Transcription but only at low or basic levels

Transcription is more complicated than just turning a gene ‘on’ or ‘off’ like a light switch. In this lesson, you’ll learn how eukaryotic transcription is regulated through the use of DNA regulatory regions, DNA methylation, and chromatin modification.

Eukaryotic Transcription Regulation

Remember that transcription is the process that creates RNA from DNA using RNA polymerase in all living organisms.

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In eukaryotic cells, the genome is housed in the nucleus. This creates a separate space for transcription, allowing for a more complicated process than in prokaryotic cells, or cells without a nucleus.Transcription, otherwise known as gene expression, is one of my favorite cellular processes.

All cells within your body have the same DNA sequence, and yet you have so many different types of cells that they all look different and act different from each other, like skin cells, heart cells, liver cells, etc. So, how does that happen? It all comes down to which genes are expressed, or transcribed, and to what level they are expressed. You see, when it comes to transcription, it’s not always as simple as whether the gene is on or off, like a light switch. A gene that is on, but only at low or basic levels of transcription, is known as basal transcription. However, a gene can be transcribed at higher rates when necessary. Think of it like a music dial. ‘Off’ is off, but ‘on’ can be a little background music or full-on party mode.

Now while we might regulate the music with a simple turn of the dial, regulating transcription is a much more complicated task, and there are several ways to do this. This is especially true in eukaryotic cells. In this lesson, we’ll delve into a few of the mechanisms used to regulate levels of eukaryotic transcription, including different DNA regulatory regions, DNA methylation, and chromatin modifications.

DNA Regulatory Regions

Transcription can be regulated by changing what transcription factors, or those proteins that control transcription levels, are bound to different parts of the DNA. Think of it this way: the dial stays the same, but the level that the music is blaring will depend on who’s controlling the tunes.To understand this best, we need to acquaint ourselves with the basic structure of a gene. Remember that only 2% of the human genome is protein-coding DNA.

Much of the remaining 98% of DNA does a lot of cool things, including transcriptional control. We’ll use a line below to represent one gene on a chromosome. For the sake of this lesson, let’s keep the gene rather simple, with a 5′ and a 3′ end, using the blue region to represent DNA that is transcribed. However, keep in mind that this blue gene represents many parts, such as the 5′ UTR, introns, exons, and 3′ UTR. Now, in addition to this region, there are multiple DNA regulatory regions. These are segments of DNA where transcription factors can bind to control transcription – to turn that dial up and down.

This line is representative of one gene on a chromosome.
DNA representation

Next to the gene is the promoter.

You may know the promoter already as the region where RNA polymerase binds to initiate transcription. Not all promoters have the same DNA sequence, even though RNA polymerase binds at all promoters. However, some eukaryotic promoters contain a specialized promoter sequence known as the TATA box. A specific transcription factor, appropriately called the TATA-binding protein, binds here to help start transcription. Other promoters without a TATA box could use different transcription factors for the same purpose. Therefore, parts of all promoters can also be DNA regulatory regions, even if they don’t contain a TATA box.Another DNA regulatory region is known as the enhancer.

This is a region of DNA where transcription factors can bind to greatly increase gene transcription. Enhancers do exactly what they sound like – they enhance transcription, beyond those basal levels. Sure, transcription could take place without them, but with them, it’s so… enhanced! Right? So, not all genes have to have enhancers, and not all enhancers are the same DNA sequence. But a really cool thing about enhancers is that they can be located really far from the gene they influence.While there are other DNA regulatory regions for controlling transcription, the promoter and enhancer are binding sites for a variety of transcription factors, and therefore, they’re really influential to eukaryotic gene expression. In addition, while many transcription factors are responsible for turning genes on, there are also many transcription factors that would turn genes off, or dial down transcription levels.

DNA Methylation and Chromatin Modification

Transcription can also be regulated by DNA methylation and chromatin modification. These methods are ways to alter the structure of DNA and chromatin to prevent or allow transcription factors to bind. In DNA methylation, a methyl group is added to some cytosine nucleotides to silence or repress a gene.

In other words, DNA methylation would turn a eukaryotic gene off or inhibit transcription. What’s really neat about this regulatory mechanism is that this regulation can be passed down to your children, in a process known as imprinting. This might be akin to passing down your love of ear-blasting music to your kids in utero.Chromatin modification is the change in chromatin structure to control transcription.

There are tons of different types of chromatin modifications, and these changes can regulate transcription by turning it on, off, up, or down. But to understand chromatin modifications, you need to remember that chromatin is your DNA wound around proteins called histones – proteins that only eukaryotes have. This helps package the DNA so that it fits inside the nucleus. It also creates a repressive structure. Imagine – it’s going to be really hard for RNA polymerase to find the promoter and start transcription with all this repressive chromatin structure in the way. It’d almost be like if you had a couple of friends blocking that dial so you can’t even get to the music, let alone turn it up really high.

Therefore, in many cases, chromatin structure is opened up to allow transcription to begin, and closed again to repress or turn off transcription. One of the ways this can happen is by adding chemical groups to these histones, such as methyl and acetyl groups. The locations of these groups on the histones determine the function. For example, not all methyl groups on histones shut off transcription like they do in DNA methylation, like we discussed earlier. Depending on where the methyl group is placed on a histone, it could turn transcription up or down.

Lesson Summary

Let’s review how we can regulate transcription in a eukaryotic cell similar to how you can regulate the volume of your favorite Michael Jackson song.

One of the ways transcription or gene expression is regulated is through the use of multiple DNA regulatory regions. These are segments of DNA where transcription factors can bind to control transcription. One example of this is actually the promoter. You may know the promoter already as the region where RNA polymerase binds to initiate transcription. Another example is an enhancer. This is a region of DNA where transcription factors can bind to greatly increase gene transcription. Enhancers can increase transcription beyond basal transcription levels, or low or basic levels.

There are other ways to regulate transcription by changing whether or not transcription factors can actually bind to those regulatory regions. DNA methylation is when a methyl group is added to some cytosine nucleotides to silence or repress a gene. When DNA methylation of a gene is passed down to offspring, it’s known as imprinting a gene. Chromatin modification is a change in chromatin structure to control transcription. There are several types of chromatin modifications, but one example is the addition of chemical groups to histones to regulate the transcription of a gene.

Learning Outcomes

Following this video lesson, you should be able to:

  • Define transcription
  • Explain how the promotor and enhancer regions can regulate transcription
  • Describe DNA methylation and chromatin modification
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