to the Lackopron, because the Lackopon really does, even if the details are different in Eukaryotes, and there's more complexity, the fundamentals are all there. And that is how a lot of transcription or regulation kind of works in essence. It's some molecules or signals come in

from the environment, which then through a cascade of mechanisms, you know, one thing affecting something else, affecting something else, eventually changes some molecule that either now starts binding to the DNA or was binding to the DNA but now stops binding. So these signaling cascades eventually terminate in something that binds to the DNA, some protein that binds to or stops binding to the DNA, often multiple proteins that bind to the DNA in different ways, which in turn affects the rate or ease at which RNA preliminase is able to transcribe that gene. So that fundamental mechanism, set of mechanisms, is still operative in eukaryotes. It's just that there's more complexity to it and more aspects to it. Also, there are more stages in eukaryotes

where there's sort of potential for intervention to regulate gene expression. I mentioned them before, right, the chromatin remodeling, post-transcriptional regulation, translational regulation, and microRNAs, these other mechanisms, right? So we're going to go through those now, as we turn to talking about eukaryotic gene regulation. But just bear in mind, again, that fundamentally, a lot of this does come down to the mechanisms of the LACOPRON and then things added onto that at different stages in the process. Okay, so now let's talk about eukaryotes and start with talking about chromatin remodeling. This is not really an issue in prokaryotes, by the way, because prokaryotes don't have

chromatin. In most prokaryotes, the DNA is just stored in as a circle. I think there's some that have linear DNA, but it's usually the structure is quite simple. It doesn't have very much DNA, and so it doesn't form these complex chromatin structure. So chromatin remodeling isn't really relevant for prokaryotes, but it's very, very important in eukaryotes. So as I explained before for gene transcription to occur, the promoter region, so that's the region of DNA where the RNA preliminaries comes in to bind, the promoter region must decondense so that the preliminaries can bind to it, right?

Now by decondense, what it means is that it has to be unwound and accessible for the RNA preliminaries to come in. Now DNA is normally stored in eukaryotes. It's normally stored in nucleosomes, which are repeated units of DNA wound around structural histone proteins. So refer back to DNA structure and function when I talked about this. I'm not going to go through the details again. But histones are these sort of protein complexes that the DNA winds around them, and then the histones with the wound DNA, there's kind of clumped together in these dense, condensed structures called nucleosomes.

When the DNA is in this condensed form, it's not really excessive. to RNA polymerase or the transcription factors, which we'll talk about it, admitted. It's not really accessible to anything. So this is good for kind of storage mode, but it's not really good for usage. You know, it's kind of like you've got your, I don't know, your old record collection boxed up and taped and covered nicely and placed it at the back of your cupboard somewhere in the attic or wherever. That's good for storage maybe, but it's not very good for making it accessible for use. So there needs to be a mechanism for a mechanism for

determining essentially which genes have we got stored up in the attic and which genes have we which genes have we got accessible and ready to go on the on the desk so to speak ready for transcription and and that's what chromatin remodeling is about it's about bringing genes out of or putting them back into storage as appropriate and as needed so chromatin remodeling is the dynamic process of either condensing or decondensing DNA so as to make the relevant and needed genes available or exposed so that they can can be transcribed as needed. Now this is regulated by many different signaling molecules

and intracellular processes. I'm not going to describe in-depth how it all works. I'll just give an overview of a few important points. So one mechanism that determines whether a particular region will be condensed or decondensed is called histone acetylation and deacetylation. So this is the process by which those histone proteins. So remember these are the protein complexes that the DNA winds around to form the nucleosomes. These histone proteins, are modified by adding or removing acetyl groups. This doesn't change them by very much. It's a fairly small modification.

It's just adding a small carbon structure, really. But it alters the structure of DNA enough to either allow for or inhibit transcription. And specifically, acetylation removes the positive charge on the histones, which decreases the interaction of them with the negatively charged DNA phosphate groups. And as a consequence, condensed chromatin is, transformed into a more relaxed form after acetylation that allows gene transcription.

