The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture.

Abstract

Tracts of the alternating dinucleotide polydeoxythymidylic-guanylic [d(TG)] polydeoxyadenylic-cytidylic acid [d(AC)], present throughout the human genome, are capable of readily forming left-handed Z-DNA in vitro. We have analyzed the effects of the Z-DNA motif d(TG)30 upon homologous recombination between two nonreplicating plasmid substrates cotransfected into human cells in culture. In this study, the sequence d(TG)30 is shown to stimulate homologous recombination up to 20-fold. Enhancement is specific to the Z-DNA motif; a control DNA fragment of similar size does not alter the recombination frequency. The stimulation of recombination is observed at a distance (237 to 1,269 base pairs away from the Z-DNA motif) and involves both gene conversion and reciprocal exchange events. Maximum stimulation is observed when the sequence is present in both substrates, but it is capable of stimulating when present in only one substrate. Analysis of recombination products indicates that the Z-DNA motif increases the frequency and alters the distribution of multiple, unselected recombination events. Specifically designed crosses indicate that the substrate containing the Z-DNA motif preferentially acts as the recipient of genetic information during gene conversion events. Models describing how left-handed Z-DNA sequences might promote the initiation of homologous recombination are presented.Homologous recombination is the process of exchange of genetic information between stretches of DNA containing sequence similarity. Although the degree of recombination is generally proportional to the length of homology, there are regions of DNA in which the rate of exchange is nonlinear with respect to distance, resulting in disparity between genetic and physical maps. The sequences responsible for this disparity, called "recombination hotspots," increase the rate of genetic exchange between homologous DNA molecules. The 8-base-pair (bp) Chi sequence in Escherichia coli is the most fully characterized recombination hotspot, shown to increase recombination in bacteriophage lambda and E. coli DNA via the RecA-RecBCD pathway (reviewed in reference 34). Recombination hotspots have also been described in fungi (12,25) and in mammalian cells (37; W. P. Wahls, L. J. Wallace, and P. D. Moore, Cell, in press).A short fragment of mammalian DNA from the human ,Bglobin gene cluster, MG-1 (29), promotes unusual recombination events during yeast meiosis (41). Molecular evidence indicates that the DNA sequence responsible is an 80-bp stretch of the simple repeating dinucleotide polydeoxythymidylic-guanylic polydeoxyadenylic-cytidylic acid, abbreviated hereafter as d(TG)n.The repeating dinucleotide d(TG)" is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria (11) but is ubiquitously present in eucaryotic chromosomes (13,29,40). It is estimated that there are on the order of 105 copies of this dinucleotide repeat, each approximately 10 to 50 bp in length, scattered throughout the mammalian genome. A striking feature of these r...

A Metric Linkage Disequilibrium Map of a Human Chromosome

“…Five predictors were found to be significant, which together explained about 7% of the variance (Table 3). The distance from (dfGT/CA) repeats, of greater than or equal to 100 bp, was the strongest predictor of LD supporting previous findings (Wahls et al 1990;Biet et al 1999;Gendrel et al 2000;Cullen et al 2002) which suggest that this sequence may promote recombination by forming Z-DNA and/or interaction with recombinases. By logistic regression, intervals containing (GT/CA) n repeats have significantly more LDUs and therefore higher rates of recombination.…”

Characterization of the promoter region of the porcine opn (osteopontin, secreted phosphoprotein 1) gene

“…The repeating dinucleotide (TG), present in the popnCAT + 51 / -180, occurs frequently (z lo5 copies) in the mammalian genome varying from 10 to 50 bp in length [54]. Although the exact function of these sequences are unknown, the observation that they form lefthanded 2-DNA indicates that the (TG), structure may be actively involved in transcriptional regulation [55].…”

Long CTG·CAG Repeats from Myotonic Dystrophy Are Preferred Sites for Intermolecular Recombination

“…Repetitive sequences have been observed previously to stimulate homologous recombination (15)(16)(17)(18)(19)(20)(21)(22)57). The formation of unusual secondary structures such as left-handed Z-DNA and intramolecular triplexes was proposed to be responsible for the association of these sequences with recombination hot spots (16,17,58).…”

“…Repetitive sequences promote homologous recombination in prokaryotic as well as eukaryotic systems, presumably by virtue of forming unusual DNA secondary structures (15)(16)(17)(18)(19)(20)(21)(22). In fact, homologous recombination has been implicated in the instability of repetitive sequences (23)(24)(25)(26).…”