Transposable Elements in Eukaryotes - Online Tutor, Practice Problems & Exam Prep

Eukaryotic cells contain two types of transposable elements: retrotransposons (class 1) and DNA transposons (class 2). Retrotransposons utilize an RNA intermediate for transposition, often linked to RNA viruses. An example is the long terminal repeat (LTR) retrotransposon. In humans, active transposable elements include short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs), which can cause mutations and diseases like hemophilia. Understanding these elements is crucial for grasping genetic variation and evolution.

Eukaryotic Transposable Elements

So, eukaryotic cells have 2 types of transposable elements. The first type is retrotransposons, otherwise called class 1 elements. Either way, they're the exact same thing. Retrotransposons are referred to this way because they use an RNA intermediate to jump. What does this mean? Initially, you start off with DNA, that DNA is then transcribed and now it's RNA, and then that RNA is turned back into DNA and then jumps. The RNA intermediate is needed for that jumping. Often, retrotransposons have their evolutionary history in RNA viruses, also called retroviruses. RNA viruses have genomic material that is just RNA. It's single-stranded, which is what "ss" stands for, single-stranded RNA, and that's their genetic material. But that RNA also encodes for something called reverse transcriptase, which we may have mentioned before. Reverse transcriptase is a protein responsible for transcribing RNA into DNA. So it is backward, which is why it is called reverse, because usually, transcription is DNA to RNA; reverse transcription is RNA to DNA. So, typically how these evolved is, you had a virus that was single-stranded RNA. It infected the cell. That RNA was reverse transcribed to DNA, and then it was integrated into the genome. Because it was DNA, the genome was like, 'Hey, there's some free DNA. Let me take that up.' That DNA is called something special when the virus puts it in there. It is called a provirus, which is the DNA from the virus that integrates into the genome. Essentially, how this works is you start off with RNA, go to DNA, and then it is inserted into the genome. An example of a retrotransposon is called a long terminal repeat retrotransposons, and this means exactly what it sounds like. It is a retrotransposon, meaning that it jumps via an RNA intermediate, but it has these long repeats on the end. And an LTR retrotransposon has these repeats on the end. Long terminal repeat transposons use the copy and paste method we talked about before to transpose.

Then the second class of transposable elements are DNA transposons or class 2 elements, and these are the ones that we are more familiar with; they are very similar to the way that the prokaryotic one jumps and they use DNA to jump. Here we have an example. Here is an LTR retrotransposon. These long terminal repeats on either end are transcribed into RNA. RNA is reverse transcribed into DNA. That DNA then integrates elsewhere in the genome, and that is how the retrotransposons actually end up jumping. So, with that, let's now turn the page.

Drosophila P Element

Okay. So now let's talk about the Drosophila p element. So the Drosophila, remember fruit flies, the p element is actually one of the first eukaryotic transposable elements identified. And so the p element is a transposon, meaning that it jumps throughout the genome, and it has the ability in fruit flies to severely disrupt the genome. And so, scientists studying these transposons have actually developed strains of them. So the strains of fly with it are called p strains. So if the fruit fly has p elements, that's called a p strain. And there are different strains of fruit flies, the different flies that have them and different fruit flies that don't. So if people studying this have figured out that if you make a male p strain, so a male fruit fly that has these p elements in them, with a female m strain, and this is a strain that doesn't have it, so a male that has it with a female that doesn't, what you get is the offspring has this phenotype called hybrid dysgenesis. And this hybrid dysgenesis just means it's, sort of, this overarching description of all the offspring. And so, this means that all the offspring are kind of screwed up. There are mutations, some of them are sterile, there's chromosomal breakage, but they have pretty serious defects in every single one of the offspring. Now, if you do the cross or the inverse of that, so if you take a female p strain, so a female with those p elements, and a male m strain, so a male without them, then and you mate them and their offspring, you get normal offspring. And so studying this, scientists were kind of perplexed, and they were, like, why? Like, what has to do with the fact that the p male female has the transposable element that makes them, like, the transposable elements not work. And so the hypothesis and what was found to be true is that the egg, so remember coming from the female p strain, has some kind of elements that can suppress the p element, and it suppresses that jumping and so the jumping doesn't occur and when the jumping doesn't occur, you get normal offspring. So, right, if you mate a p male and a female m, what you get is hybridogenesis where all these offspring, transposons have jumped into all these different genes. They're called chromosomal breakage and mutations of a variety of different things, sterility, and these are very sickly flies. Whereas, if you do the inverse cross, the egg contains, p element suppressors. So those transposons do not jump, so there's no jumping. And when they don't jump, that means that all the genes are normal. So you get normal offspring from this cross. This is a super important, super important way that scientists have studied transposable elements. So with that, let's now turn the page.

