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Why there are gene deserts has remained a mystery. They were discovered when whole genome sequencing showed that genes are not evenly distributed. A substantial fraction of mammalian genomes contains gene deserts, defined as long regions (>500 kb) containing no protein-coding sequences. Gene deserts occupy ≈38% of human, 34% of mouse, 23% of rat, and 20% of dog genome (29). It is extremely unlikely that gene deserts reached their observed maximal size of 5.1 Mb with 545 deserts larger than 640 kb by chance (30), which raises the question of what selective pressure might be acting.Animal cells are universally exposed to NaCl, and the level of NaCl may be high in animals exposed to marine or desiccated terrestrial environments. During evolution of mammals, osmoregulatory mechanisms developed that maintain osmolality of most extracellular fluids close to 300 mosmol/kg. Nevertheless, even in mammals, NaCl concentration is constantly very high in some tissues, particularly the renal medulla. Given our finding that DNA breaks induced by high NaCl are concentrated in gene deserts, we suggest that, as the size of genomes has increased, newly formed regions are susceptible (for unknown reasons) to high NaCl-induced DNA breaks and evolve to contain fewer genes, thus limiting mutations and preventing genomic instability. This suggestion is supported by several observations.i) The neutral mutation rate (30) and the rate of genome rearrangements associated with appearances of new centromeres (31) are both higher in gene deserts than in regions containing genes.
ii) Before the evolution of vertebrates, the sizes of genomes grew in proportion to the number of genes. However, gene deserts began appearing in fish and increased in size to occupy ≈38% of the genome in humans (29). Over the same period, osmoregulatory mechanisms developed that maintain systemic osmolality close to 300 mosmol/kg. Estimates from molecular clocks of the rates of evolution show that the rates decreased significantly in vertebrates before the origin of Osteichthyes (32). That could have been due to a combination of decreased rate of mutations in protein coding regions owing to more precise osmoregulation and the low abundance of functional genes in gene deserts where they would be susceptible to NaCl-induced breaks.
iii) Recently, a model was proposed relating the rate of molecular evolution and the maximal size of genomes (33). The theory assumes that for an organism to be viable, essential genes must be functional. Further, it predicts that populations become extinct because of lethal mutagenesis when the mutation rate exceeds approximately six mutations per replication in essential parts of the genome in mesophilic organisms and one or two mutations in thermophilic ones. The theory therefore predicts that mutation rate limits essential genome size; in other words, the higher the mutation rate, the smaller the sustainable size of the genome. This theory implies that increasing the size of the genome required that genes not evolve in regions, like the present gene deserts, that are more susceptible to DNA breaks and mutations.
Our finding that high NaCl-induced DSBs are located in gene deserts is an example of nonrandom induction of DNA breaks in higher organisms. Although we are uncertain why high NaCl breaks DNA, the gene deserts apparently have properties that render them more susceptible. Limitation of high NaCl-induced DNA breaks to gene deserts helps explain why they apparently are less harmful than are the random breaks induced by genotoxic agents like UV radiation, ionizing radiation, and oxidants. Further, our finding suggests a possible role of high NaCl in evolution of the structure of the animal genome.
Perspective. More studies are required to decipher why double-strand breaks occur predominantly in gene deserts during exposure to high NaCl. Possibilities that we are considering include decreased DNA repair in gene deserts similar to that in heterochromatin (34), presence of specific target sequences for nucleases activated by high NaCl, and high NaCl-induced alterations of chromatin in gene deserts that makes the DNA there more susceptible to damaging agents.
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