Z-DNA-forming sequences generate large-scale deletions in mammalian cells

Abstract

Spontaneous chromosomal breakages frequently occur at genomic hot spots in the absence of DNA damage and can result in translocation-related human disease. Chromosomal breakpoints are often mapped near purine-pyrimidine Z-DNA-forming sequences in human tumors. However, it is not known whether Z-DNA plays a role in the generation of these chromosomal breakages. Here, we show that Z-DNA-forming sequences induce high levels of genetic instability in both bacterial and mammalian cells. In mammalian cells, the Z-DNA-forming sequences induce double-strand breaks nearby, resulting in large-scale deletions in 95% of the mutants. These Z-DNA-induced double-strand breaks in mammalian cells are not confined to a specific sequence but rather are dispersed over a 400-bp region, consistent with chromosomal breakpoints in human diseases. This observation is in contrast to the mutations generated in Escherichia coli that are predominantly small deletions within the repeats. We found that the frequency of small deletions is increased by replication in mammalian cell extracts. Surprisingly, the large-scale deletions generated in mammalian cells are, at least in part, replication-independent and are likely initiated by repair processing cleavages surrounding the Z-DNA-forming sequence. These results reveal that mammalian cells process Z-DNA-forming sequences in a strikingly different fashion from that used by bacteria. Our data suggest that Z-DNAforming sequences may be causative factors for gene translocations found in leukemias and lymphomas and that certain cellular conditions such as active transcription may increase the risk of Z-DNA-related genetic instability.DNA repair ͉ genetic instability ͉ non-B DNA ͉ translocation

Epigenetic Regulation by Z-DNA Silencer Function Controls Cancer-Associated ADAM-12 Expression in Breast Cancer: Cross-talk between MeCP2 and NF1 Transcription Factor Family

“…concentrated near the transcription start sites (26) and have been implicated in gene regulation (27)(28)(29)(30), chromatin remodeling (31), recombination (32,33) and large-scale deletions (34). It is interesting to note that many cancer-associated genes, including EGFR, ER-a, Cyr61, ACCA, prolactin, MMP-9, heme oxygenase 1, and HMGA2, contain dinucleotide repeat elements that have been identified as regulatory elements (Supplementary Table S1); but how these sequences regulate gene expression remained poorly understood.…”

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

“…However, CG repeats, found at high frequency in CpG islands, can form non-B DNA secondary structures that are associated with elevated rates of rearrangements in mammalian cells (Wang et al 2006). Through their propensity to accumulate double-strand breaks, the hairpin loops, Z-DNA, and other structures generated in CG-rich regions could potentially play key roles in the fragility of reused EBRs.…”

“…Through their propensity to accumulate double-strand breaks, the hairpin loops, Z-DNA, and other structures generated in CG-rich regions could potentially play key roles in the fragility of reused EBRs. Active transcription increases the mutability of CG repeats (Wang et al 2006), and CpG islands are typically associated with the promoters of highly and widely expressed genes (for review, see Antequera 2003). As a result, a large fraction of islands reside in domains of open chromatin (Roh et al 2005;Heintzman et al 2007).…”

The Cucurbit[7]Uril‐Based Supramolecular Chemistry for Reversible B/Z‐DNA Transition

“…Long stretches of alternating purine‐pyrimidine sequences have been reported to be infrequent in genomes 24. Therefore, the B/Z transition in short stretches of DNA is biologically more important than the cooperative transition in long stretches of DNA.…”