LTR retrotransposons are sub-divided on the basis of gene order and sequence similarity into the Ty1-
copiagroup and the gypsygroup, named after prototype examples discovered in Drosophilaand yeast.^64
Both groups are also found in plants, fish, amphibia and reptiles but neither has been described in mam-
mals (including humans) or in birds.
6.8.3.2.3 Transposition Mechanisms. Only the transposition cycle for LTR retrotransposons will
be discussed here, since it is much better understood than LINE transposition mechanisms (Figure 6.48).^64
First, an integrated DNA copy of the retrotransposon in the host genome is transcribed into an RNA.
Transcription is initiated within one LTR and terminated in the other. It thus contains the entire genetic
information of the transposable element. Some of this RNA is spliced before export into the cytoplasm and
some is exported unspliced. Both spliced and unspliced RNAs can be translated into the various protein
products encoded by the retrotransposon. Most of the protein produced comprises the components of an
intracellular virus-like particle. This process is similar to that seen for many retroviruses. A subset of the
full-length unspliced retrotransposon RNAs is encapsidated into this particle, along with two enzymes
necessary for transposition, namely reverse transcriptase and integrase.
Reverse transcription is carried out by the encapsidated reverse transcriptase. The process is completed
when the RNA has been converted into a linear unintegrated DNA. Insertion of this DNA into a new chromo-
somal location is catalysed by the integrase protein. As a rule, retrotransposons insert at random sites into
their host genome, although some LTR retrotransposons of Drosophilaand Saccharomyceshave prefer-
ences for particular insertion sequences or genomic regions.
6.8.3.2.4 Retrotransposons and the Human Genome. Approximately half of human genome
consists of repeated elements interspersed among the genes. Much of this interspersed DNA is comprised
of Class I transposable elements, predominantly SINEs(approximately 1 million copies or 10–15% of the
genome), LINEs(15–20% of the genome) and pseudogenes of human retroviruses (ca.1% of the genome).^67
6.8.3.2.5 Retroviruses. Retroviruses were first identified as agents involved in the onset of cancer about
80 years ago.^30 More recently the AIDS epidemic has been shown to be due to the HIV retrovirus. In the
early 1970s it was discovered that retroviruses could replicate their RNA genomes viaconversion into
DNA, which becomes stably integrated in the DNA of the host cell. It is only comparatively recently that
248 Chapter 6
Figure 6.48 The life cycle of LTR retrotransposons. All intermediates are intracellular. Shaded boxes and circles
indicate genes and their protein products respectively