Targetprimed

Targetprimed, often encountered as target-primed reverse transcription (TPRT), is a mechanism by which non-LTR retrotransposons, most notably LINE-1 elements, integrate new copies into the genome. The term describes how reverse transcription is initiated at the site of a DNA nick created by the retrotransposon’s endonuclease, providing a primer for cDNA synthesis directly at the insertion target.

In TPRT, the endonuclease encoded by the retrotransposon makes a nick in the genomic DNA, creating a free 3'-hydroxyl group. This 3'-OH serves as the primer for reverse transcription of the element’s RNA by the element’s reverse transcriptase. The resulting cDNA is synthesized at the target site and integrated into the genome. The insertion is often accompanied by short target site duplications caused by staggered cuts in the DNA. Most insertions are 5' truncated, reflecting premature termination of reverse transcription.

TPRT is the predominant mechanism driving LINE-1 retrotransposition in many mammalian genomes. Non-autonomous elements such as Alu and SVA mobilize using LINE-1-encoded machinery, relying on the same reverse transcription process for insertion, though they do not encode their own full transposition enzymes. As a result, TPRT contributes to genomic diversity and evolution but can also disrupt genes, regulatory regions, or chromosomal integrity, potentially contributing to disease.

In genome analyses, TPRT insertions are identified by signatures such as target site duplications and poly-A tails at the 3' end of the inserted sequence. While first characterized in LINE-1 biology, the concept of target-primed reverse transcription informs understanding of various non-LTR retrotransposon activities across species.