So acetylated DNA tends to be in a more relaxed form which allows it more easily to be transcribed. Now there's another mechanism called DNA methylation which refers to adding methyl groups to selected cysteine residues on the DNA. Again this is a fairly small biochemical change it doesn't change the structure that much but it changes it enough so that it can affect the the ease with which the DNA is accessible. So inactive genes tend to be more heavily methylated than active genes. So we've got two mechanisms here that I've just explained. Acetylation tends to switch on the DNA, whereas methylation tends to switch off the DNA,

in the sense of making it more condensed. And both of these mechanisms operate together, so methylation, demethylation, and acetylation, deacetulation. Now you may be wondering, well, what regulates acetylation and and methylation, while those in turn will be regulated by a whole host of signaling processes and cascades within the cell itself. And in fact, I did an episode where I talked about these. So if you refer back to the episode on cell signaling, which was episode 118, I talk about some of these intracellular signaling cascades in that episode. So one way to understand this would be to listen to that episode and then come back and listen to this or whichever order you do it in and think about

DNA acetylation and methylation, which affects chromatin remodeling, is one of the endpoints of the signaling cascades. So there's a molecule that affects the receptor of a cell, which then affects an intracellular receptor, and then affects secondary messages and so on within the cell. And eventually that will terminate in some molecule triggering acetylation and or methylation or deacetylation demethylation in some particular region of the genome. So the processes by which those are regulated are very complicated and similar to the processes that regulate kind of anything in a cell. But the end point here is particular parts like particular regions or particular chromosomes. The chromatin can be decondensed or it can be condensed so as to make certain genes accessible or less accessible to transcription. So that's the chromatin remodeling part.

But that's only the first step because that just makes it available for transcription. It doesn't mean that it necessarily will be transcribed to any significant. amount. So that leads us to the next section where we talk about transcriptional regulation. Transcriptional regulation is generally the part of control of gene expression that receives the most attention it seems. And when we talked about the Lack operons in the prokaryotes, so all of that, all of the operon stuff that would fall under this category of transcriptional regulation. So it's kind of all you have in the prokaryotes. In the ucarriots, there's more things going on before and after that. But nevertheless, transcriptional regulation is still a very important component

or aspect of the overall control of gene expression. And indeed, control of transcriptional initiation, so the starting of the process of transcription is the usual way that transcription is regulated in eukaryotes. So it's kind of the most important mechanism of gene expression. Most eukaryotic genes are off by default, which means that in most cells at most times, most genes won't be actively transcribed. So generally, in order to start transcribing a gene actively, there'll need to be some signal that activates it. There are some exceptions called housekeeping genes, which are kind of

generally on in most cells, and they're the ones that are required to just for the cell to sort of function. But most genes aren't like that, and they need special signals to turn them on. Now, as I said before, the overall process is broadly similar to operons in prokaryotes. However, nearly all eukaryotes MRNA are monocystronics, so that means that unlike the operons where there's multiple genes in one MRNA transcript that is under the control of a single promoter, eukaryotic MRNA transcripts only have a single protein on them, and so each gene has its own promoter. That means that the overall process of regulation is much more complicated as there are going to be more components interacting and more points of control necessary.

So what I'm going to do now is I'll just talk through some of these important components and introduce some more of the complexity, whilst hopefully trying to make it a bit manageable. So I've already introduced you to transcription factors. These are proteins that bind to specific DNA sequences in order to regulate the expression of a given gene. Transcription factors are able to recognize specific DNA sequences from the outside. I mentioned this before, without having to unwind the DNA or unzip it. The way it does this is effectively transcription factors are proteins, and so their function is determined by their precise shape, the precise shape of the search. of the particular part of the molecule.

