Retrotransposons characterization

Some well-characterized eukaryotic DNA transposons from sources as diverse as yeast and fruit flies have a structure very similar to that of retroviruses these are sometimes called retrotransposons (Fig. 26-33). Retro-transposons encode an enzyme homologous to the retroviral reverse transcriptase, and their coding regions are flanked by LTR sequences. They transpose from one position to another in the cellular genome by means of an RNA intermediate, using reverse transcriptase to make a DNA copy of the RNA, followed by integration of the DNA at a new site. Most transposons in eukaryotes use this mechanism for transposition, distinguishing them from bacterial transposons, which move as DNA directly from one chromosomal location to another (see Fig. 25-43). 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

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. 

Characterize retrotransposons. Once a positive clone has been identified, it can be used as a probe to isolate full-length copies of the element from a genomic library. These clones can also be characterized by phylogenetic screening. 

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. 

Laha T, Kewgrai N, Loukas A, Brindley P.J. Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in genome of the human blood fluke, Schistosoma mansoni. BMC Genomics. 2005 g 154. doi 10.1186/1471-2164-6-154. 

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