Repetitive DNA elements

Kramer, F. and Schnieder, T. (1998) Sequence heterogeneity in a repetitive DNA element of Fasciola. International journal for Parasitology 28, 1923-1 929. 

Marin, M., Carat, B., Pettersson, LJ. and Ehrlich, R. (1993) Isolation and characterization of a middle repetitive DNA element from Echinococcus granulosus. Molecular and Biochemical Parasitology 59, 335-338. 

Spotila, L.D., Hirai, H., Rekosh, D.M. and LoVerde, P.T. (1989) A retroposon-like short repetitive DNA element in the genome of the human blood fluke, Schistosoma mansoni. Chromosoma 97, 421 —428. 

This method is useful for the isolation of interspersed repetitive DNA elements whose copy number is on the order of tens of thousands, but it will not be practical for the isolation of less abundant elements. As long as the copy number is high enough, SINEs, LINEs, and the retroviral-like elements can all be isolated using this approach. 

Palmeri D, Carroll KD, Gonzalez-Lopez O, Lukac DM. Kaposi s sarcoma-associated herpesvirus Rtatetramers make high-affinity interactions with repetitive DNA elements in the Mta promoter to stimulate DNA binding of RBP-Jk/CSL. J Virol. 2011 85 11901-15. 

Indeed, a bDNA assay for diagnosis of African trypanosomiasis was developed and compared with buffy coat microscopy for detection of T brucei in human blood samples (Harris etal., 1996). Two repetitive DNA sequences found only in the T. brucei complex, a 177-bp satellite repeat and the ribosomal mobile element, were selected as targets in the bDNA assay. The assay used the standard bDNA components capture probes, target probes, amplifier molecules, and alkaline phosphatase-labeled probes. Various blood fractions and sample preparation methods were examined. Ultimately, buffy coat samples resulted in the highest sensitivity. Although typanosomes do not infect leukocytes, they cosediment with them. 

Callaghan, M.J. and Beh, K.J. (1994a) A middle-repetitive DNA sequence element in the sheep parasitic nematode, Trichostrongylus colubriformis. Parasitology 109, 345-350. 

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). 

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... 

In general the definition of a transposable element is not that any one particular element has been proved to transpose, rather that a particular repetitive DNA sequence can be demonstrated to be interspersed in genomic DNA and have sequence similarity with established classes of trans-... 

As their name implies, interspersed genome-wide repeats are repetitive sequences that are scattered around the genome. Most of these sequences are the result of transposition (Section 18.1), a mechanism whereby certain DNA sequences can be duplicated and move within the genome. Transposable DNA elements, referred to as transposons, excise themselves and then insert at another site. More commonly, however, transposition mechanisms involve an RNA transcript intermediate. These latter DNA elements are called RNA transposons or retrotransposons. The most abundant retrotransposon in humans is the Alu sequence. Alu sequences, whose lengths are about 280 bp, are present in about 500,000 copies. The function of Alu sequences and other retrotransposons is unknown. It is suspected that they are molecular parasites whose primary purpose is their own propagation. 

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