GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE281nnn/GSE281921/primaryOK200Other Mus musculusHomo sapiensOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281921GEOGSEfalseSingle-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes [BrdU-IP Repli-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.2026/07/13GSE281921GSM9344436GSM8632850GSM9344437GSM8632852GSM8632851GSM8632854GSM8632853GSM8632856GSM8632855GSM8632858GSM8632857GSM86328592079521273281921 Mus musculusHomo sapiens