Short interspersed nuclear elements

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). 

Several publications describe assays for genomic animal DNA. Analysis of short interspersed nuclear elements (SINEs) allows specific detection of DNA from many species, including cattle, horse, pig, deer, and dog. SINEs are repeated, unblocked, and dispersed throughout the genome sequences. They represent retroposons (included in the genome transcripts of intracellular RNA) and constitute more than 20% of the genome of humans and other mammals. Unique sequences could be identified for every species and used for the development of a species-specific PCR assay (Walker et al., 2003). For this application the laboratory has to prepare its own control samples with the DNA extracted from reference samples. 

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