Eukaryotic Chromatin Modifications: Study with Video Lessons, Practice Problems & Examples

Eukaryotic chromatin modifications, such as histone acetylation and DNA methylation, play crucial roles in regulating gene expression. Histone acetylation loosens chromatin, promoting euchromatin formation and enhancing transcription by allowing RNA polymerase access. Conversely, DNA methylation typically occurs on cytosine residues, blocking transcription and leading to heterochromatin formation. These modifications illustrate the complex mechanisms eukaryotes use to turn genes on and off, impacting cellular functions and development.

Eukaryotic Chromatin Modifications

In this video, we're going to begin our lesson on eukaryotic chromatin modifications. And so eukaryotes can regulate gene expression by modifying the structure of their chromatin. And so recall from our previous lesson videos that chromatin are loosely packed or, loosely coiled nucleosomes, which is basically just DNA wrapped around units of 8 histone proteins. And so if you don't recall this, then make sure to go back and watch those older lesson videos on DNA before you continue here. Now modifications can actually impact, the transcription process. And so, histone modifications and DNA sequence modifications are made to control transcription, but these modifications are taking place at the chromatin level affecting the histone proteins or the DNA sequence. And really this leads to two different types of chromatin. It leads to heterochromatin and also it leads to euchromatin. Now heterochromatin is going to be a condensed region of the genome with really really low transcriptional activity. And so heterochromatin is not going to be transcribed. And euchromatin is basically the opposite, it is a lightly packed region of the genome with high transcriptional activity and histone and DNA modifications. And so if we take a look at our image down below, we can distinguish between heterochromatin and euchromatin. And so again over here on the left-hand side, we have this miniature version of our map of the lesson. And again we're starting off with chromatin modifications, which is going to take place in the nucleus since that is where the chromatin is found. And so heterochromatin is basically like turning off the light switch. It turns off transcription. It turns off genes. And so it's going to represent really really tightly packed, chromatin, heterochromatin, super super tightly packed and that's gonna have really really low transcriptional activity. And this is simply because the transcriptional machinery, like RNA polymerase and things of that nature, will not be able to fit and access the DNA that it needs to access because it's so tightly packed. And so heterochromatin, this tightly packed DNA, is a way to lower transcriptional activity and turn off genes, a form of regulation. Now euchromatin on the other hand is a way to turn on the light switch, to turn on genes so that transcriptional activity is high. And so notice that over here, the chromatin is much more loosely packed. And because it is loosely packed, it's going to have high transcriptional activity. And so you can see that the transcriptional machinery, like RNA polymerase, for example, is capable of accessing the DNA that needs to be transcribed. And so because the DNA is loosely packed, it's gonna have high transcriptional activity and that is a way of turning on the genes. And so, this here concludes our brief introduction to eukaryotic chromatin modifications, but as we move forward, we're gonna continue to talk about specific modifications that can take place that will lead to either heterochromatin or euchromatin. And so I'll see you all in our next video.

Histone Acetylation

In this video, we're going to introduce a specific type of chromatin modification, which is histone acetylation. Histone proteins that are found within nucleosomes of chromatin actually contain a long polypeptide tail, and this long polypeptide tail that extends off the histone proteins can actually be chemically acetylated. Acetylation refers to the process of the addition of an acetyl group. You can see down below in our image, an acetyl group is just a specific type of functional group, the one that you see right here. In our image down below, we're going to represent acetylation and acetyl groups by using a star symbol to represent the acetylation. Now, histone acetylation actually impacts the chromatin structure because what it does is it loosens the chromatin structure and that helps the chromatin take on a euchromatin formation, making the DNA accessible to RNA polymerase and allowing that DNA to be transcribed at a high rate. In our example down below, notice that we're focusing on how histone acetylation loosens the chromatin structure forming euchromatin.

If we take a look at our image down below, again, on the left-hand side, we're showing you our miniature version of the map. You can see that chromatin modifications, which include histone acetylation, take place within the nucleus of the eukaryotic cell. Here, we're showing you the chromatin in a heterochromatin form where the nucleosomes are really tightly packed together. But notice that extending off of each of these histones are these little tails, called the histone tails. These histone tails are capable of being modified by cellular enzymes. In this formation, the heterochromatin, the DNA is basically in an off state, and it's not going to be transcribed very much. However, through acetylation, which is represented by this arrow right here, acetylation can help turn the DNA into an ON confirmation, the chromatin structure into an ON confirmation because it changes the chromatin to a euchromatin state where it is more loose and the DNA is more accessible to RNA polymerase and more accessible to transcription. You can see the little stars here on the histone tails represents the acetylation. Acetylation is going to be a way to help allow for transcription to occur.

The removal of the acetyl groups in a process called deacetylation is actually going to result in the opposite. It's going to result in tight packing of the chromatin structure, basically reverting the chromatin back to a heterochromatin state. On the left over here, we have the heterochromatin, which we talked about in our last lesson video. Over here on the right, we have the euchromatin. Notice that acetylation will help promote a euchromatin state where transcription is more active. Then deacetylation is going to promote a heterochromatin state where the DNA is not going to be transcribed as much. Histone acetylation is a chromatin modification that can occur to help regulate gene expression. We'll be able to get some practice applying this as we move forward in our course. So, I'll see you all in our next video.

Histone acetylation is associated with:

• A. Activate transcription in that region, RNA Polymerase can easily interact with DNA.
• B. Repressed transcription in that region, RNA Polymerase cannot easily interact with DNA.
• C. Tightly-packed nucleosomes.
• D. No change in chromatin structure or transcription rates.