Human Transposable Elements

Okay. So now let's talk about human transposable elements. So you may be surprised that humans also contain them, but humans also contain active transposable elements. So these are elements that are still moving in the genome. Now, it doesn't happen often, but they still do move. Obviously, if it happened often, we would be all sorts of mutated, but it doesn't happen often, but we still do contain them. So the two most important ones, or the 2 most common ones at least, are called SINEs and LINEs, and this stands for Short Interspersed Nuclear Elements or Long Interspersed Nuclear Elements, and that just is describing the size of them. So SINEs are shorter, LINEs are longer. Now, both of these are retro transposons. Do you remember from when we talked about retro transposons? That is going to be and that, is just an interesting fact about these two types of human transposable elements. So the most common SINE in human is called ALU, and there's about 300,000 copies of this throughout the genome, and, these are the copies, so these can jump around. The most active LINE is called L1, there's about 20,000 copies of these and these can still jump around as well. And so the majority of all the transposable elements in the human genome actually don't move. Right? They've been mutated. They lost some of their transposase, they lost some of their repeats, they don't move, they're just stuck there sort of filling up the genetic material. But some do, and when they do, they can actually cause disease. So there are cases of things like hemophilia is a great example, so it's a very genetic disease, but there have been, at least one case of a man developing hemophilia without any genetic history of the disease, and scientists were like, oh, this is very weird. What happened is that one of these, transposable elements had actually jumped into the gene causing that mutation and causing hemophilia. So it's very rare, but it can happen. And, but however, most of the time when these transposable elements are still jumping in our genomes, they actually just move to what's known as safe havens, and these are regions of the genome that aren't going to cause any harm. So an example, like if you had to guess where a gene could jump where it wouldn't cause any harm, what would you say? You'd say, potentially, introns. Right? Introns are cut out, they're not coding, they're not going to hurt any genes or proteins or anything. So most transposable elements are jumping into places like introns where they're not causing any harm to the organism, but occasionally, very rarely, they do jump into areas that can cause disease in humans. And so I just wanted to show you this graph to give you an idea of how many, transposons are actually in the human genome. So this is just a various, this is kind of the key. Right? So if we look at protein coding genes here in this grain, that's 2%. Right? And 2% that it codes for all the proteins that make us who we are. But if you start looking at other things, these are introns. Right? And then we start looking at the transposons, which is this. We start this, and there's even more over here. Right? This dark purple here and the green here. This all right here are transposable elements, and that is how many of them are actually in the human genome. Now the majority of these do not do anything. Right? They're completely inactive, but they, some of them are active, especially some of these SINEs and LINEs are active, and can cause disease. So I think it's sort of overwhelming, I think, to realize how much of our genome are these transposable elements. And because there's so many in our genome, you can imagine that they have a huge impact on our evolution, and that is because transposable elements jump. They move around the genome, so they're causing this sort of dynamic phenotype, whereas they can cause mutations. If they insert into a gene, that is going to either, you know, that can activate it, can hurt a gene. They can jump inside a gene regulatory region and sort of suppress a protein or activate a protein more, and that obviously is gonna affect evolution of that organism and all its offspring. They can cause chromosomal rearrangements, which can cause serious defects, but also can cause, you know, some benefits occasionally, very rarely, but it can. And if it does, that is definitely a way that causes or promotes evolution. And they actually have the ability to relocate. So they're sitting in the genome, and if there are genes really close by, like, right next to them, they can actually relocate those genes to new regions of the genome, and when they do those genes are going to be activated by different promoters. They're going to be suppressed by different factors, and so that is going to affect evolution, obviously, of that individual organism and all the offspring that come after. So transposable elements are super, super, super important, sort of evolution drivers in the history of humans, but also in the history of many other organisms on the planet. So with that, let's now move on.

