Fig. 7: Loss of NDX is associated with increased rather than decreased R-loop levels.

a Pile up plots showing DRIP signal intensities over the identified peaks in Col-0 and ndx1–4 plants. RNase H-treated samples are also shown. Color scale corresponds to RPGC (reads per genomic content) values. b Statistical evaluation of DRIP peak intensities in Col-0 and ndx1–4 plants. AUC (area under curve) values were calculated for each peak and their distributions were compared. AUCs, which are proportional to DRIP peak intensities, were significantly higher in the ndx1–4 mutant (p < 0.0001, Mann–Whitney U test, two-sided). Bounds of boxes describe the interquartile range with the median; whiskers indicate minimum and maximum values; outliers are not shown. Sample size n = 15,049 peaks identified in Col-0 and ndx1–4 plants. c Detection of RNA-DNA hybrids in Col-0 and ndx1–4 plants using slot blot hybridization. 200 ng, 100 ng, and 50 ng of gDNA were slotted onto a nitrocellulose membrane with and without RNase H-treatment, stained with S9.6 antibody and goat anti-mouse-HRP secondary antibody. Equal loading was determined by methylene blue staining. d Band intensities were quantified by ImageJ (average values are shown). Error bars: SD. Statistics: Student’s t test, two-sided. Sample size n = 3 biologically independent replicates. e, f Genome browser tracks and DRIP-qPCR validation of DRIP peaks identified in Col-0 (red) and ndx1–4 (blue) samples. Error bar: SEM. Sample size n = 2 biologically independent experiments.