Fig. 1: SFPQ suppresses R-loop formation in repeat elements.

A C₀t-1 RNA-FISH performed in U-2 OS cells transiently transfected with indicated siRNAs (left panel). Quantification of focal C₀t-1 signal intensity (right, top panel) and number of C₀t-1 foci per nucleus (right bottom panel). B C₀t-1 RNA-FISH combined with anti-p-ATR (Thr1989) immunostaining performed in U-2 OS cells transiently transfected with indicated siRNAs. Images were obtained by super-resolution microscopy. Right panel, quantification of number of C₀t-1 foci co-localizing with p-ATR (Thr1989) per nucleus. C Combined immunofluorescence with anti-SFPQ and anti-CREST (centromere) antibodies in U-2 OS cells transfected with indicated siRNAs. Images were obtained by super-resolution microscopy. Right panel, quantification of co-localization events. D Representative images of combined immunofluorescence with anti-SFPQ and anti-TRF2 antibodies in U-2 OS cells transfected with indicated siRNAs. Images were obtained by super-resolution microscopy. Right panel, quantification of co-localization events. E Anti-SFPQ ChIP-qPCR analysis using control and RNaseH1 depleted U-2 OS cells. Indicated sequence categories were amplified using specific PCR primer pairs. F Quantitative DRIP-PCR analysis after siRNA mediated SFPQ knock-down in U-2 OS cells. RNaseH1, treatment of genomic DNA with recombinant RNaseH1 prior to DRIP. Indicated repeat regions were amplified using specific primers. Mean values are shown, error bars indicate standard deviation. N = number of independent experiments. n = number of analyzed nuclei. An unpaired, two-sided Student’s t test was used to calculate statistical significance; p-values are shown. Scale bar (1 μm) applies to all images in respective immunofluorescence panels. DNA was stained using DAPI (4’,6-diamidino-2-phenylindole). Arrowheads and zoomed images indicate co-localization events. Source data are provided with this paper.