Which of the following is true regarding reverse transcriptase?

• A. It is required for transposition of DNA transposons
• B. It synthesizes DNA from RNA
• C. It is encoded within long-terminal repeats of retrotransposons
• D. The provirus uses it to insert into the genome

Which of the following elements is a transposable element in Drosophila?

• A. Ds element
• B. Alu element
• C. P element
• D. Ac element

Which of the following is an example of a safe haven for transposon movement?

• A. Intron
• B. Exon
• C. Promoter
• D. Enhancer

Which of the following would occur if an Alu element jumped into the AG splice site of a human gene?

• A. Splicing would occur, and the protein would be unaffected
• B. Translation would not occur on any part of the mRNA
• C. Splicing would not occur and the protein would be altered
• D. Chaperone proteins would correct the damage, and the protein would be unaffected

Here’s what students ask on this topic:

What are the two types of transposable elements in eukaryotes?

Eukaryotic cells contain two types of transposable elements: retrotransposons (class 1) and DNA transposons (class 2). Retrotransposons use an RNA intermediate for transposition. This process involves transcribing DNA into RNA, then reverse transcribing RNA back into DNA, which is then inserted into a new location in the genome. Retrotransposons are often linked to RNA viruses, such as retroviruses. An example of a retrotransposon is the long terminal repeat (LTR) retrotransposon. DNA transposons, on the other hand, do not use an RNA intermediate and instead move directly as DNA. They are similar to the transposable elements found in prokaryotes.

How do retrotransposons move within the genome?

Retrotransposons move within the genome using an RNA intermediate. The process begins with the transcription of the retrotransposon DNA into RNA. This RNA is then reverse transcribed back into DNA by the enzyme reverse transcriptase. The newly synthesized DNA is then inserted into a new location in the genome. This method of transposition is often referred to as a 'copy and paste' mechanism because the original retrotransposon remains in its original location while a new copy is inserted elsewhere. This process is similar to the lifecycle of RNA viruses, such as retroviruses.

What is the significance of the Drosophila P element in genetic studies?

The Drosophila P element is significant in genetic studies because it was one of the first eukaryotic transposable elements identified. It has the ability to disrupt the genome of fruit flies, causing mutations, sterility, and chromosomal breakage. Scientists have used P elements to create strains of fruit flies with and without these elements, known as P strains and M strains, respectively. By crossing these strains, researchers observed phenomena such as hybrid dysgenesis, where offspring exhibit severe genetic defects. The P element has been instrumental in understanding the mechanisms of transposition and the genetic regulation of transposable elements.

What are SINEs and LINEs in the human genome?

SINEs (Short Interspersed Nuclear Elements) and LINEs (Long Interspersed Nuclear Elements) are types of retrotransposons found in the human genome. SINEs are shorter sequences, with the most common example being the Alu element, which has about 300,000 copies in the genome. LINEs are longer sequences, with the most active example being the L1 element, which has about 20,000 copies. While most transposable elements in the human genome are inactive, some SINEs and LINEs can still move and cause mutations. For instance, they can jump into genes and disrupt their function, potentially leading to diseases like hemophilia.

How do transposable elements contribute to genetic variation and evolution?

Transposable elements contribute to genetic variation and evolution by moving within the genome and causing mutations. When they insert into or near genes, they can disrupt gene function, alter gene expression, or cause chromosomal rearrangements. These changes can lead to new traits, some of which may be beneficial and subject to natural selection. Additionally, transposable elements can relocate nearby genes to new genomic locations, exposing them to different regulatory environments. This dynamic activity can drive evolutionary changes by creating genetic diversity within populations, influencing the adaptability and evolution of organisms.