Retrotransposons mammalian

As described in Section B,l, mammalian DNA contains many retrotransposons (retroposons) that lie within short direct repeats characteristic of transposons. However, they contain a poly(A) tail at the 3 end, an indication of their relationship to RNA transcripts, and are discussed in Chapter 28. 

Although a number of mammalian retrotransposons have been discovered by chance, a variety of approaches have been developed specifically to survey the genome for the presence of retrotransposons as well as to facilitate their isolation and characterization. Of the three methods outlined here in detail, two (conserved restriction sites and phylogenetic screening) could lead to isolation of all three types of retrotransposons, whereas the third method [polymerase chain reaction (PCR) amplification of reverse transcriptase] will exclude the SINEs. An unrelated method that has been particularly useful for isolation of SINEs7 will not be detailed. 

The presence of retrotransposon-derived repetitive DNA in such abundance in mammalian genomes is a mystery in terms of its origin as well as its role in the evolution of the genomes it inhabits. These mysteries will best be solved by detailed comparative studies of a number of elements in an evolutionary context. Already, phylogenetic analysis has led to an improved understanding of the structure and dynamics of retrotransposi-tion of LINE and SINE elements of vertebrate genomes.4 11 12 22-24 We have detailed three useful methods for the isolation of interspersed repetitive... 

DNA/retrotransposons from mammalian genomes. In addition, methods to characterize and study the phylogenetic distribution of these elements are presented. These methods are applicable to screening any mammalian genome and should facilitate the much needed examination of genome evolution in a wide variety of species. 

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