DSBs can result from extrinsic causes, including certain viruses, ionizing radiation, and chemical sources, or from intrinsic causes, such as reactive oxygen species produced by cellular respiration or replication fork collapse at genome fragile sites ^{[16][17][18][19]}[19,20,21,22]. Alternatively, they can be a consequence of specific mechanisms and examples include programmed genome reorganization, such as RAG-1,2 endonuclease-mediated V(D)J somatic recombination, as it occurs in the immune system ^[20][21][23,24]. In the brain, DSBs can also be formed by specific mechanisms, such as retrotransposon mobilization (e.g., LINE-1 transposition in neural progenitors and mature neurons ^[22][23][25,26]) and RNA retroinsertion, as in somatic APP gene recombination ^[24][27]. Specific DSB generation mediated by endonucleases to control gene expression, as described for DNA topoisomerase II β (TOP2β) and Spo11 in the promotors of neuronal activity-induced genes ^[25][26][27][28,29,30], have also been shown.

DSBs constitute a potentially serious threat to cell survival and, therefore, must be properly repaired. DSBs are repaired by either homologous recombination or nonhomologous end-joining (NHEJ). NHEJ involves the direct ligation of the two DNA ends that frequently alter the original DNA sequence. A defective DNA damage response severely impacts nervous system development ^[28][31], and alterations in factors involved in the DSB response have been implicated in a range of diverse human syndromes, including neuropathology and neurodegeneration (e.g., ataxia telangiectasia) ^[29][30][31][32,33,34]. The importance of DSBs and their consequences for neurons are clearly evidenced by the phenotype of mice carrying DNA repair mutations. These mice present a marked, and in some cases lethal, embryonic phenotype, characterized by a high level of neuronal cell death, impaired development, and even acellularity in the central nervous system ^[15][32][15,35]. Indeed, mouse models with NHEJ mutations (e.g., XRCC4 and DNA lig IV) display a dramatic neural phenotype, in some cases with embryonic lethality ^[33][34][36,37], and severe immunodeficiency, although the remaining organs and tissues are largely unaffected, suggesting an important role of NHEJ in neural development.

Together, the neurogenic process provides an environment permissive to DSB generation and subsequent genetic alterations. The specificity of these neural DNA alterations is supported by the observation that genetic changes emerge specifically during in vitro stem cell differentiation towards neural lineage [3] but are completely absent during differentiation towards fibroblasts. This accumulation of DSBs during neural development suggests that neurons possess mechanisms to cope with DSBs, which may even have a particular function or be generated as a side-effect of another, as-yet-unknown process.

3. DSBs and Early Neural Cell Death

Several studies have shown that the number of neurons with somatic mutations decreases after development; both the number of CNVs per neuron [3] and the number of aneuploid neurons ^[35][36][37][67,68,69] are lower in the newborn and young adult brain than during embryonic development [9]. These observations suggest the involvement of cell death processes, which may selectively target non-viable mutations in a manner analogous to apoptosis following V(D)J recombination ^[38][70]. In fact, many authors, ourselves included, have shown that neural precursors and newborn neurons actually undergo a specific wave of apoptosis during early embryonic development ^{[32][39][40][41][42]}[35,71,72,73,74]. Although the purpose of this early wave of neuronal cell death has not been clearly established, the findings in mutant models that lack apoptosis genes have underscored its importance. The dysregulation of cell death in this context specifically impairs proper CNS generation, affecting neural precursor cell proliferation and early neuronal differentiation ^[15][39][43][15,71,75]. Specifically, the dysregulation of cell death results in neural malformations including cerebral hyperplasia, exencephaly, and neural tube defects, as well as defective retinal structure and visual system connectivity ^{[15][32][39][44][45][46]}[15,35,71,76,77,78]. Early neuronal cell death in the mouse retina parallels the onset of DSB generation (Figure 2), and that apoptosis occurs during a specific time window ^[47][48]. In the developing chicken retina, the onset of cell death is carefully programmed and intrinsically determined, specifically the death of newborn neurons is determined, in a cell-autonomous manner, by the time the neuron is generated and it is independent of the niche in which it was situated ^[48][49][79,80].