Structure of LTR retrotransposons

Figure 1: basic structure of a full-length LTR retrotransposon

The typical structure of a full-length LTR retrotransposon is shown in Figure 1:

1. LTR Region: 5'LTR and 3'LTR are two similar regions. They are identical while the element inserts into the host genome, and once inserted, they begin to evolve independently. Mutations and indels thus are often found. A typical LTR retrotransposon has a structure called TG..CA box, with TG at the 5' extremity of 5'LTR and CA at the 3' extremity of 3'LTR.
2. TSR Region: TSR(target site repeat) is a 4~6bp short direct repeat string flanking the 5' and 3' extremities of an element. It is the sign of insertion of transposable elements.
3. PBS: Near 3' end of the 5'LTR, there is a ~18bp sequence complemented to the 3' tail of some tRNA. The site is very important because tRNA binding process is the first step of initiating reverse transcription.
4. PPT: Polypurine tract is a short rich purine segment, about 11~15 bp in length. Like PBS, this region is important for reverse transcription.
5. Protein domains: In a typical virus genome there are three polygenes: gag, pol and env. Among them, pol is most conserved. Inside pol there are three important domains: IN(integrase), RT(reverse transcriptase) and RH(RNase H), which are enzymes for reverse transcription and insertion. RT and IN are regarded essential for autonomous LTR elements to fulfill their function.
6. These signals may become blur or even undetectable for evolutionary events.