Non-LTR Retrotransposons

Non-LTR retrotransposons account for approximately 17% of the human genome. These class I transposons lack the long terminal repeats characteristic of LTR retrotransposons. They are subdivided into two categories: Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs), both of which occur abundantly in humans and other mammals.

LINEs are autonomous retrotransposons that encode proteins essential for their own mobilization, including reverse transcriptase and endonuclease. SINEs are non-autonomous and cannot encode these proteins; instead, they rely on proteins encoded by LINE elements for transposition. However, SINEs contain structural features like 3' AT-rich sequences that enable LINE-encoded proteins to recognize and mobilize them through the same nick-and-copy process.

L1 elements contain two open reading frames: ORF1 encodes a protein with RNA binding and chaperone activities, while ORF2 encodes a protein with reverse transcriptase and endonuclease domains. Both proteins are essential for L1 mobilization. They associate with L1 RNA to form an L1 ribonucleoprotein (RNP) that facilitates the transposition process through target-site primed reverse transcription.

Target-site primed reverse transcription is the mechanism by which L1 elements integrate into the genome. The L1 ribonucleoprotein uses its endonuclease activity to make staggered nicks at AT-rich target sites. The reverse transcriptase then uses the loose 3' end of one DNA strand as a primer to synthesize a complementary DNA copy of the L1 RNA, resulting in integration and target site duplication.

Random insertion of non-LTR retrotransposons into genes can disrupt gene expression and cause genetic dysfunction. For example, L1 insertion into the factor VIII gene causes hemophilia, while L1 integration into the tumor suppressor gene APC has been found in colon cancer patients. SINE elements like Alu cause chromosomal aberrations and have been linked to congenital defects such as neurofibromatosis.

The vast majority of LINE and SINE elements are truncated at their 5' end due to erroneous reverse transcription during transposition. These truncated retrotransposons are usually silent, meaning they do not affect gene expression after insertion into the genome. This truncation effectively inactivates most retrotransposons, preventing them from causing genomic disruption.

Methylation of L1 elements is significantly reduced in cancerous cells, a condition called hypomethylation that leads to genomic instability. Hypomethylated L1 levels have been investigated as biomarkers for malignancies including breast, colon, and skin cancer. This reduced methylation allows normally silenced retrotransposons to become active, contributing to the genomic instability characteristic of cancer cells.