Basically, you can think of it as if each transcription factor has a gene that it's paired with. It's usually not that simple, but let's just simplify it a bit. So a single transcription factor will have a single gene that it targets, and the shape of the transcription factor will be tailored to the outside shape of the bumps made by the particular combination of nucleotide residues in part of, like in a region of the gene that that trancheonels that transcription factor targets. So obviously a gene can be hundreds or even thousands of nucleotides long, so the protein won't recognize all of it, but there'll be some segment of it, that some sequence of nucleotides that the transcription factor is able to recognize. So it's sort

of tailored to this specific shape that it's looking for, the sequence of precise bombs. It's actually able to recognize the presence and absence of a particular sequence of hydrogen bonds, which is how it determines which of the two DNA nucleotides are present is by the signature of hydrogen bonds. You remember the AT and the G and the C, right? It's able to tell which is present in a given location. And so the transcription factor can tell this just from the groove of the outside of the double helix, and it's able to bind there when it finds just the right one, which is just the right shape. And that shape then reveals the presence of that gene. Now, it's not so simple that a single transcription factor will target a single gene.

they'll often target many different genes that contain a particular sequence of nucleic acids. There are, in fact, many different components, structural components of transcription factors and other gene regulatory proteins as well, which enable them to bind to certain patterns in the DNA. So these are called, these special structural motifs are called DNA binding motifs. And they're basically special structures found in the proteins that are specifically have specifically developed in order to find and bind to certain patterns of nucleic acids or certain structures in the DNA. Examples include helix turn helix.

So this is a helix and alpha helix in the protein. And then there's kind of a, like a turn, like a U-turn around. The protein structure has a sort of a loop that turns around. And then there's another helix. So helix turn helix. There's something called a zinc finger, which is so named because it was originally discovered around zinc. it's a particular structure of helices and loops.

There's beta sheets that can form particular structures, and there's something called Lucene zipper motifs as well, which is sort of too long alpha helices that form a cross structure. Anyway, the point is I'm just trying to illustrate that there's many different domains that have very precise structures, which have been studied, you know, down to atomic level resolution, like a very high degree of precision. Proteins may have multiple of these, right,

that enable them to bind to specific site, specific combination, of nucleic acids and thereby enlabeling them to target and bind to particular sites in the DNA. So this is very important because the transcription factors need to be specific to particular DNA sequences in order to find the right genes, right? And so this is how they can do that. It's by this very precise shape of the transcription factor, which are determined by many factors, including the presence of particular structural motifs. So now let me talk through the process of transcriptional regulation. regulation in a little bit more detail. The key components or the key players here, most of them you've already seen in the example, in the case of the Lackopron that we talked about for prokaryotes. So there's the promoter, that's the region of DNA that

the RNA preliminase binds to, that initiates transcription for that particular gene. One difference is that in eukaryotes, RNA preliminaries can pretty much never bind to the promoter by itself. It always needs various transcription factors to help it bind. And so the promoter is a bit more complicated than in progeria. It has the region for RNA preliminaries itself, and then there's sort of special regions for various transcription factors to bind that kind of help it to bind and to be in the right position. There are also activators and repressors. So activators are the proteins which bind to DNA regions that help to enhance transcription and repressors of proteins that buy.

bind to sites on the DNA that inhibit transcription. So we met both of those in the Lackopron case. One difference in the case of eukaryotes is that in addition to the activators and new repressors, there are also co-activators and co-repressors. So these are complexes that generally don't bind to the DNA itself, but they bind to the thing that binds to the DNA, right? So co-activators will bind to activators and co-repressors will bind to repressors. So what will happen is, that the quantity of these co-activators and co-repressors that are present will determine sort of how much of a signal boost the activators and repressors give. The more of these that are present, the more will bind to the forming complex. I'll explain in a minute what I mean by the complex,

but everything sort of has to come together in one physical location on the DNA for transcription to start. So the more of these co-activators that are present, the more kind of votes you have, if you want to put it that way, or the more enhanced will be the binding of the RNA preliminace, and therefore the initiation of transcription, the more co-repressors you have, then the more inhibited it will be. And again, by enhanced and inhibited, I mean, we talk, I talk about votes in a loose way. But what we're really talking about is bringing the, what is actually happening is bringing the RNA preliminaries into precisely the right position on the DNA in an energetically favorable manner, you know, in a short period of time, so that it can begin transcription and, you know,

