Repetitive DNA

Repetitive DNA.—The eukaryote genome contains, on average, 30% repetitive sequences. These can be divided into highly repetitive and moderately repetitive classes. Highly repetitive sequences occur at the centromeres of the chromosomes and are generally assumed to be involved in the organization and separation of chromosomes at meiosis and mitosis. 

Jelinek, T. P. Toomey, L. Leinward, C. H. Duncan, P. Biro. P. Choudary, S. Weissmin, L. Rubin, C. Houck, P. Deininger, and C. Schmid, Proe.JVdl/. dead. Set. VSA, 1980, 77,1398. 

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The DNA in a eukaryotic genome can be divided into different sequence classes. These are unique-sequence, or nonrepetitive, DNA and repetitive-sequence DNA. In the haploid genome, unique-sequence DNA generally includes the single copy genes that code for proteins. The repetitive DNA in the haploid genome includes sequences that vary in copy number from two to as many as 10 copies per cell. 

Besides unequal crossover and transposition, a third mechanism can effect rapid changes in the genetic material. Similar sequences on homologous or nonhomol-ogous chromosomes may occasionally pair up and eliminate any mismatched sequences between them. This may lead to the accidental fixation of one variant or another throughout a family of repeated sequences and thereby homogenize the sequences of the members of repetitive DNA families. This latter process is referred to as gene conversion. 

J. Versalovic, T. Koeuth, and J. R, Lupski, Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acid Re.K. 79 6832 (1991). 

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. 

Elder, J.F. and Turner, B.J. (1995) Concerted evolution of repetitive DNA sequences in eukaryotes. Quarterly Review of Biology 70, 297-320. 

Tautz, D. (1993) Notes on the definition and nomenclature of tandemly repetitive DNA sequences. In Pena, S.D.J., Chakraborty, R., Epplen,J.T. and Jeffreys, A.J. (eds) DNA Fingerprint State of Science. Birkhauser Verlag, Basel, Switzerland, 21 pp. 

The genomic DNA sequences used in these tests are generally regions containing repetitive DNA... 

Eukaryotic chromosomes have two important special-function repetitive DNA sequences centromeres, which are attachment points for the mitotic spindle, and telomeres, located at the ends of chromosomes. 

Telomeres are stretches of highly repetitive DNA found at the ends of linear chromosomes. As cells divide and age, these sequences are shortened, contributing to cell death. 

Mbp of DNA containing perhaps 40,000 proteincoding genes. However, 97% of the genome is repetitive DNA and other DNA that, at present, has no recognizable function. The genome project will reveal all of these sequences and will doubtless provide us with many surprises. 

For repetitive DNA sequences, such as alphoid repeats, especially for identification of centromeric regions on chromosomes, as well as in mterphase nuclei, I routinely prepare labeled probes by PCR using a centromeric DNA-specific set of primers. For single-copy gene mapping by FISH, it is essential to use DNA cloned into either cosmids or in yeast artificial chromosome vectors (YAC) m order to obtain the level of sensitivity that will enable visualization of signal with a fluorescence microscope... 

The method described here is ideally suited for detection of both alphoid repeats at the centromeric regions of all chromosomes, and moderately repetitive DNA sequences within the arms and telomeric regions... 

Repetitive DNA. A DNA sequence that is present in many copies per genome. 

Satellite DNA. A DNA fraction the base composition of which differs from that of the main component of DNA, as revealed by the fact that it bands at a different density in a CsCl gradient. Usually repetitive DNA or organelle DNA. 

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). 

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