Fig. 5: DDR at ALT telomeres induced by FANCM deficiency is mediated by XPF.

a Representative images of TRF2 and XPF co-immunostaining in U2OS cells transfected with FANCM siRNAs for 3 days. Arrows indicate the colocalization events. b Quantification of colocalization events in (a). The number of XPF-TRF2 colocalization per nucleus (left). The intensity of XPF foci that are colocalized with TRF2 (right). P-values by two-sided Mann-Whitney test. Bars, mean ± SEM. n, cell number (left) or number of XPF foci (right). Data of three independent experiments. c DRIP-qPCR to detect telomeric R-loops in U2OS cells after transfection with control, XPF, or FANCM siRNAs for 3 days. Relative R-loop levels were normalized to the same amount of genomic DNA treated with RNase H prior to DRIP. P-values by two tailed Student’s t-test. Bars, mean ± SD. Representative of three independent experiments. Other replicates show similar trends and are provided in the Source Data file. d Quantification of APBs in U2OS cells transfected with siRNAs. APB foci were determined by large TRF2 foci with PML staining shown in Supplementary Fig. 5d. n, cell number. Bars, mean ± SEM. P-values by two-sided Mann-Whitney test. Data of three independent experiments. e Representative images of immuno-DNA FISH to detect the co-localization of γH2AX and telomeres in U2OS cells after transfection with control, XPF, or FANCM siRNAs for 3 days. Arrows indicate the colocalization events. f Quantification of γH2AX foci at telomeres in (e). n, cell number. Bars, mean ± SEM. P-values by two-sided Mann-Whitney test. Data of two independent experiments. g Quantification of top 5% telomere intensity foci in (e). n, cell number. Bars, medians. P-values by two-sided Mann-Whitney test. Representative of three independent experiments. Other replicates show similar trends and are provided in the Source Data file. a–g Mean or median values of each group shown on the top of figures.