Transposons

Did you know there are segments within our DNA that are mobile or can jump to other locations within a genome? Yes, these are transposons or transposable elements which were earlier referred to as “junk DNA” or “selfish DNA”. These transposons are getting noticed since the advent of whole-genome sequencing due to their numerous copies in eukaryotic cells. After many researches on transposable elements (TEs), it has been accepted that these TEs can cause genetic and genomic variations.

You can think of a transposon in your body or genome as a random word that is inserted in a sentence. As that random word can change the meaning of the sentence, a transposon can meddle with your bodily function or disrupt it.

The transposons are a hot topic amongst biologists who are working in the field of gene manipulation. Be it bacteria or humans, transposable elements have accumulated with the passage of time and are shaping genomes due to their mobilization. So let us learn more about what are transposons and delve into the types of transposons.

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Who Discovered Transposons?

Transposons were first discovered by Barbara McClintock (an American scientist and cytogeneticist) in 1940 while she was studying cytogenetics in maize, specifically corn). Before this discovery, it was broadly believed that genes lined up within a chromosome in an unchanging manner and occupied specific positions. She disagreed with this belief and found that certain genes called transposons can move to different places within the chromosome. She made this discovery on kernels of corn and observed that due to these jumping genes the offspring plants can differ in colour due to activated or deactivated genes. 

She realized that these TEs are not like genetic recombination but they caused a change in the location of the gene itself within chromosomes. She conducted standard genetic breeding experiments with something called the Ac/Ds system in maize and found that the breakage occurs at specific sites on maize chromosomes. When a Ds element is transposing due to the influence of a nearby Ac element, it may get inserted into the C allele which destroys its ability to produce pigment. Once the Ds element transposes into the C allele, the resulting kernel is colourless (neither yellow nor white). This is because neither the C allele nor Ct confers pigment.

Transposon Definition 

All organisms contain mobile genome sequences which are called transposons. These transposable genes are adorned with a variety of names like jumping genes, mobile genes, mobile genetic elements, etc. A TE is a DNA sequence that can change its position within the genome which can cause mutations and a change (increase or decrease) in the amount of DNA in the genome. Although these jumping genes are found in an integrated site in the genome. Also, most transposons eventually become inactive and stop moving.

All organisms (prokaryotic and eukaryotic) have TEs and in some species genes they are found in high proportions (The TEs account for more than 80% of genomes in maize and other plants, 10% in many fish species, and 45% of the human genome.). Though science has not concluded on what can cause genome size to increase which is TE-induced, stress is supposed to amplify TEs. Various genetic alterations can occur due to TEs based on the process of transposition (insertions, deletions, duplications, translocations, or excisions in the site of integration). 

Characteristics of Transposons 

TEs move around a genome with no regard for homology and their insertion can cause chromosomal fusions, deletions, inversions, and other complicated rearrangements. 

• TE modifies gene structure hence causes gene expression.

• TEs can create novel genes since they cause mobilization, reshuffling, and rearrangements.

• In a few rare cases, TEs can cause disease due to mutations. 

• They are mobile genetic materials that many times carry an antimicrobial resistance gene.

• TEs can insert randomly and move from chromosomes to plasmids and vice versa. By transductions, conjugation, and transformation the TEs can be moved from one bacterium to another.

• TEs are DNA sequences that code for enzymes that result in self-duplication and insertion into a new DNA site.

• Transpose elements are involved in transposition events (this includes both replication and recombination) that mostly give rise to two copies of the original TE. One copy is retained at the parent site while another copy reaches the host chromosome.

• Since TEs carry the genes which are responsible for RNA synthesis, it could activate some previously dormant genes.

• A transpose element cannot replicate without the host chromosome as phages or plasmids since a TE does not have a site for origins of replication.

• A TE can insert at any position in the plasmid or host chromosome since no homology exists between a TE and its target site of insertion. TEs rarely insert at base-specific target sites.

Types of Transposons 

There are four distinct types of transposon elements:

• Simple Transposons 

They are also called the Class II or insertion sequence (IS) transposons which consist only of DNA that directly move from one place to another. These TEs have shorter sequences (between 800 to 1500 bp) and do not code for proteins. The genetic information which is needed for their transposition is carried within the sequences. Such sequences are identified in many bacteria, F factor plasmids, and bacteriophages. These transposons move by a “cut and paste” method(cut is similar to the command ctrl+X on your PC) where the transposon gets cut out from its location and gets inserted into a new location (like the command ctrl+V on your PC). This process requires a transposase (an enzyme) which is encoded within these transposons. The transposase binds to 

• both ends of the transposon that has inverted repeats i.e. identical sequence readings running in opposite directions.

• A sequence of DNA that is present in the target site. Some transposases require that the target site has a specific DNA sequence while others can insert a transposon anywhere in the genome.

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Once the transposon is ligated to the host DNA, the gaps get filled up by Watson-Crick base pairing which results in each end of the transposon having identical direct repeats.

• MITEs 

These are miniature inverted-repeat transposable elements or class III transposons. After the recent completion of the genome sequence of C.elegans and rice, it is revealed that their genomes have thousands of copies of recurring motifs with the following features:

• There are almost identical sequences of 400 base pairs.

• They are small to encode any protein and how they are copied and moved to a new location is still uncertain.

• The rice genome has more than 100,000 MITEs and some of the mutations in certain strains of rice are due to a MITE getting inserted in the gene.

• MITEs also exist in the genomes of humans, apples, and Xenopus.

• Tn or Complex Transposons  

The complex transposons are several thousand base pairs long. They have genes that code for one or more proteins, some of them might include resistance factors in bacteria that act against antibiotics. Their distinct characteristics are:

• Presence of inverted, identical terminal repeats which can range from 8 to 38 base pairs. These inverted repeats are unique to the different transposons of this type.

• There is a short sequence (less than 10 base pairs) present on either side of the transposon.

• Retrotransposons 

These transposons apply a “copy, paste, and send to” method to move around but here the copy being made is of RNA and DNA (unlike other transposons described above). These RNA copies are then transcribed back into DNA by a reverse transcription mechanism. They are then inserted into new locations in the genome. These transposons have similarities with a few retroviruses like HIV and their method of action is also similar (though there is no transcription process in viruses). 

• A lot of retrotransposons have LTRs (long terminal repeats) at their end which can have more than 1000 base pairs in each of them.

• Retrotransposons create direct repeats at the new site where they get inserted.

• 40% of the entire human genome is made up of retrotransposons and is an ongoing source of genetic variations.

• Amongst all the mobile elements family, the retrotransposons remain actively mobile in primate genomes and humans.

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Key Feature

Transposons are repeating DNA sequences with the ability to migrate from one site in the genome to another (transpose). Transposon movement can cause mutations, affect gene expression, cause chromosome rearrangements, and grow genome sizes due to higher copy numbers.