keeping it there. And all of these protein complexes fundamentally are about pushing it and bringing it and confining it into that position. Whereas anything that represses that will essentially push it out of the way or make it more difficult or less energetically favorable. So that's what's sort of happening at a physical level. We talked about inducers as well in the lack operon case. So these are small molecules that will bind to repressors or activators, causing them to be activated essentially or deactivated. and inducers can also bind to co-repressors or co-activators. Something that's new to the Eukaryote case are insulators. So insulators are DNA regions, so they're not proteins, they're DNA regions,

which block the effect of transcription factors, activators and repressors from influencing distant genes. So this is very important because obviously if we have transcription factors which are affecting a particular gene in a particular location on the DNA in your chromosome, you don't want these transcription factors to also be affecting all of the other genes in the region. You want it to be targeted to the specific gene that we're focused on. And so what's necessary is some mechanism of limiting the influence, like spatially limiting the influence of transcription factors, activators and repressers.

And insulators do this. They're these special regions of DNA which sort of act as like walls between different genes so that transcription factors affecting one gene won't also affect a neighboring gene, or at least there'll be minimal effect. So this is typically accomplished by chromatomy modeling, nucleosome modifications, or formation of DNA loops, which sort of physically forms boundaries between the two locations. So there's a variety of mechanisms by which that occurs. Now, a moment ago I mentioned the formation of this sort of complex,

the initiation complex for transcription. And one of the important points with regard to eukaryotic RNA transcription initiation is that it's not just the RNA preliminaries binding to the promoter. That does need to happen, but it can't happen by itself. It requires a whole complex of enhances and promoters and so forth. And there's a special protein complex called the mediator. The mediator is a co-activator, although there's other co-activators as well, to be complicated, but it's a particularly large co-activator complex.

And basically what the mediator does is it forms kind of this central, like a nexus, or a substrate where all of the other things kind of come together. So what you should imagine is, so there's a gene, right? That's where the actual genetic material is stored, and then just upstream of that is the promoter. That's the location where the RNA preliminaries actually binds. Surrounding this, generally upstream, but some could be downstream as well. Surrounding this are regulatory sequences of DNA relevant to that gene.

So these regulatory sequences don't actually contain the code for the protein itself, but they are sites where actually, activators, repressors, and such, so various transcription factors will bind. And so you've got all of these different regulatory DNA sites to which different proteins are bound to. The mediator then kind of brings them all together. So these regulator proteins are bound to different parts of the DNA, different regulatory sequences. They all in turn are brought together and bind to different parts of the mediator. So you've got all these activators, repressors, co-activators, co-repressors, inducers, all brought together by the mediator,

which then also interacts with the RNA preliminase itself. And effectively, if you've got enough favorable factors, then the whole thing kind of fits together, and the RNA preliminers is able to start transcription. It's able to bind to the promoter and begin transcription. If you don't have enough of these favorable factors, then the RNA preliminase won't be able to get into the right position in enough time, and it will dissociate the whole thing kind of,

it'll fizzle out it. It sort of won't go through. So it's not just like the RNA preliminaries comes in and gets going. It's a very complicated, like an intricate kind of dance arrangement between many, many different regulatory proteins and sequences of DNA. And it has to be just in the right shape for it all to work. The reason why it's so complicated is because this allows for the integration of many, many different regulatory signals. Because each of these repressers, activators, co-repressors, co-activators, inducers, and the mediator itself, they're all kind of endpoints of different signaling processes. So the more activators you have and the more co-activators, then the more different sort of signaling pathways can contribute to increasing the chance of transcribing

or increasing the amount of transcription of that particular gene. Conversely, the more repressors and co-repressors you have, then the more different signaling pathways you can have contributing to the inhibition of the transcription of that gene. So this gives rise to the notion of combinatorial control, and this refers to the way in which regulatory proteins, work together to determine the expression of a single gene. So it's not like the Lackoperon case where it was essentially, is lactose present yes or no, is glucose present yes or no. There were basically just two factors and it was quite simple. In eukaryotic gene regulation, it's much more complicated. It's not

yes or no like that. It's the combinatorial combination of many, many different signals, many different transcription factors. Gene expression is not determined by any single activator or enhancer, but the particular combination of activators and suppressors that are present at any given time. This gives rise to the notion of gene regulation is really a form of computation. So all of these complex networks and connected mechanisms of the activators and the enhancers and repressors and so forth form processes which you can think of as performing computations. It's like integrating all the inputs and determining whether the result is sort of high enough to transcribe the gene or low enough.

