What is Transposon’s Target Site Duplication (TSD)?

“When the transposon inserts at the target DNA, duplication leads to generate identical sequences on both the sides, which is known as target site duplication of transposons.”

Transposons, often known as the Transposable elements or Mobile genetic elements can move from one place to another into the genome, first discovered in the Maize plant. It’s a part of the Junk DNA having a function in regulating gene expression. Structurally it is made up of three components.

Transposase encoding region, terminal region and target site duplication are three basic structural components of transposons. The terminal repeats present on both ends help in the recognition of transposase protein while the gene region encodes protein transposase. 

The definite function of target site duplication is still unknown for scientists. It might have a role in the process of evolution, scientists believed. I have explained everything regarding transposons in the previous article besides the TSD. So the idea to write the present article is to make you understand the importance of target site duplication. 

It’s a small topic, though very important to understand, the present article concentrates on the mechanism and importance of target site duplication of transposons.

Let us start the topic,

Definite structural units of transposons are gene body and terminal repeats however, TSD occurs when it inserts into the target location. The transposase protein, encoded by the gene body part, governs the process of transposition.

Means, at which rate and at which location the TE inserts depends on the enzyme- transposase. We can say, Excision and insertion are two functions of it. Both catalytic reactions occur simultaneously.

Excision removes individual transposons from one location followed by its insertion at another location in the genome. Note that the process of the removal varies in transposons and target sites.

[epcl_box type=”information”]The target site is a DNA sequence at which our transport will be inserted. [/epcl_box]

The two types of transposons viz DNA and retrotransposons perform transposition through replicative or non-replicative mechanisms.

In the replicative mechanism the copy of a transposon is left behind at the original position while in the non-replicative transposition, instead of a copy, a gap occurs at the original position.

Read more on replicative and non-replicative transposition:

  1. Replicative Transposition of DNA transposons and Retrotransposons
  2. Non-Replicative (Cut and Paste) Mechanism of Transposition

Interestingly, during either type of transposition, the excision process occurs similarly.

[epcl_box type=”information”]The transposase creates double-stranded excision on the terminal repeats and single-stranded excision on the target DNA. [/epcl_box]

Single-strand excision leads to the formation of TSD -target site duplication in an organism’s genome.

Let us understand the mechanism stepwise,

In the first step, each transposase protein binds to the terminal ends of the transposon. Inverse, direct and “in the same direction” are three types of terminal repeats. 

Depending upon the nature of the repeat, the transposase protein recognizes it and works.

In the next step, the protein complex stretches both ends inward and creates a circular loop-like structure, and cuts both ends of the transposon, immediately.

Here, the protein cuts the double-stranded DNA directly and removes it from that position.

In the next step, the complex moves towards the target site. The insertion site or the target site is randomly selected. Scientists don’t have any significant data about whether the transposition is specific or random. However, it is generally AT-rich. 

Once it finds and settles on the location (target site), it starts the second round of cleaving. Here, each transposase cuts each single DNA strand. See the figure below,

The graphical representation of the process of target site duplication in transposons.
The graphical representation of the process of target site duplication in transposons.

The TSDs are usually 5 to 9 nucleotides long, occur at different locations on two different DNA strands (See the image carefully). It generates sticky DNA ends.

In the next step, the transposase protein inserts the transposon between both the sticky ends. The transposase detached without filling gaps. 

[epcl_box type=”information”]The transposase can only fill gaps in the 3′ to 5′ direction, therefore, the target site duplication gap cannot be filled by the enzyme.[/epcl_box]

Gaps can’t remain as well. Cells’ natural DNA repair mechanism takes responsibility to do so. The multifunctional DNA polymerase binds to the 3′ end, uses it as a primer and fills gaps. Now in the final step, the ligase enzyme joins the transposon with the newly synthesized DNA. Now, carefully examine the figure below, I have explained how the duplication occurred at the molecular level. 

The molecular process of target site duplication occurs in transposons.
The molecular process of target site duplication occurs in transposons.

The molecular process of target site duplication occurs in transposons.

The figure explains how the process happens, here once gaps occur, sticky ends are formed, the polymerase fills the gaps and the ligase completes the process by sealing it.

Note that the target site duplication region is a portion of the insert (the part of the genome where the transposon is inserted), but it migrates along with the TE when it moves to another location.

So technically, it takes some portion of a DNA sequence with it and transports it to another location in the genome. Consequently, it creates a new mutation which results in a new allele.

And as we know how natural selection works, if this new variation is useful, it will remain there and be inherited in offspring.

So it’s a process of creating new mutations by generating target site duplication and favoring evolution.

Most eukaryotes have retrotransposons while most prokaryotes have DNA transposons. 

For more detail on the transposons please refer to our previous articles:

Transposons: A Jumping Entity and a Foe with Benefits

  • Overview, history, different types of transposons, LINEs-SINEs, retrotransposons, DNA transposons 

Transposase, Transposons and Antibiotic Resistance in Bacteria

  • Bacterial transposons, IS elements, composite transposons, Mu phage, transposon and antibiotic resistance

Transposons in eukaryotes

  • The general structure, transposon in Drosophila (P element, retrotransposon), TY elements in Yeast, transposon in Maize (Ac/Dc elements, spm/dspm elements), human transposons

Role of transposons in evolution

  • How transposon involved in the process of evolution


Transposons were an integral part of our genome, and now are inactive and Junk. However, several TEs still are active in other organisms. We can say transposons and transposition are one of the evolutionary forces in which the target site duplication plays an important role.

We can say the process of TSD induces new variation in nature. Three points are still unclear and unexplored; not all the target sites duplicated migrate with transposons, how much amount of host DNA will be transferred and how transposase protein recognizes the target DNA.

We are far behind in transposon research, and we still don’t know we have to use it for gene transfer and gene expression assays, more things to come in the future. 

I hope these topics will help you to understand the basic mechanism behind the process of transposition.

Some of the Quick FAQs:

What are the terminal repeats? 

The terminal repeats are the short inverted or direct sequences present on both ends of the transposon. Terminal repeats are recognized by transposase protein for transposition.

What is a “copy and paste” mechanism of transposition? 

It is a replicative mode of transposition in which the transposon is inserted in a new location by leaving a copy of it at the original, native position.

What is a “cut and paste” mechanism of transposition?

Cut and paste is a non-replicative/ conservative mode of transposition in which transposons migrate uni-direction, creating a gap at the native position.

What is composite transposon?

Composite transposons are bacterial transposons, made up of two Insertional sequences (IS) elements.

What is the consequence of transposition? 

It creates mutation or new variation in nature.

What is the target site duplication? 

A target site duplication is the identical sequences present on both end ends of the transposon, originating due to the insertion of a transposon.


Linheiro RS, Bergman CM. Whole-genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS One. 2012;7(2):e30008. doi:10.1371/journal.pone.0030008

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