DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts

Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 11/2011; 108(51):20796-801. DOI: 10.1073/pnas.1114677108
Source: PubMed


High concentration of NaCl increases DNA breaks both in cell culture and in vivo. The breaks remain elevated as long as NaCl concentration remains high and are rapidly repaired when the concentration is lowered. The exact nature of the breaks, and their location, has not been entirely clear, and it has not been evident how cells survive, replicate, and maintain genome integrity in environments like the renal inner medulla in which cells are constantly exposed to high NaCl concentration. Repair of the breaks after NaCl is reduced is accompanied by formation of foci containing phosphorylated H2AX (γH2AX), which occurs around DNA double-strand breaks and contributes to their repair. Here, we confirm by specific comet assay and pulsed-field electrophoresis that cells adapted to high NaCl have increased levels of double-strand breaks. Importantly, γH2AX foci that occur during repair of the breaks are nonrandomly distributed in the mouse genome. By chromatin immunoprecipitation using anti-γH2AX antibody, followed by massive parallel sequencing (ChIP-Seq), we find that during repair of double-strand breaks induced by high NaCl, γH2AX is predominantly localized to regions of the genome devoid of genes ("gene deserts"), indicating that the high NaCl-induced double-strand breaks are located there. Localization to gene deserts helps explain why the DNA breaks are less harmful than are the random breaks induced by genotoxic agents such as UV radiation, ionizing radiation, and oxidants. We propose that the universal presence of NaCl around animal cells has directly influenced the evolution of the structure of their genomes.

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Available from: Natalia I Dmitrieva
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    • "Mammalian (renal) and marine invertebrate cells that use organic osmolytes thrive, even with unrepaired breaks (Dmitrieva and Burg, 2008), and it appears that they restrict breakage to 'gene deserts' – chromosomal regions with no genes. This may explain why osmolyte-using cells survive at high osmolalities despite persistent breaks (Dmitrieva et al., 2011). However, the mechanism for restricting breaks to these gene deserts is not known, nor is a causal connection with compatible osmolytes. "
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