Copy number variants are produced in response to low-dose ionizing radiation in cultured cells

Despite their importance to human genetic variation and disease, little is known about the molecular mechanisms and environmental risk factors that impact copy number variant (CNV) formation. While it is clear that replication stress can lead to de novo CNVs, for example, following treatment of cultured mammalian cells with aphidicolin (APH) and hydroxyurea (HU), the effect of different types of mutagens on CNV induction is unknown. Here we report that ionizing radiation (IR) in the range of 1.5-3.0 Gy effectively induces de novo CNV mutations in cultured normal human fibroblasts. These IR-induced CNVs are found throughout the genome, with the same hotspot regions seen after APH- and HU-induced replication stress. IR produces duplications at a higher frequency relative to deletions than do APH and HU. At most hotspots, these duplications are physically shifted from the regions typically deleted after APH or HU, suggesting different pathways involved in their formation. CNV breakpoint junctions from irradiated samples are characterized by microhomology, blunt ends, and insertions like those seen in spontaneous and APH/HU-induced CNVs and most nonrecurrent CNVs in vivo. The similarity to APH/HU-induced CNVs suggests that low-dose IR induces CNVs through a replication-dependent mechanism, as opposed to replication-independent repair of DSBs. Consistent with this mechanism, a lower yield of CNVs was observed when cells were held for 48 hr before replating after irradiation. These results predict that any environmental DNA damaging agent that impairs replication is capable of creating CNVs.