or what amount of transcription, like how many MRNA products will be produced in a unit of time. And this is happening in all of your cells all of the time. And because cells are differentiated in eukaryotes, then different cells will arrive at sort of different conclusions, even if they're receiving the same input, which, of course, they may not, because different cells have different receptors on the surfaces, there are different locations in the body and so forth. So not only do different cells get different signals, but they can integrate the same signals differently to produce different results. So this complex integration of signals, as well as preservation of memory states, so cells once they're differentiated, stay differentiated.

This allows for genetic circuits to act like biological computers, integrating information from many sources, and using it to determine the correct levels of activation for many, many different genes. The memory, by the way, that I just mentioned, is what enables a cell to stay differentiated once its parent cells become differentiated in the developmental process. One of the simplest ways in which a cell ensures that its daughter cells will remember what type of cell they are and stay that type of cell is by using a positive feedback memory mechanism. So effectively you have a transcription regulator which activates transcription of its own gene. You have a gene which produces a protein product which is in fact a transcription factor that

activates that very same gene. So that's positive feedback. Once you've got that gene present it will remember that it has to be a protein product. has that gene present because it keeps activating the production of that gene. So obviously there will have to be some signal that turns that on in the first place. You have to get it going somehow. That can be produced by some other cell or some environmental pressure or some environmental signal, whatever, in the developmental pathway.

But once that's happened, the cell is able to remember that that signal was present because of this positive feedback mechanism. And of course, it can be more complicated than this, right? It doesn't have to just be a one-step process. It could be many steps that allows it to remember. So cells have memory, not encoded in the sequence of nucleotides in the DNA, but encoded rather in the particular combination of genetic activation or repression that it's accumulated through both its own history as well as the developmental history of its mother cells. and this type of molecular cellular memory and ability to inherit from mother cell to daughter cell to inherit these signals is called epigenetics or epigenetic inheritance

and some forms of epigenetic inheritance can actually be transmitted through not just from one cell to another but actually to to offspring like as in humans or other animals I won't talk about that in too much detail here, but it typically involves things like chromatin remodeling and acetylation and deacetylation, methylation, de-methylation, things like this, which can be inherited, because obviously we don't just inherit the DNA of our parents. We also inherit a cell, well, initially we are a cell, right, a zygote, a single cell. Apart from the small genetic contribution from the father, all of the rest of that cell comes from our mother. and that means that the pattern of genetic activations and chromatim remodeling,

at least part of that, can be transmitted as well. So there are ways of inheriting characteristics over generations that don't actually involve the sequence of nucleic acids themselves, but rather a sequence, but rather involves transmission of mechanisms for gene regulation. So hopefully from going through these different processes, you've got an idea of how complex and intricate the process of control of transcriptional regulation is in eukaryotes and how it's really much more complicated than just the idea that, oh, well, the DNA contains a blueprint for producing proteins. It does obviously, but it's so much more than that because of the fact that cells have a memory for the developmental specialization that they've become. differentiated into, as well as environmental signals, they can remember that, and they use that sort of history to then determine how they integrate signals that come in, and that combination

then determines how, through complex processing of information, how to actually use the genetic information that they have to produce a particular combination of proteins. So it's much more complicated than just a static blueprint. Let's finish off the episode now just by talking about post-transcriptional regulation and then briefly translational or post-translational regulation. So post-transcriptional regulation is the component of control of gene expression that occurs after transcription of MRNA. So we've got our MRNA transcript and now we need to turn it into an actual protein, right? So there's a number of steps that need to happen for that to occur in eukaryotes.

