Retrovirus-like elements

All of the mammalian transposable elements that have been characterized to date seem to be the result of transpositions that proceeded through an RNA intermediate. This process is known as retrotransposition or retroposition. Three classes of these retrotransposable elements are known in mammals (1) SINEs, or short interspersed repeated sequences such as the human Alu family and rodent Bl (2) LINEs, or long interspersed repeated sequences such as LI in a variety of mammalian species and (3) retrovirus-like elements, such as THE 1 in humans and mys and IAP in rodents. Retrovirus-like elements have long terminal repeats (LTRs) that often surround two open reading frames (ORFs) like those of retroviruses, but they lack the ability to leave one cell and enter another. LINEs also have two ORFs, but have no LTRs. SINEs have no LTRs and no ORFs. Transposition of all of these elements must involve reverse transcription of the RNA intermediate in some cases the required reverse transcriptase is apparently encoded by the element itself. 

Phylogenetic screening has been used successfully to isolate retroelements that have been active in recent evolutionary time. In a phi-screen of the white-footed mouse, Peromyscus leucopus, the retrovirus-like element mys was identified by virtue of its hybridization to Peromyscus DNA but its lack of hybridization to Mus (the outgroup) DNA.13 In a phi-screen of human DNA using Galago as an outgroup, both the 5 end of the LI element and the retrovirus-like element THE 1 hybridized differentially,... 

One advantage of this method is that it does not require library construction unless one wishes to use the PCR product to isolate the entire element. Additionally, this method can be used to detect both repetitive and low-copy elements. Using these primers, however, it will not be possible to detect retroposons such as SINE elements or retrovirus-like elements such as THE 1 that do not have a region of amino acid similarity to reverse transciptase. 

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