retrotranspositio

Retrotransposition is the process by which a DNA sequence is copied through an RNA intermediate and inserted at a new genomic location, leaving a copy at the original site. This mechanism is carried out by retrotransposons, mobile genetic elements that can shape genome structure and evolution. In many organisms, retrotransposons comprise a substantial fraction of the genome and can influence gene expression, chromatin organization, and genomic spacing.

Retrotransposons are typically categorized as autonomous or non-autonomous. Autonomous elements, such as LINEs (long interspersed nuclear elements), encode the proteins needed for reverse transcription and integration. Non-autonomous elements, including many SINEs (short interspersed nuclear elements), lack coding capacity and rely on the enzymatic machinery provided by autonomous elements. A distinct class, the LTR retrotransposons, has long terminal repeats and resembles endogenous retroviruses; they also carry genes for reverse transcriptase and integrase. The common lifecycle involves transcription of the element into RNA, translation of its encoded proteins, reverse transcription of RNA into cDNA, and integration of the cDNA at a new site via integrase or related endonucleases. Insertion events can disrupt genes, alter regulatory regions, or generate genetic variation through duplication or recombination.

Genomes regulate retrotransposition through mechanisms such as DNA methylation, histone modifications, and RNA interference to limit activity. Although many insertions are neutral or deleterious, some become advantageous by providing new regulatory elements, influencing gene expression, or contributing to novel genes. Endogenous retroviruses, a subset of LTR retrotransposons, have been co-opted in host biology and have roles in placental development and immune regulation, illustrating the diverse impact of retrotransposition on evolution and function.