GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE281nnn/GSE281920/primaryOK200Other Mus musculusHomo sapiensOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281920GEOGSEfalseSingle-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes [scRepli-seq]Common fragile sites (CFSs) are genomic regions susceptible to chromosome breaks. However, because they were identified using cell populations, low-frequency fragile sites (non-CFSs) could have been overlooked. Here we perform single-cell genome-wide mapping and classification of aphidicolin-induced chromosome breaks. In human osteosarcoma cells, 42% of breaks exhibit features of CFSs. The remaining 58% are non-CFSs that are ‘rare’ and replicate throughout the S-phase. Among non-CFSs, we identify early-S replicating breaks associated with transcription-replication conflicts, as well as two additional break classes. One is dependent on transcription and coincides with early-to-late-S replication timing (RT) transition regions, while another class exhibits late-S RT with its frequency increasing upon transcription inhibition. Intriguingly, we find that distinct RT landscapes are associated with aphidicolin-induced RT behavior and break classes. Our data reveal the frequencies, RT landscapes, and mechanistic differences among distinct break classes, providing a comprehensive view of genomic regions prone to breakage under replication stress.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 Mus musculusHomo sapiens