Retrotransposonencoded

Retrotransposon-encoded elements are mobile genetic sequences that amplify themselves in genomes via an RNA intermediate and a reverse transcription step. They are ubiquitous in eukaryotes and contribute to genome size, structure, and variation. Their activity is tightly regulated because insertions can disrupt genes or regulatory regions, or alter chromosomal stability.

Retrotransposons are broadly classified into two classes based on their transcriptional and enzymatic organization: long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons. LTR retrotransposons encode at least two enzymatic domains as part of a Pol polyprotein along with Gag; the Pol domain typically includes reverse transcriptase, RNase H, and integrase, and some elements also encode a protease. Non-LTR retrotransposons include LINEs (long interspersed nuclear elements) that usually contain two open reading frames: ORF1p and ORF2p; ORF2p contains endonuclease and reverse transcriptase activities, which drive retrotransposition. SINEs (short interspersed nuclear elements) do not encode proteins themselves and mobilize using the enzymatic machinery supplied in trans by autonomous elements such as LINEs.

The proteins encoded by retrotransposons—retrotransposon-encoded reverse transcriptase, integrase, and related factors—drive replication and insertion into new genomic sites. Activity is often silenced by epigenetic mechanisms and small RNA pathways, but occasional reactivation can create copy-number variation, disrupt genes, or create new regulatory motifs. Some inserted retrotransposon sequences have become co-opted by the host, contributing to gene regulation, exon shuffling, or even novel genes, as seen in various evolutionary lineages. The term retrotransposon-encoded highlights the coding capacity of these elements alongside their RNA intermediates.