Extended Data Fig. 4: Epistatic study between BRG1 and known R loop-preventing factors.
a, Depletion controls by WB in double-knockdown experiments. siRNAs and antibodies used are indicated (n = 2). b, Representative S9.6 IF in HeLa cells transfected with the indicated siRNAs combined either with siC (−) or siBRG1 (+) (n = 3; except for siC, siTHOC1, siTHOC1+siBRG1, siUAP56 and siUAP56+siBRG1 where n = 4). Scale bar, 5 μm. c, Representative γH2AX IF in HeLa cells treated as in (b) (n = 3; except for siC and siFANCD2 where n = 4). Scale bar, 10 μm. d, Quantification of nuclear S9.6 signal intensity through cell cycle in siTHOC1 single depletion and siTHOC1+siBRG1 double depleted HeLa cells. Data presented as box plot (n = 3). Scale bar, 10 μm. (Mann-Whitney U test, two-tailed). e, Quantification of nuclear S9.6 signal intensity through cell cycle in siUAP56 single depletion and siUAP56+siBRG1 double depleted HeLa cells. Data presented as box plot (n = 3). Scale bar, 10 μm. (Mann-Whitney U test, two-tailed). f, Representative RNAPII S2P+PCNA PLA example images in wild-type HeLa cells. Control PLAs are also shown (n = 1). Scale bar, 10 μm. g, Quantification of RNAPII S2P+PCNA PLA in control cells (siC) and BRG1-depleted cells (siBRG1) either transfected with an empty plasmid (−) or a plasmid allowing expression of a siRNA-resistant wild-type (WT) or catalytically dead (K785R) version of BRG1. Data presented as scatter plot (n = 3). Scale bar, 10 μm. (Mann-Whitney U test, two-tailed). h, Representative RNAPII S2P+PCNA PLA example images in HeLa cells treated as in (b) (n = 3; except for siC (n = 6) and siSETX (n = 4)). Scale bar, 10 μm. P-values are indicated. Other details as in Figs. 1 and 2.
