retroelement

A retroelement is a genetic element that propagates within a genome via an RNA intermediate, using reverse transcription to insert new copies of itself at new genomic locations. Retroelements are a major class of transposable elements and are found in many eukaryotic genomes. In humans and other mammals, they contribute a substantial portion of the genome and influence genome structure, function, and evolution.

The major groups of retroelements include: LINEs (long interspersed nuclear elements), which are autonomous and encode the proteins needed for reverse transcription and integration; SINEs (short interspersed nuclear elements), which are non-autonomous and rely on the LINE machinery for mobilization (examples include Alu elements in humans); and LTR retrotransposons, which are flanked by long terminal repeats and include endogenous retroviruses (ERVs) that are remnants of ancient viral infections. ERVs are integrated viral sequences that can be defective or occasionally still capable of expression; some have been co-opted for host functions.

Mechanistically, retroelements are transcribed by RNA polymerase II, reverse-transcribed into DNA, and then inserted into the genome by a specialized integration process. Some LINEs use target-primed reverse transcription to integrate. LTR retrotransposons and ERVs resemble retroviruses in their life cycle but typically lack infectious intermediates in modern genomes.

Biological impact includes genome expansion, insertional mutagenesis, and modulation of gene expression and regulation. Epigenetic silencing by DNA methylation and histone modifications helps contain their activity. Retroelements are pervasive across genomes and have played a significant role in evolution, sometimes contributing novel regulatory elements and protein-coding sequences.