DNA Methylation

In this video, we're going to introduce another type of eukaryotic chromatin modification, which is DNA methylation. In addition to histone modifications like histone acetylation and histone deacetylation, the actual DNA sequence, not just the histones, can also be chemically modified to regulate transcription. The most common DNA modification is methylation, and methylation is really just the process of adding a methyl group or a CH₃ group, to another substance. Typically, when it comes to DNA methylation, it turns out that the nucleotides, cytosine, are the ones that are most susceptible to methylation. The cytosine residues are the ones that are going to be methylated. DNA methylation is a way to prevent transcription by blocking RNA polymerase's access to the promoter. DNA methylation will turn off a gene or turn off transcription. In our image down below, we can see in our example that methylation of cytosine nucleotides is going to block transcription and turn off a gene. Notice that we have acetylated histone modifications on the left-hand side. The stars, the green stars from our last lesson video, represent acetylation. Acetylation we know is going to turn on genes. Genes are going to be turned on by acetylation because the DNA is going to take a euchromatin state, and that is going to promote transcription. The gene's turned on by acetylation by promoting transcription. The RNA polymerase will be able to bind to this open and available DNA and will be able to transcribe genes in this DNA that is available here. This is a way of turning on the gene. However, methylation of specific cytosine residues, cytosine nucleotides. Methylation of cytosine, which methylation is adding a CH₃ group to, the molecule. It's going to be represented using one of these red star shapes. Notice that the DNA itself can actually be methylated. This modification occurs to the DNA sequence directly, not to the histones. DNA can be methylated and the DNA methylation is a way to turn the gene off. The genes are going to be turned off. Notice that the methylation is blocking RNA polymerase from binding to the DNA. The RNA polymerase will not be able to transcribe the DNA, and the gene is being turned off through methylation of cytosine nucleotides. Through acetylation and methylation, eukaryotic organisms have a very complex way to be able to regulate their genes, turn the genes off and turn the genes on depending on the type of modification that's made. This here concludes our introduction to DNA methylation, and we'll be able to get some practice applying these concepts as we move forward in our course. So I'll see you all in our next video.

Transcriptional repression by methylation of DNA involves the methylation of which nucleotide?

• A. Adenine.
• B. Uracil.
• C. Cytosine.
• D. Thymine.
• E. Guanine.

Which of the following causes transcription to be increased for a specific gene?

• A. Histones in that region are deacetylated.
• B. DNA is methylated in the regulatory region of the gene.
• C. Histones in that region are acetylated.
• D. The chromatin structure is tightly packed.
• E. B and D.

Here’s what students ask on this topic:

What is the difference between heterochromatin and euchromatin?

Heterochromatin and euchromatin are two forms of chromatin that differ in their structure and function. Heterochromatin is tightly packed, leading to low transcriptional activity because the transcriptional machinery, like RNA polymerase, cannot access the DNA. This form of chromatin is associated with gene repression. In contrast, euchromatin is loosely packed, allowing for high transcriptional activity as RNA polymerase can easily access the DNA. Euchromatin is associated with active gene expression. These structural differences are crucial for regulating gene expression in eukaryotic cells.

How does histone acetylation affect gene expression?

Histone acetylation affects gene expression by loosening the chromatin structure, which promotes the formation of euchromatin. This process involves the addition of acetyl groups to the histone tails, reducing the positive charge on histones and decreasing their affinity for the negatively charged DNA. As a result, the chromatin becomes less condensed, making the DNA more accessible to RNA polymerase and other transcriptional machinery. This increased accessibility enhances transcriptional activity, thereby turning genes on. Conversely, the removal of acetyl groups, known as deacetylation, leads to chromatin condensation and gene repression.

What is DNA methylation and how does it regulate gene expression?

DNA methylation is the addition of a methyl group (CH₃) to the DNA molecule, typically at cytosine residues. This modification is a key mechanism for regulating gene expression. Methylation of DNA generally leads to gene repression by blocking the binding of RNA polymerase and other transcriptional factors to the promoter region of the gene. This prevents the initiation of transcription, effectively turning the gene off. DNA methylation is crucial for various cellular processes, including development, differentiation, and maintaining genomic stability.

What role do histone modifications play in chromatin structure and gene expression?

Histone modifications, such as acetylation, methylation, phosphorylation, and ubiquitination, play a significant role in regulating chromatin structure and gene expression. These chemical modifications occur on the histone tails and can either loosen or tighten the chromatin structure. For example, histone acetylation loosens chromatin, promoting euchromatin formation and enhancing transcription. In contrast, histone methylation can either activate or repress transcription, depending on the specific amino acids modified and the number of methyl groups added. These modifications serve as signals that recruit other proteins to either activate or repress gene expression, thus playing a crucial role in cellular functions and development.

How does DNA methylation differ from histone acetylation in gene regulation?

DNA methylation and histone acetylation are both crucial for gene regulation but operate through different mechanisms. DNA methylation involves the addition of methyl groups to cytosine residues in the DNA, leading to gene repression by blocking RNA polymerase and other transcription factors from accessing the DNA. This results in a more condensed chromatin structure, known as heterochromatin. On the other hand, histone acetylation involves the addition of acetyl groups to histone tails, which reduces the histones' affinity for DNA, leading to a more open chromatin structure, known as euchromatin. This enhances transcriptional activity by making the DNA more accessible to RNA polymerase.