It's much simpler in prokaryotes, so most of these steps aren't relevant to prokaryotes, but eukaryotes, again, there's more going on. So the first thing that happens once we produced our raw MRNA product is 5 prime capping. This is the term that's used to refer to modification of the residue at the very far 5 prime end of the MRNA, and it makes it chemically more similar to the 3 prime end. And this is a method of protection from degradation, which targets foreign RNA. So effectively, if you have a naked 5 prime end of your genetic material, that's a signal that you shouldn't be there, and there will be enzymes that will come.

come in or be recruited and they'll start chewing you up. So in order to prevent that, the cell needs to modify the fire prime end so that it looks like a three prime end and so that sort of protects it. That's called adding a five prime cap. This also helps with transporting or marking the MRI for transport out of the nucleus because remember transcription occurs in the nucleus but translation occurs in the cytoplasm so it needs to move out of the nucleus. And the process of transport out of the nucleus is just one of the many ways in which post-transcription or regulation can occur. So that capping process, again, can be regulated.

If it's not capped properly, then the MRNA transcript will just be degraded. The next step is polyadinolation. So that's adding a tail, so the repeated 20 to 30 repeats of adenosine nucleotides that are added to the three prime end of the tail. This, again, helps to protect it from degradation and gives it greater stability. The length of that tail determines its stability, so generally longer tails, mean it's more stable, it's better protected. So again, regulating that process of how many adenosines you add is another mechanism for regulating, effectively how long the MRNA will be present for, because eventually that tail gets chewed off and the messenger RNA will be degraded.

So the longer the tail you add, effectively, the longer it will last for. I mean, other things being equal, right? So that's another mechanism of post-transcription or regulation. Again, it's not the case that you just transcribe M Messenger RNA once and then it's gone. It can be transcribed many times. So anything that affects the longevity or the stability of a specific transcript will affect how many protein products you get from that one transcript. And so that's another important mechanism by which post-transcription or regulation is affected, that changes the amount of protein product you get even from a single MRI transcript.

Another very important mechanism in prokaryotes is called alternative splicing. Splicing is a process that removes the introns from the MRI transcript. introns are non-coding regions that are transcribed, they're part of the RNA transcript, but they need to be removed in order to get just the protein coding sequence, which is the bit that actually gives rise to the protein product. It's very sort of counterintuitive that introns even exist. Introns don't exist in prokaryotes, they're just in eukaryotes. It's sort of like, if you imagine, a book, but 90% of the book isn't actually the text that you want.

it's sort of random gibberish that's inserted at random points. And so, you know, the first five pages might be the start of the introduction, and then there's 20 pages of gibberish inserted randomly until you get to the next point where the introduction continues. That's effectively what introns are. And so you might wonder, well, why do they even exist? They seem completely pointless, right? There's also some debate about exactly why they exist,

but they do seem to perform important functions. One of them is alternative splicing, which effectively means, that you don't always have to use all of the exons. The exons are the parts that actually they're coding material, right? You don't actually always have to use all of them. You can just use some of them and you can put them in different orders. And this allows you to produce different proteins from the same pre-MRNA transcript. So suppose you have five exons in your RNA, right? Well, you can splice them in different ways. You can include one, two, three, and five, or you can include one, three, and five, or just one and five, right? There's many different

combinations. This gives you a lot of flexibility so that the same MRI transcript can give rise to different proteins depending on how you splice them. It's also thought that introns serve structural, that they basically serve a structural purpose to change the relative shape and distance and things between the exons which can serve a regulatory purpose. Because remember DNA isn't just sitting there waiting to be read, it's a complex three-dimensional structure and so it needs to be in the right position at the right time for the right enzymes to come in and so forth. I don't know how much

research that has been into that precisely the sort of regulatory structural role of introns, but I believe that's another mechanism as well. There are still more mechanisms of post-transcriptional regulation. So there's something called RNA editing, which to be honest, I had never even heard of before researching for this specific episode. So there you go. So RNA editing is the direct alteration of the nucleic acid sequence of MRNAs after transcription. It's catalyzed by special enzymes, which are guided by these short separately coded RNAs. So it's like they get a little transcript

which says modify these residues and then these enzymes go and they find the position of the mRNA to bind to and then modify these residues. Again, it's a little strange. It's like you publish the book and then you make some modifications and edits manually in pen or something. You wonder, well, why not just change the DNA directly?

