retroelements

Retroelements are mobile genetic elements that propagate through an RNA intermediate and are reverse-transcribed and inserted at new genomic locations. They are widespread in eukaryotic genomes and often constitute a substantial fraction of DNA. In humans, retroelements account for roughly 40 to 50 percent of the genome, with the majority represented by autonomous LINEs, non-autonomous SINEs such as Alu elements, and endogenous retroviruses derived from ancient infections.

Classification and examples: Long terminal repeat (LTR) retrotransposons carry long terminal repeats flanking internal coding regions; non-LTR retrotransposons include LINEs and SINEs. LINE-1 elements are autonomous and encode proteins for reverse transcription and integration; Alu elements and related SVA elements are non-autonomous and rely on LINE-1 machinery. Endogenous retroviruses (ERVs) are remnants of ancestral retroviral infections that have become fixed in the germline and may be transcriptionally active in some contexts.

Lifecycle and regulation: Retroelements are transcribed by host RNA polymerase II, and their RNA is reverse-transcribed and inserted into new genomic sites, often via target-primed reverse transcription. Host defense mechanisms such as DNA methylation, histone modifications, and small RNA pathways (piRNA) suppress their activity. Many copies are inactive due to mutations.

Impact: Insertion can disrupt genes or alter expression and contribute to genetic disease, while over evolutionary timescales retroelements drive genome expansion and rearrangement. Some retroviral genes have been domesticated to serve host functions, such as env-derived proteins implicated in placental development in mammals.