DNA Breaks Due to Replication Stress Limit the Developmental Potential of Human Preimplantation Embryos

Human cleavage stage embryos frequently acquire chromosomal aneuploidies during mitosis. We recently showed that double strand breaks (DSBs) introduced by Cas9 result in frequent chromosomal alterations. Here we show that spontaneous DSBs arise de novo during embryonic DNA replication and show as chromosomal breaks that occur primarily, in centromeric, and gene-poor areas, with the latter harboring long genes implicated in neurodevelopmental disorders, including CNTN5, IMMP2L, LRP1B, RYR2, CSMD1. While transcription-replication conflicts are not required for chromosome fragility, fragile, gene-poor regions contain long-traveling replication forks, and complete replication late in G2 phase, hours after most of the genome has been duplicated. Incomplete replication at these sites in both human and mouse zygotes, results in DSBs, whole and segmental chromosome errors, micronucleation, chromosome fragmentation and poor embryo quality. Thus, failure to complete DNA replication is a mechanism of developmental failure, and a source of detrimental genetic alterations in humans.