TRANSPOSONS: TYPES AND CHARACTERISTICS - GEOGRAFÍA - 2025

The transposon or transposable elements are fragments of DNA that can change its location in the genome. The event of moving is called transposition and they can move from one position to another, within the same chromosome, or change chromosome. They are present in all genomes, and in significant numbers. They have been extensively studied in bacteria, yeast, Drosophila, and corn.

These elements are divided into two groups, taking into account the element's transposition mechanism. Thus, we have the retrotransposons that use an RNA intermediate (ribonucleic acid), while the second group uses a DNA intermediate. The latter group are the sensus stricto transposons.

The "jumping genes" or transposons were discovered in maize (Zea mays). Source: pixabay.com

A more recent and detailed classification uses the general structure of the elements, the existence of similar motifs, and the identity and similarities of DNA and amino acids. In this way, subclasses, superfamilies, families and subfamilies of transposable elements are defined.

Historical perspective

Thanks to the investigations carried out in maize (Zea mays) by Barbara McClintock in the mid-1940s, the traditional view that each gene had a fixed place on a particular chromosome, and a fixed place in the genome, could be modified.

These experiments made it clear that certain elements had the ability to change position, from one chromosome to another.

Originally, McClintock coined the term "controlling elements", since they controlled the expression of the gene where they were inserted. The elements were later called jumping genes, mobile genes, mobile genetic elements, and transposons.

For a long time, this phenomenon was not accepted by all biologists, and it was treated with some skepticism. Today, mobile elements are fully accepted.

Historically, transposons were considered "selfish" DNA segments. After the 1980s, this perspective began to change, as it was possible to identify the interactions and the impact of transposons on the genome, from a structural and functional point of view.

For these reasons, although the mobility of the element can be deleterious in certain cases, it can be advantageous for populations of organisms - analogous to a "useful parasite".

General characteristics

Transposons are discrete pieces of DNA that have the ability to mobilize within a genome (called the "host" genome), generally creating copies of itself during the mobilization process. The understanding of transposons, their characteristics and their role in the genome, has changed over the years.

Some authors consider that a “transposable element” is an umbrella term to designate a series of genes with diverse characteristics. Most of these only have the necessary sequence for their transposition.

Although they all share the characteristic of being able to move around the genome, some are capable of leaving a copy of themselves in the original place, leading to the increase of transposable elements in the genome.

Abundance

The sequencing of different organisms (microorganisms, plants, animals, among others) has shown that transposable elements exist in virtually all living beings.

Transposons are abundant. In the genomes of vertebrates, they occupy from 4 to 60% of all the genetic material of the organism, and in amphibians and in a certain group of fish, transposons are extremely diverse. There are extreme cases, such as corn, where transposons make up more than 80% of the genome of these plants.

In humans, transposable elements are considered the most abundant components in the genome, with an abundance of almost 50%. Despite their remarkable abundance, the role they play at the genetic level has not been fully elucidated.

To make this comparative figure, let's take into account the coding DNA sequences. These are transcribed into a messenger RNA that is finally translated into a protein. In primates, the coding DNA comprises only 2% of the genome.

Types of transposons

Generally, transposable elements are classified based on the way in which they move through the genome. Thus, we have two categories: elements of class 1 and those of class 2.

Class 1 items

They are also called RNA elements, because the DNA element in the genome is transcribed into a copy of RNA. The RNA copy is then converted back into another DNA that is inserted into the target site of the host genome.

They are also known as retro-elements, since their movement is given by the reverse flow of genetic information, from RNA to DNA.

The number of these types of elements in the genome is enormous. For example, the Alu sequences in the human genome.

The rearrangement is of the replicative type, that is, the sequence remains intact after the phenomenon.

Class 2 items

Elements of class 2 are known as DNA elements. This category includes transposons that move by themselves from one place to another, without the need for an intermediary.

The transposition can be of the replicative type, as in the case of class I elements, or it can be conservative: the element is split in the event, so the number of transposable elements does not increase. The items discovered by Barbara McClintock belonged to class 2.

How does transposition affect the host?

As we mentioned, transposons are elements that can move within the same chromosome, or jump to a different one. However, we must ask how the fitness of the individual is affected due to the transposition event. This essentially depends on the region where the element is transposed.

Thus, mobilization can positively or negatively affect the host, either by inactivating a gene, modulating gene expression, or inducing illegitimate recombination.

If the fitness of the host is drastically reduced, this will have effects on the transposon, since the survival of the organism is critical for its perpetuation.

Therefore, it has been possible to identify certain strategies in the host and in the transposon that help to reduce the negative effect of the transposition, achieving a balance.

For example, some transposons tend to insert into nonessential regions of the genome. Thus, the series impact probably minimal, as in heterochromatin regions.

On the host side, strategies include DNA methylation, which manages to reduce the expression of the transposable element. Also, some interfering RNAs can contribute to this work.

Genetic effects

The transposition leads to two fundamental genetic effects. First of all, they cause mutations. For example, 10% of all genetic mutations in the mouse are the result of retroelement rearrangements, many of these are coding or regulatory regions.

Second, transposons promote illegitimate recombination events, resulting in the reconfiguration of genes or entire chromosomes, which generally carry deletions of genetic material. It is estimated that 0.3% of genetic disorders in humans (such as inherited leukemias) arose this way.

The reduction in host fitness due to deleterious mutations is believed to be the main reason why transposable elements are not more abundant than they already are.

Functions of transposable elements

Transposons were originally thought to be parasite genomes that had no function in their hosts. Nowadays, thanks to the availability of genomic data, more attention has been paid to their possible functions and to the role of transposons in the evolution of genomes.

Some putative regulatory sequences have been derived from transposable elements and have been conserved in various vertebrate lineages, in addition to being responsible for several evolutionary novelties.

Role in the evolution of genomes

According to recent research, transposons have had a significant impact on the architecture and evolution of the genomes of organic beings.

On a small scale, transposons are capable of mediating changes in linkage groups, although they can also have more relevant effects such as considerable structural changes in genomic variation, such as deletions, duplications, inversions, duplications and translocations.

Transposons are considered to have been very important factors that have shaped the size of genomes and their composition in eukaryotic organisms. In fact, there is a linear correlation between the size of the genome and the content of transposable elements.

Examples

Transposons can also lead to adaptive evolution. The clearest examples of the contribution of transposons is the evolution of the immune system and transcriptional regulation via non-coding elements in the placenta and in the brain of mammals.

In the vertebrate immune system, each of the large numbers of antibodies is produced by means of a gene with three sequences (V, D and J). These sequences are physically separated in the genome, but they come together during the immune response through a mechanism known as VDJ recombination.

In the late 1990s, a group of researchers found that the proteins responsible for VDJ junction were encoded by the RAG1 and RAG2 genes. These lacked introns and could cause the transposition of specific sequences into DNA targets.

The lack of introns is a common feature of genes derived by retrotransposition of messenger RNA. The authors of this study argued that the vertebrate immune system arose thanks to transposons that contained the ancestor of the RAG1 and RAG2 genes.

It is estimated that some 200,000 insertions have been exapted in the mammalian lineage.

References

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