Eukaryotic Chromatin Modifications - Online Tutor, Practice Problems & Exam Prep

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 gene silencing. These modifications create a dynamic system for gene regulation, enabling eukaryotic organisms to turn genes on or off as needed, thus influencing cellular functions and responses.

Eukaryotic Chromatin Modifications

In this video, we're going to begin our lesson on eukaryotic chromatin modifications. Eukaryotes can regulate gene expression by modifying the structure of their chromatin. 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. If you don't recall this, then make sure to go back and watch those older lesson videos on DNA before you continue here. Modifications can actually impact the transcription process. 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. This leads to 2 different types of chromatin. It leads to heterochromatin and also it leads to euchromatin. Heterochromatin is going to be a condensed region of the genome with really low transcriptional activity. Heterochromatin is not going to be transcribed. Euchromatin is basically the opposite, it is a lightly packed region of the genome with high transcriptional activity and histone and DNA modifications.

If we take a look at our image down below, we can distinguish between heterochromatin and euchromatin. Over here on the left-hand side, we have this miniature version of our map of the lesson. We're starting off with chromatin modifications, which is going to take place in the nucleus since that is where the chromatin is found. Heterochromatin is basically like turning off the light switch. It turns off transcription. It turns off genes. It's going to represent really tightly packed chromatin, heterochromatin, super tightly packed and that's going to have really low transcriptional activity. 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. 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.

Notice that over here, the chromatin is much more loosely packed. Because it is loosely packed, it's going to have high transcriptional activity. You can see that the transcriptional machinery, like RNA polymerase, for example, is capable of accessing the DNA that needs to be transcribed. Because the DNA is loosely packed, it's going to have high transcriptional activity, and that is a way of turning on the genes. This here concludes our brief introduction to eukaryotic chromatin modifications, but as we move forward, we're going to continue to talk about specific modifications that can take place that will lead to either heterochromatin or euchromatin. 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. This long polypeptide tail that extends off the histone proteins can actually be chemically acetylated. Acetylation is just 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. 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, is going to take place within the nucleus of the eukaryotic cell. Here, what we're showing you is 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, and these are called the histone tails. These histone tails are capable of being modified by cellular enzymes. In this formation over here, 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 represent the acetylation. Acetylation is going to be a way to help, allow for transcription to occur.

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. 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. 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, which is really just the process of adding a methyl group, or a CH₃ group, to another substance. Typically, in DNA methylation, 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, thereby turning off a gene or transcription. In our image below, we can see in our example that methylation of cytosine nucleotides is going to block transcription and turn off a gene.

Notice on the left-hand side, we have acetylated histone modifications. The stars, the green stars from our last lesson video represent acetylation. We know acetylation is going to turn on genes because the DNA is going to take a euchromatin state, which promotes transcription. Genes are turned on by acetylation, promoting transcription. RNA polymerase will be able to bind to this open and available DNA and transcribe genes in this DNA that is available here, thus turning on the gene.

However, methylation of specific cytosine residues, cytosine nucleotides, occurs by adding a CH₃ group to the molecule. This will be represented using one of these red star shapes. Notice that the DNA itself can actually be methylated. This modification occurs directly to the DNA sequence, not to the histones. DNA can be methylated, and DNA methylation is a way to turn the gene off. The genes are going to be turned off, and methylation is blocking RNA polymerase from binding to the DNA. Consequently, 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 regulate their genes, turning genes on and off depending on the type of modification made. This conclusion introduces 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 silencing. In contrast, euchromatin is loosely packed, allowing for high transcriptional activity as the DNA is accessible to RNA polymerase. 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 involves the addition of acetyl groups to the histone proteins, specifically to the lysine residues on their tails. This modification loosens the chromatin structure, converting it into euchromatin. The relaxed structure allows RNA polymerase and other transcriptional machinery to access the DNA, thereby promoting transcription and increasing gene expression. Conversely, the removal of acetyl groups, known as deacetylation, tightens the chromatin into heterochromatin, reducing gene expression by making the DNA less accessible.

What role does DNA methylation play in gene regulation?

DNA methylation involves the addition of a methyl group (CH₃) to cytosine residues in the DNA sequence. This modification typically occurs at CpG sites and is associated with gene silencing. Methylation blocks the binding of transcriptional machinery, such as RNA polymerase, to the DNA, thereby preventing transcription. This process is crucial for regulating gene expression, maintaining cellular identity, and silencing transposable elements. DNA methylation is a key mechanism in epigenetic regulation, influencing cellular functions and developmental processes.

What enzymes are involved in histone acetylation and deacetylation?

Histone acetylation is catalyzed by enzymes known as histone acetyltransferases (HATs). These enzymes add acetyl groups to the lysine residues on histone tails, leading to a relaxed chromatin structure and increased gene expression. Conversely, histone deacetylation is carried out by histone deacetylases (HDACs), which remove acetyl groups from histones. This results in a more condensed chromatin structure, reducing gene expression. Both HATs and HDACs play crucial roles in the dynamic regulation of chromatin structure and gene expression.

How does chromatin structure influence transcriptional activity?

Chromatin structure significantly influences transcriptional activity by determining the accessibility of DNA to transcriptional machinery. In a tightly packed form known as heterochromatin, the DNA is less accessible, leading to low transcriptional activity and gene silencing. In contrast, a loosely packed form called euchromatin allows RNA polymerase and other transcription factors to access the DNA, resulting in high transcriptional activity and active gene expression. Modifications such as histone acetylation and DNA methylation dynamically regulate these chromatin states, thereby controlling gene expression.