A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes.

Abstract

By Southern blotting and hybridization analysis using 32P-labeled poly(dT-dG)-poly(dC-dA) as a probe, we have found, in eukaryotic genomes, a huge number of stretches of dTdG alternating sequence, a sequence that has been shown to adopt the Z-DNA conformation under some conditions. This sequence was found in all eukaryotic genomes examined from yeast to human, indicating extraordinary evolutionary conservation. The number of the sequence ranged from about 100 in yeast to tens of thousands in higher eukaryotes. Comparison of nucleotide sequences of dT-dG alternating regions and its flanking regions in several cloned genes showed that the repeated element [the Z(T-G) element] consists only ofdT-dG alternating sequence with variable length. The presence of another purine-pyrimidine alternating sequence was also surveyed in eukaryotic genomes by Southern blot hybridization using 32P-labeled poly(dG-dC)-poly(dGdC) as the probe. The stretches of dC-dG alternating sequence [the Z(C-G) element] were found to be moderately repetitive in human, mouse, and salmon genomes. However, a few and no copies of the Z(C-G) element were found in yeast and calf genomes, respectively. These results provide evidence for the abundance of potential Z-DNA-forming sequences in nature.Recent physicochemical studies of DNA conformation have shown that some synthetic DNAs with certain primary sequences have a novel conformation, called the Z form (1-4). Although the Z conformation was first observed with poly(dGdC) and most studies on Z-DNA have been done with it, other synthetic purine-pyrimidine alternating sequences such as poly(dT-dG)-poly(dC-dA) (2, 5, 6) and poly(ds4A-dT) (2) have also been shown to adopt the Z conformation. Until recently, however, there has been little direct evidence that such Z-DNA-forming sequences exist in native DNA. Nordheim et at (7) have shown that a specific antibody against brominated poly(dG-dC)-poly(dG-dC), a polymer that forms a Z-DNA under physiological conditions, reacts with interband regions of Drosophila polytene chromosomes. Recently, we have shown that the human genome has approximately 105 copies of stretches of dT-dG alternating sequence (8). A tandem block of 17 T-G (9) and 27 T-G dinucleotides (10) were found in human globin and in mouse immunoglobin genes, respectively, but the general occurrence of these sequences in the genomes was not investigated.Here we report that one of the Z-DNA-forming sequences, a long stretch of dT-dG alternating sequence is the sole unit of a repeated element [designated the Z(T-G) element] that is highly conserved throughout eukaryotic genome evolution. Furthermore, another Z-DNA-forming sequence, a stretch of dC-dG sequence, was found to be at least a part of another repeated element [designated the Z(C-G) element] and is moderately repeated in human, mouse, and salmon genomes but not in yeast or calf DNA.MATERIALS AND METHODS Materials. Calfthymus DNA, salmon sperm DNA, and poly-(dG-dC)-poly(dG-dC) were purchased from Sigma. Poly(dTdG)-poly(dC-dA) was o...

Target sites for the transposition of rat long interspersed repeated DNA elements (LINEs) are not random

“…Therefore, an (A+T)-rich stretch that contains a TACTCA or singly-substituted variant thereof, followed by a simple PQ stretch, typifies at least one class of LINE target sites. We roughly estimated the number of such sites in the rat genome as follows: Mammalian genomes contain from about 0.1 x 10 (22) to 1 x 106 (20) copies of (GT) , where n is 25 (22) or 8 (20). GC stretches are n far fewer (22), and assuming that AT stretches, which were not determined, are as abundant as GT stretches, then the rat genome could contain from 0.2 x 106 to 2 x 106 copies of simple PQ stretches.…”

“…We roughly estimated the number of such sites in the rat genome as follows: Mammalian genomes contain from about 0.1 x 10 (22) to 1 x 106 (20) copies of (GT) , where n is 25 (22) or 8 (20). GC stretches are n far fewer (22), and assuming that AT stretches, which were not determined, are as abundant as GT stretches, then the rat genome could contain from 0.2 x 106 to 2 x 106 copies of simple PQ stretches. Only some of these would be in a region of DNA that is both (A+T)-rich and contains a TACTCA or version thereof.…”

PCR‐amplified microsatellites as markers in plant genetics

“…It has been shown that eukaryote genomes are densely interspersed with simple sequences which consist of stretches of tandemly repeated nucleotide motifs which can be as short as 4, 3, 2 and even 1 nucleotide (Braaten et a/., 1988;Hamada et a/., 1982;Schafer et a/., 1986;Tautz and Renz, 1984;Vergnaud, 1989). When such regions, which have been termed 'microsatellites' (Litt and Luty, 1989), are individually amplified by means of the polymerase chain reaction (PCR) (Saiki et a/., 1988), using a pair of flanking unique oligonucleotides as primers, they almost invariably show extensive polymorphism due to site-specific length variation, as a consequence of the occurrence of different numbers of repeat units.…”

Protein and microsatellite single locus variability in Salmo salar L. (Atlantic salmon)

“…One type of repetitive element, referred to as microsatellites, corresponds to tandemly repeated DNA motifs of one to five base pairs in length evenly distributed in the genome of all investigated eukaryotic species (Hamada et a!., 1982;Weber, 1990;Wong et a!., 1990;Wintero et a!., 1992; Estoup et al, 1993;Slettan et a!., 1993).…”