Accumulation of transcription-dependent DNA–RNA hybrids and dsRNA in mitochondria of HeLa and U2OS cells depleted of SUV3 and PNPase. (A) IF of DNA–RNA hybrids using the S9.6 antibody and (B) dsRNA using the J2 antibody in HeLa cells transfected with siC (control), siSUV3, and siPNPT1. Mitochondria are stained with MitoTracker. (C) IF with MitoTracker and S9.6 and J2 antibodies in siC, siSUV3, and siPNPT1 in U2OS cells. (D) Effect of transcription-blocking agents in the formation of S9.6 granules in HeLa cells seen by IF. Cells were treated with 50 ng/mL EtBr for 5 h or 100 μM cordycepin for 2 h before fixation. Nuclei were stained with DAPI. (Scale bar, 10 μm.) (E) Box plots represent the median and quartile levels of total S9.6 granules per cell or (F) granule intensity obtained from three independent experiments. ****P < 0.0001; *P < 0.05 according to Mann–Whitney U test. AU, arbitrary units.