Replication-stress-induced chromatin loops protect fork stability

Cell culture, treatments and thymidine analogue incorporation Cell lines and culture MRC5 SV40-immortalized human fibroblasts and HCT116 human colorectal cancer cells were cultured in a 1:1 mixture of Dulbecco’s modified Eagle’s medium (DMEM) and Ham’s F10 (Invitrogen), supplemented with 10% FCS (Biowest) and 1% penicillin–streptomycin (Sigma-Aldrich) (Supplementary Table 6 ). Cells were maintained at 37 °C in a humidified incubator with 5% CO 2 . Human RPE1-hTERT TP53 −/− shBRCA2 cells were cultured in DMEM/Nutrient Mixture F-12 (Invitrogen) supplemented with 10% FCS and 1% penicillin–streptomycin at 37 °C and 5% CO 2 . U2OS (WT and TKO) cells were cultured in DMEM supplemented with 10% FCS and 1% penicillin–streptomycin under the same incubation conditions. HAP1 cells 25 were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% FCS and 1% penicillin–streptomycin. All cell lines used in this study were routinely tested for mycoplasma contamination and tested negative. Thymidine analogue incorporation For BrdU incorporation, asynchronously growing cells were incubated in their respective culture medium containing 100 µM BrdU for 20 or 40 min (Supplementary Table 7 ). Immediately after the BrdU pulse, cells were either fixed or subjected to replication stress by replacing the medium with fresh medium containing 1 mM or 4 mM HU. …