retrotransposonsretrotransposonencoded

Retrotransposons are transposable elements that move within genomes through a copy-and-paste mechanism that uses an RNA intermediate. They are mainly categorized as long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons, the latter including LINEs and SINEs. Many retrotransposons encode proteins needed for their replication; non-autonomous elements rely on enzymes supplied by autonomous elements.

Autonomous elements such as LINE-1 encode proteins in two open reading frames, including ORF2p with endonuclease and reverse transcriptase activities and ORF1p, a nucleic-acid-binding protein. Non-autonomous elements, like Alu and SVA, lack these enzymes and depend on LINE machinery for mobilization.

The typical cycle starts with transcription by RNA polymerase II, followed by translation of encoded proteins, reverse transcription of the RNA, and integration into the genome. LINEs use target-primed reverse transcription and endonuclease activity, while LTR retrotransposons produce Gag-Pol polyproteins that are processed into functional enzymes and integrate via integrase. In contrast to infectious retroviruses, retrotransposons are generally non-viral and non-infectious.

Retrotransposons influence genome structure and function by increasing genome size, generating insertional polymorphisms, and contributing regulatory elements. They can affect gene expression, splicing, and chromatin state, and some sequences have been exapted for host functions. Host defense includes DNA methylation, histone modification, and small RNA pathways such as piRNA.

In humans, LINE-1 elements remain active in some tissues, Alu and SVA elements depend on LINE machinery, and endogenous retroviruses contribute additional regulatory and evolutionary elements. This dynamic interplay shapes genome evolution and diversity.