7.15:
Non-LTR Retrotransposons
Non-LTR retrotransposons are a type of class I transposons that currently account for approximately 17% of the human genome. Unlike LTR retrotransposons with their characteristic long terminal repeats, non-LTR retrotransposons gain their name from the lack of these motifs. Non-LTR retrotransposons themselves are subdivided into two categories – Long Interspersed Nuclear Elements, or LINEs, and Short Interspersed Nuclear Elements, or SINEs.
While LINEs are autonomous and can encode proteins essential for their mobilization, SINEs are non-autonomous retrotransposons and require proteins encoded by other elements for their mobilization. For example, L1 elements – a type of LINE retrotransposon and one of the few autonomous transposons active in humans – are approximately 6kb long elements containing two open reading frames. ORF1 encodes for a protein with RNA binding and chaperone activities. ORF2 encodes for a protein with reverse transcriptase and endonuclease domains.
Both of these proteins are essential for the mobilization of the L1 element. Inside the nucleus, the RNA polymerase II first transcribes the L1 element into an L1 RNA, which is then polyadenylated and transported to the cytoplasm to be translated into ORF1 and ORF2 proteins. Both of these proteins then associate with the L1 RNA to form an L1 ribonucleoprotein, or RNP. The L1 RNP is imported back into the nucleus where it uses its endonuclease activity to make staggered nicks at the AT rich target site.
The reverse transcriptase then uses the loose 3’ end of one of the DNA strands as the primer for reverse transcription of the L1 RNA. This process is called target-site primed reverse transcription. The L1 RNA is then digested while a cellular DNA polymerase starts extending the 3’ OH end of the complementary DNA strand using the newly synthesized DNA strand as the template. Finally, the ends of the newly synthesized L1 element are sealed by the host enzymes – resulting in target site duplication.
In contrast to LINEs, SINEs are only around 100-400 bp in length and cannot encode proteins required for their transposition. However, most SINE elements contain structural features such as a 3’ AT-rich sequence that upon transcription enables them to be recognized by the LINE encoded proteins. This facilitates their integration into the genome via the same nick-and-copy process as LINE elements.
7.15:
Non-LTR Retrotransposons
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes – Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1 elements (LINE) and the Alu elements (SINE).
Transposition is typically a chance occurrence, which means the location where the transposable element is inserted is random. Transposons that are randomly inserted into genes can interfere with gene expression and cause genetic dysfunctions. A classic example is the insertion of the L1 retrotransposon into the factor VIII gene that causes hemophilia. L1 integration in the tumor suppressor gene Adenomatous polyposis coli (APC) has also been found in colon cancer patients. The SINE element Alu causes chromosomal aberrations and also has been linked to congenital defects like neurofibromatosis.
The cellular mechanism for repression of retrotransposons involves chemical modifications such as methylation of LINE elements or producing truncated retrotransposons. The vast majority of LINE and SINE elements in the human genome are truncated at their 5’ end due to erroneous reverse transcription. Such retrotransposons are usually silent, meaning they do not affect gene expression after insertion.
The occurrence of retrotransposons in cancerous cells has been exploited to develop retrotransposons like L1, as cancer biomarkers. It has been observed that methylation of L1 is significantly reduced in cancerous cells. This type of hypomethylation leads to genomic instability. Hypomethylated L1 levels have been investigated as biomarkers for malignancies like breast, colon, and skin cancer.
Suggested Reading
- Ardeljan, Daniel, Martin S. Taylor, David T. Ting, and Kathleen H. Burns. "The human long interspersed element-1 retrotransposon: an emerging biomarker of neoplasia." Clinical chemistry 63, no. 4 (2017): 816-822.
- Sigalotti, Luca, Elisabetta Fratta, Ettore Bidoli, Alessia Covre, Giulia Parisi, Francesca Colizzi, Sandra Coral, Samuele Massarut, John M. Kirkwood, and Michele Maio. "Methylation levels of the" long interspersed nucleotide element-1" repetitive sequences predict survival of melanoma patients." Journal of translational medicine 9, no. 1 (2011): 78.
- Kazazian, Haig H., and John V. Moran. "The impact of L1 retrotransposons on the human genome." Nature genetics 19, no. 1 (1998): 19.