retrotransposones

Retrotransposons are genetic elements that move within a genome by copying themselves through an RNA intermediate and reintegrating the copy into new locations. They are inherited vertically and can accumulate over evolutionary time, contributing to genome size and structural variation. Retrotransposons are grouped into two major classes based on the presence or absence of long terminal repeats (LTRs): LTR retrotransposons and non-LTR retrotransposons.

Non-LTR retrotransposons include LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements). LINEs typically encode the enzymes required for their own mobilization, including reverse transcriptase and endonuclease, whereas SINEs do not encode proteins and rely on the enzymatic machinery provided by LINEs for propagation.

LTR retrotransposons are structurally similar to retroviruses and carry long terminal repeats flanking internal genes for reverse transcriptase and integrase. They propagate via an RNA intermediate and reintegrate into the genome through mechanisms shared with retroviruses, although they usually lack an env gene that enables cell-to-cell transmission.

In the human genome, LINE-1 elements are autonomous, while Alu and SVA elements are non-autonomous and mobilized with LINE-1 proteins. Retrotransposons can disrupt genes, alter regulatory landscapes, and promote chromosomal rearrangements, contributing to genetic disease and natural variation. Epigenetic mechanisms, notably DNA methylation, often suppress their activity in somatic cells, while activity can occur in germ cells or during early development.

Retrotransposons have shaped genome evolution by providing regulatory sequences, splice sites, and new exons, and by mediating recombination. Some viral sequences have been domesticated to serve host functions, including roles in placental development and immune regulation. They remain a major topic in the study of genome dynamics.