Well, again, it seems that this is a mechanism for providing extra flexibility. so that you can sometimes do the edits and sometimes not, and that you can change them based on different signals. So another mechanism of post-transcriptional regulation is RNA transport. As I mentioned before, RNA needs to be transported out of the nucleus before it can be translated. In UKario, it's only about one-twentieth of the total RNA that's initially transcribed actually even leaves the nucleus. The rest of it stays in the nucleus. Much of that is excised introns or damaged RNAs that have something wrong with them, or others are just

just never transported out because they don't get the right signals, right? And so they'll eventually be degraded in the nucleus. So there are many different regulatory processes that can keep the mRNA from being exported, and so that will affect the rate of translation as well. Finally, there are a special type of regulatory RNA called microRNAs, which have only fairly recently been discovered. So these are very small RNA molecules, about 21 nucleotides in length, that can degrade specific messenger RNAs.

So it's different from RNA editing. It doesn't edit the nucleic acid sequence of the MRNA. And it's not alternative splicing. It doesn't splice the exons together differently. What it actually does is causes specific mRNA sequences to be degraded and it's targeted towards those sequences. So mature microRNAs form a complex. It's called an RNA-induced silencing complex or risk. So it contains various proteins along with the microRNA itself, which guides the risk to specific. M RNAs that have the complementary nucleotide sequence. So again, it's like these, it's like RNA editing, except in this case, the risk, salmene complex, has a bunch of proteins, and then it's got the, like a special place where you slip in the transcript. In this case, the transcript is the

microRNA, which contains the sequence, and that sequence will be complementary to a particular nucleotide sequence in a specific messenger RNA, which is essentially telling it, go and kill this messenger RNA, go and find any messenger RNAs that match this, and and take them out. And so they degrade the complementary messenger RNAs by either an internal nuclease or by recruiting other nucleases which come in and chop it up. And again, this is a little counterintuitive because you might be thinking, well, we just went through the complex dance and combination of processes needed to produce that MRNA

transcript in the first place. And we went to all the trouble of producing that, and now we're just going to go and chop it up. What was the point? Why didn't we just not produce it in the first place? Well, once again, biology is messy and doesn't always make sense in the way that we would design it, right? But the existence of microRNAs provides an additional mechanism, some additional flexibility. And it seems the way that it works is that it's actually in a sort of a complementary balance

where you have messenger RNAs that are being produced from a particular gene, and those, so the messenger RNAs are ready to be translated. And at the same time, you have microRNAs chopping up those messenger RNAs for the that particular gene. And so the rate at which messenger RNAs are actually ready and exported from the nucleus and actually give rise to protein product is determined by the relative balance of the production of the transcripts versus the destruction of the transcripts. And so this is actually quite common in many biological processes where the chemical processes where the combination of two sort of mutually inhibitory processes is the precise point where those balance determines the

rate at which something happens and thereby allowing you more flexibility and more redundancy as well for controlling that process. Effectively, this is like instead of just having a break or just having an accelerating, you have a brake and accelerator, which you use both at the same time, which is not how you're actually supposed to drive, by the way, but that's how cells work, right? They use the break and the accelerator both constantly at the same time and just change the relative amounts of those. So that seems to be what microRNAs are for, though there's still a lot of research about those. So all of those processes that I just talked about, you know, the control of the capping, the polyandenolation, alternative splicing, RNA editing, selective RNA transport out of the nucleus, and microRNAs. All of those are methods of altering either the actual sequence of the mRNA or altering the amount of it that is allowed to exist and exported from the nucleus and also altering its stability.

So all of these things will affect the actual protein products that are produced by this. that messenger RNA and the amount of those things that are produced. So this is all again downstream of the actual transcription. So that's why it's post-transcriptional regulation, right? It's all up to the point where finally the edited and modified and spliced message RNA is exported from the nucleus and is actually translated to form a protein. But even then, even at the point where we finally got our protein product, we're still not quite done because there are post-translating or regulation mechanisms as well. Not so many, it must be said. So by this point, normally the cell is kind of done with the regulation side of things and it's ready to actually use the

proteins, but there are still mechanisms, some mechanisms that are operative to alter the proteins after they've been synthesized from the messenger RNA. And this is especially important for rapid short-term adjustments in protein synthesis, because basically the further back you go, the longer it takes for these processes to have an effect on the actual amount of protein product. But sometimes you need to control the amount of protein product or the amount of operational protein product very quickly. And so modifying the protein itself after translation can be effective for that. So one mechanism is to actually modify the ribosome recruitment itself. So you might have the MRNA transcript, but you change the rate at which ribosomes can come in and actually translate it.

