Epigenetics, Chromatin Modifications, and Regulation: Videos & Practice Problems

Epigenetics involves chromatin modifications that regulate gene expression through DNA packaging. Eukaryotic DNA exists as euchromatin (loosely packed, active) and heterochromatin (tightly packed, inactive). Key modifications include chromatin remodeling, histone acetylation (promotes transcription), and methylation (often represses transcription). Genetic imprinting and X-inactivation exemplify chromosomal-level regulation, where entire chromosomes can be silenced, affecting gene dosage and expression. Understanding these mechanisms is crucial for grasping gene regulation and its implications in genetics and development.

Chromatin

Hi. In this video, we're going to be talking about epigenetics, chromatin modifications, and regulation. So, most of you are aware that DNA has to be packaged. Right? Normally, our DNA is so long and just like spread out, but we see it in the form of chromosomes, and so it has to be packaged so that it fits into those chromosome forms and fits into the nucleus. And so, some of you may have already seen the videos in which I talk about chromatin packaging, which are super important if your book presents them, but if not, don't worry about it because we're going to talk about some of the overviews here. So eukaryotic DNA packaging can regulate gene expression. So this packaging isn't just so that the DNA fits into the cell and can divide in the form of chromosomes, but actually so that it can regulate gene expression as well.

There are two forms of chromatin, which chromatin is defined by DNA and protein. Two forms, and the first is euchromatin, and the second is heterochromatin. This refers to how tightly packaged the DNA is. So euchromatin is loosely packaged, and heterochromatin is tightly packaged. Now obviously, if you have loosely packaged DNA and tightly packed DNA, that's going to affect gene expression. So the loose DNA has all this more open space, proteins can come in and initiate transcription, RNA polymerase can come in and transcribe genes. So these euchromatin regions of the chromosome are generally where genes are being expressed. Whereas heterochromatin is tightly packaged, and so that means that all these proteins that are needed for transcription initiation, for anything, essentially, are not going to be able to get in, and so they are not going to be transcribed, these genes are not going to be expressed.

So here we have an example of this. You can see eukaryotic proteins can come in, they can bind to these regions, and start transcribing and make these genes active, whereas in heterochromatin, the proteins cannot bind to the DNA because it's so tightly packaged, these are going to be silent, and whatever is in this region of the DNA is not going to be expressed. So you might say, okay, is everything always euchromatin or heterochromatin, or does it change back and forth? And it actually changes back and forth, and so there are three types of chromatin modifications that can sort of change whether it's euchromatin or heterochromatin and affect gene expression. So the first one is called chromatin remodeling, and this is the process of moving nucleosomes to new DNA sequences. So, most of you should know what a nucleosome is, but in case you don't, nucleosomes are these yellow proteins here. So you can see DNA is in red, and these yellow proteins are in here. So the yellow protein is called a nucleosome, and this is what DNA wraps itself around to package either loosely or tightly. So nucleosomes are associated with every single DNA sequence. It's just whether these are all packaged loosely or tightly. So chromatin remodeling can actually move nucleosomes to new DNA sequences. And why would it need to do that? Let's say that this region here has a promoter, and so that promoter needs to have proteins bind to it so that it can promote transcription. Right? That's what a promoter does. But if it's wrapped around a nucleosome, this means that different factors, like this blue protein here, can't come in and bind it. So chromatin remodeling will actually push this nucleosome either this way or this way to a new sequence so that the DNA region with the promoter on it, it says 'promoter' in case you can't read my ridiculously messy handwriting, so that these but the main really important one you should know about is the SWI/SNF complex. It's a protein complex, meaning it has a lot of proteins in it, and they reposition nucleosomes. So that is the first type of chromatin modification. Let's turn the page and get to the second.

Histone Protein Modifications

Okay. So now we're going to talk about histone protein modification. So just in case you need a refresher, what are histone proteins? Do you remember where they are? Right, they are in the nucleosome, and that is what the DNA is wrapped around to be able to package. So histone protein modifications can affect how tightly DNA is packaged, and remember, we already said that if DNA is packaged too tightly, gene expression won't occur. So this definitely regulates gene expression.

So, how are histone proteins modified? Well, histone proteins actually have tails, they have these little protein tails that hang off of them, and they contain a bunch of different amino acids, but the two important ones are lysines and arginines. And these 2 amino acids can be modified through a bunch of different ways, most of which we're not talking about, but the two most important ones are through the addition of methyl or acetyl groups.

So, let's talk about acetylation first. Acetylation of the acetyl groups results in open chromatin. So this is what you need to know, you need to be able to connect acetylation with open chromatin, and if the chromatin is open, what does that mean for transcription? Is that going to activate it or suppress it? Right. It's going to activate or promote transcription. Now acetylation is reversible, and there are enzymes called histone deacetylases that come in, can remove that acetyl group. When the acetyl group is gone, what is that going to do with the chromatin? It's going to close it back up again and repress transcription. So you have an acetyl group there, a bunch of acetyl groups there, that open this region of the chromosome, it's going to promote that transcription of those genes present there. If the acetyl group is not there, it can be closed, and if it's closed, that means that transcription of those genes won't occur. Obvious gene regulation.

