LTR Retrotransposons

Most eukaryotic genomes contain a unique group of transposable elements called Retrotransposons, or Class I transposons.

Unlike DNA-only transposons or Class II transposons, the retrotransposons employ a "copy and paste" mechanism - which means that a copy of the transposon moves to a new site on the genome. 

There are two types of retrotransposons - Long terminal repeat, or LTR, retrotransposons, and non-LTR retrotransposons - both of which use different transposition mechanisms.

The LTR retrotransposons consist of a 5-7kb long protein-coding region flanked at both ends by long terminal repeats, typically 250-600 bp in length.

These LTRs contain enhancer and promoter sequences for transcription. 

The coding region is very similar to that of the retroviral genome, consisting of genes closely related to the gag and pol of retroviruses. Hence, LTR retrotransposons are also known as retroviral-like retrotransposons. 

However, unlike retroviruses, LTR retrotransposons do not encode the “env” gene, and hence, cannot form a viral envelope. 

While the pol gene encodes enzymes such as protease, reverse transcriptase, integrase, and RNase H; the gag gene encodes structural proteins that can form a virus-like particle. 

The mechanism of transposition of the LTR elements also resembles retroviral replication in the host cells.

First, the host cell RNA Polymerase II binds to the 5’ LTR and starts transcribing the retrotransposon into a single RNA strand. 

The RNA intermediate is then processed by the host cell enzymes to add a 5’ cap and a 3’ polyA tail. 

The mature RNA is then transported to the cytoplasm and translated into proteins. The mRNA and the protein products then assemble to form a virus-like particle. It is inside this virus-like particle that the RNA is reverse transcribed into a single-stranded DNA copy. 

This is followed by the degradation of the RNA strand by RNase H, and synthesis of a complementary DNA strand leading to a double-stranded DNA. 

This linear, double-stranded DNA is bound by the integrase at both ends to form a stable complex called an intasome that can be transported back into the nucleus and inserted into a new location on the host genome. 

LTR retrotransposons can make several copies of themselves in the same cell using this mechanism of replication.