Although technically that's translational regulation and not post-translational regulation, but let's not get into the technicalities of that. So as with transcription regulation, there's many mechanisms that can affect the rate at which MRNA transcripts are actually translated. But even downstream from that, once you have your actual protein product, there are still mechanisms that can affect the operation of that protein product. So there are a vast array of post-translational modifications that are made to proteins. I won't talk about those here because I have discussed them in the episode where I think it was

protein structure and function or it might have been a DNA structure and function. I've talked about post-translational modification. So all of those things that are modifications that are made to proteins can also affect the function of those proteins and so are connected to gene regulation, although I think that they're normally sort of treated in terms of proteins rather than gene regulation, but still they're connected. The very last stage of genetic regulation, although again it's sort of stretching the definition at this point, the very last stage is determining where the proteins end up. And so it's just, this then leads us into talking about intracellular protein sorting and the internal membrane

system of the cell. And I'll refer you then to episode 117 where I talked about that. But again, that's still kind of part of the process of determining what the protein product is and how it functions and where it ends up. So there's no real, very precise demarcation between where gene regulation ends and protein sorting and modification begins. So finally, that brings us to an end of our journey talking about mechanisms of eukaryotic gene regulation. So let me just give a brief summary. Remember that the basic point here is determining how much of a given gene is transcribed at a given time in a given cell and that needs to be regulated by a and responsive to a wide range of different signals, both internal to the organism and external

from the environment. And in a eukaryotic organism there are many different points in the process of protein production at which control over gene regulation and protein production can be affected. So the first is chromatin remodeling. So this determines whether the chromatin and the DNA is effectively open and active and available to be transcribed or closed and condensed and not available to be transcribed. And so that can be affected by methylation and acetylation as we discussed. The sort of main stage is transcription regulation. So this determines the initiation of transcription at a given gene, and it is determined by the combination of the activators, repressors,

co-activators, co-repressors, the mediator, which brings everything together, the inducer molecules, which all determine effectively to what extent the promoter is able to bind to the right location and stay affixed to the promoter region of the gene, and ready to begin translation. We talked about how, unlike prokaryotes, sort of switched on or switched off mostly. In eukaryotes, it's a complex combination of multiple signals which will, you need a sufficiently, a sufficiently intense sort of signal in order for

a given gene to be transcribed at a given time. And we talked about how cells can act as computers and they have memories, which are like positive, positive feedback mechanisms that allow them to just kind of remember what specialisation they are, and those are determined in development. And I emphasized how the cell is a complex computer and not just a sort of static template for determining what proteins are produced. And we talked then about post-transcriptional regulations, so the various mechanisms that operate after the production of the message RNA for determining how much of that MRNA transcript actually is exported from the nucleus and how stable it is and also even what it codes for. So we talked about capping, polyadenolation, alternative splicing, RNA editing, RNA transport and microRNAs. And then we briefly talked about translational regulations, so determining the rate at which a given MRNA transcript is translated into a protein, even once it's reached the cytoplasm, there's many mechanisms for that.

And then we talked about post-translational modifications to the protein itself, as well as where it's directed to in the cell, or even outside of the cell, as being a sort of continuation of the gene regulatory process. So hopefully you now have a bit of a richer picture of how genetic regulation is controlled and how the cell, and indeed the organism as a whole, is constantly integrating different signals to determine which genes need to be transcribed and then ultimately translated at which times and then how much of a given protein is needed. And this is a constant kind of fine-tuning and adjustment process. and the DNA is extremely active and responsive to different things that are happening in the environment. And it's not just the sort of, it is a static store of information, but it isn't just that. It's much more than that. So, hopefully you found this episode interesting. If you would like to support the show, there's a few ways to do that.

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