So the second type is methylation, this is the process of adding methyl groups. Now, most often, methylation causes closed chromatin but notice I said most often because occasionally it can support open chromatin. But this is where it gets confusing, because some professors want you to just sort of know for the test, acetylation causes open, methylation causes closed. So I suggest that before you get to a major test, that you go to your professor and say, hey, does methylation occasionally cause open chromatin, and what is the answer you're looking for on the test? Because some professors want you to know that there is this, you know, most of the time it causes closed, but can cause open. And some of the professors just say, let's make it easy for them. Acetylation causes open, methylation causes closed. So make sure you know what your professor wants you to believe that methylation does, before you get to a test. So, methylation often causes closed chromatin. Now, methylation when it's on there, what it does, like the functionality of how this is going to activate or suppress transcription, is when there's a methyl group there that creates a binding site. So other proteins can bind to that methyl group, and then proteins come in and they can either activate or suppress transcription depending on the proteins that are binding to that area. Now obviously, there's a bunch of different amino acids. It's not just 1 lysine, and it's not just 1 arginine. Histones are made up of a ton of amino acids, and there's a bunch of histone proteins in the nucleosome, each one of them have tails, so there's all these huge combinations, which we refer to as the histone code. Now they, so it's the combination of all the histone modifications that affect gene regulation. And I only talked about methylation and acetylation, but there's actually over a 150 different types of modifications that can occur on a histone protein, amino acid, and then on top of that, there's multiple amino acids. So this, this code is huge, and we haven't broken it yet. We don't know how to read it yet. And so, what kind of what signals cause activation and what signals cause suppression is not at all well understood. But there is one pattern that we can say for certain that we know, and that's the pattern of CpG islands. So most CG dinucleotides, and dinucleotide just means we're referring to 2 nucleotides here, cytosine and guanine. So, in the genome, the majority of these are actually methylated. Sorry if you can hear that siren that's outside. But anyways, most of these are, methylated. So throughout the entire genome, if you have a pair of cytosine and guanine, the majority, like, overwhelming majority, you're going to be methylated. But there are regions of unmethylated cytosine and guanine dinucleotides, and we call these CpG islands. So regions where cytosine and guanine are not methylated. And they are not, when they are not methylated, they are very often found in promoter regions, which makes sense because promoters need to be able to activate genes. So you don't want this methylation occurring in a promoter because that could really cause a closed chromatin and result in the suppression of the gene that the cell may want to actually activate. So here's an example. So here is the nucleosome, and each one of these is a type of histone protein, and you can see that they have these tails on them. Some of them have 1, some of them have 2. And as you go along here, you can get all different types of combinations. Right? You can get, like, this is a lysine here with acetylation and methylation on it. You have a lysine up here with just acetylation. You have a ton of lysines and arginines up here with just acetylation. You have things I didn't talk about including phosphorylation, the one I don't really know much about, the ubiquitination that occurred occur on here. And so all of this, all this whole combination here means something. This is going to say, okay, activate this gene or suppress it. Right? But we don't know just by looking at this whether or not this gene would be activated or suppressed, we would have to actually do an experiment to determine that. And so this histone code is a code that scientists are currently working on trying to figure out, but you can say it's extremely complex, and, obviously it's not going to be easy to figure out. So with that, let's quickly get to the 3rd form, and that is actually the histone variants. Variants. So histone proteins are generally very well conserved. The same histoproteins throughout pretty much every organism, every eukaryotic organism, even further than that. And, histone variants are very rare, and what they are is just like their variants. Right? They're histone proteins, but they're not quite the same as the universal histone proteins that are used. But, generally, they're found in unique chromosomal regions. So an example of this is the centromere, which is always very tightly, I mean, just like extremely tightly packaged heterochromatic, contains its own H3 histone protein variant. So H3 is just a type of histone protein, and there's a special one found at the centromere. Why is it there? No one really knows, but people suspect that it has something to do with the centromere. It has this, you know, very tightly, just like abnormally tightly packaged DNA, and that that histone variant may play a role in that. We don't know for sure, but that's just kind of the idea. So histone variants are the third way that gene regulation can be controlled, because the centromere, obviously, nothing in the centromere location is getting transcribed, and that could be potentially due to this histone variant. So with that, let's now move on.

Other Chromatin Modifications

Okay. So now we're going to talk about other chromatin regulatory mechanisms. We talked about individual amino acids getting modified, but DNA packaging can cause entire chromosomal effects. A great example of this that you're probably already familiar with is X inactivation. We know that females, human females, get two copies of the X chromosome. We don't need both copies, so one has to become inactivated, and that inactivated X chromosome is called a Barr body. Now that entire chromosome is inactivated due to heterochromatin. This is DNA packaging on an entire chromosome level that shuts off an entire chromosome and prevents all those genes from being transcribed in order to prevent a huge overdose of gene dosage in females.

