What Is a Target Site Duplication in Genomics?

A target site duplication (TSD) is a short segment of DNA copied at the boundaries of a mobile genetic element after it inserts into a new genomic location. These duplications are a hallmark of transposition, where DNA sequences called transposable elements move within a genome. The length of these duplicated sequences is short, ranging from a few to several hundred base pairs.

The formation of a TSD is part of the integration mechanism. A transposase enzyme makes a staggered cut in the host’s DNA, creating single-stranded overhangs. After the transposable element is inserted, the host cell’s DNA repair machinery fills in the gaps, which duplicates the target site sequence and results in two identical copies flanking the element.

The Mechanism of Target Site Duplication Formation

This process begins when an enzyme, like a transposase or integrase, recognizes a specific location on the host’s DNA and makes a staggered cut across the two DNA strands. This cut at offset positions generates short, single-stranded overhangs.

After the target DNA is cleaved, the transposable element is positioned between these overhangs. The enzyme then ligates, or joins, the element’s ends to the host DNA, integrating it into the new genomic location. This leaves two single-stranded gaps on either side of the newly inserted element.

The host cell’s DNA repair systems are recruited to resolve these gaps. A DNA polymerase synthesizes new DNA to fill in the missing nucleotides, using the exposed overhangs as a template. The enzyme DNA ligase then seals the nicks in the sugar-phosphate backbone, completing the repair and creating a direct repeat of the target DNA on both sides of the element.

Transposable Elements as Drivers of Target Site Duplications

Transposable elements (TEs) are the drivers of TSD formation. These mobile genetic sequences are categorized into two main classes based on their method of movement. Class I retrotransposons move via a “copy-and-paste” mechanism involving an RNA intermediate, while Class II DNA transposons use a “cut-and-paste” mechanism.

Despite different mobilization strategies, both classes generate TSDs upon insertion. The length of the TSD is a characteristic feature of the specific TE type. For example, Mariner DNA transposons create specific TSDs, while Alu retrotransposons are associated with TSDs ranging from 10 to 20 base pairs. This consistency allows researchers to predict the TE type by analyzing the length of the flanking repeats.

A TSD serves as a permanent footprint of a transposition event. Even if the TE itself is mutated or deleted over time, the flanking TSDs can remain as evidence of the original insertion. This makes TSDs valuable markers for studying TE activity and the history of genomic changes.

Genomic Consequences and Significance of Target Site Duplications

The presence of a TSD indicates a TE insertion, an event with significant effects on the genome. If a TE inserts into a protein-coding region, it can disrupt the gene’s reading frame or introduce stop signals, often leading to a non-functional protein. This insertional mutagenesis is a common way TEs cause new mutations.

TE insertions and their associated TSDs can also influence gene regulation. The insertion can alter the spacing between regulatory elements and the genes they control or introduce new regulatory sequences contained within the TE. This can lead to changes in how much a gene is expressed, which can contribute to evolutionary novelty.

Evolutionarily, TSDs are markers of past TE activity that have shaped genomes. The accumulation of TEs is a driver of genome expansion and plasticity. The identical repeats of TSDs can also be sites of genomic instability, potentially facilitating deletions or other rearrangements through recombination. In genetic research, the predictable formation of TSDs is exploited as a tool to confirm successful gene delivery or to create mutations for study.