There's a second term that you're going to come across, and that's genetic imprinting. What this means is you get one copy of every chromosome from your father and your mother. One copy will be inherited as inactive, so that entire chromosome will be inactive when you inherit it. Depending on which parent it came from, it can either come from the mom or the dad, they'll also have that as an inactive chromosome. When you get one copy that's inactive and one that's active, that means that genes are expressed as if there's only one allele. Because if you have one active and one inactive, only the allele on the active chromosome will be expressed. If that's a recessive allele, that means that the recessive allele is going to be expressed even if the allele on the inactive one was dominant, but it's not being expressed so you can't see it.

An example of genetic imprinting can be seen in these mice right here; aren't they cute? I'm not a big mouse fan, but anyways these are genetically engineered mice. If you take their genome and sequence it, you're going to get the exact same genome between these mice. They look so different because one of these mice has genetic imprinting, so that means one of their chromosomes is entirely inactive. That results in genetically identical mice looking so different because an entire chromosome has now been inactivated. This results in recessive alleles or a single allele, showing forth when there should have been two, to make them look like each other. So, that is genetic imprinting and different ways of entire chromosomal modifications that can affect gene expression. So, with that, let's now move on.

Chromosomal regions that form heterochromatin contain:

• A. Highly expressed genes
• B. Associations with the nucleolus
• C. Few genes
• D. Lots of open chromatin

Answer: (C)

Which of the following are examples of epigenetic marks?

• A. Acetylated guanines in DNA
• B. Methylated nucleotides in histone tails
• C. Methylated amino acids in histone tails
• D. All of the above

Answer: (C)

CpG islands are defined as which of the following?

• A. Highly methlayed CG dinucleotides
• B. Groups of unmethylated CG dinucleotides
• C. Methylated CG dinucleotides found in gene coding regions
• D. CG nucleotides that become methylated to activate the gene

Answer: (B)

Which of the following terms is associated with closed chromatin?

• A. CpG islands
• B. Heterochromatin
• C. Methylation
• D. Euchromatin

Answer: (B)

Here’s what students ask on this topic:

What is the difference between euchromatin and heterochromatin?

Euchromatin and heterochromatin are two forms of chromatin that differ in their packaging and gene expression. Euchromatin is loosely packed, allowing proteins like RNA polymerase to access the DNA and initiate transcription, making it transcriptionally active. In contrast, heterochromatin is tightly packed, preventing access to transcriptional machinery and thus rendering the genes in these regions transcriptionally inactive. The dynamic nature of chromatin allows regions to switch between euchromatin and heterochromatin states, thereby regulating gene expression in response to cellular needs.

How does histone acetylation affect gene expression?

Histone acetylation involves the addition of acetyl groups to lysine residues on histone tails. This modification reduces the positive charge on histones, decreasing their affinity for the negatively charged DNA. As a result, the chromatin structure becomes more open (euchromatin), allowing transcription factors and RNA polymerase to access the DNA and initiate transcription. Therefore, histone acetylation generally promotes gene expression. Conversely, histone deacetylases (HDACs) can remove these acetyl groups, leading to chromatin condensation (heterochromatin) and transcriptional repression.

What is chromatin remodeling and how does it regulate gene expression?

Chromatin remodeling refers to the dynamic modification of chromatin architecture to allow access to the DNA. This process involves repositioning or removing nucleosomes, which are complexes of DNA wrapped around histone proteins. Chromatin remodeling complexes, such as the SWI/SNF complex, can move nucleosomes to expose or hide DNA regions, including promoters and enhancers. By altering nucleosome positioning, chromatin remodeling regulates the accessibility of transcription factors and RNA polymerase to the DNA, thereby controlling gene expression.

What is genetic imprinting and how does it affect gene expression?

Genetic imprinting is an epigenetic phenomenon where only one allele of a gene is expressed, depending on its parental origin. This selective expression is due to DNA methylation and histone modifications that silence one allele, either from the mother or the father. As a result, the expressed allele functions as if it were the only copy, which can affect traits and development. For example, in mice, genetic imprinting can lead to phenotypic differences despite identical genetic sequences, as one chromosome is inactivated, revealing recessive traits.

What is X-inactivation and why is it important?

X-inactivation is a process in female mammals where one of the two X chromosomes is randomly silenced to balance gene dosage between males (XY) and females (XX). The inactivated X chromosome condenses into a structure called a Barr body, becoming transcriptionally inactive due to heterochromatin formation. This ensures that females do not produce double the amount of X-linked gene products compared to males, maintaining cellular and developmental balance. X-inactivation is crucial for normal development and preventing disorders related to gene dosage imbalance.