Fig. 4: ChIP-seq assays of RAD51 and RPA1A show that unstable genomic DNA reshapes the distribution of HRR events in atxr5 atxr6 vs. Col-0.
a Venn graph shows the overlap between RAD51 and RPA1A enriched regions in host genomes. b Co-IP assay validated the interaction between RPA1A and RAD51 in planta. FM-FVE77 and Coomassie blue staining of blots serve as negative and loading controls, respectively. The experiments were repeated twice with similar results. c Peak reads distributions of RAD51 and RPA1A ChIP-seq in various locus categories in Col-0 and atxr5 atxr6. The y axis represents the percentage of reads mapped to loci of various categories. ncRNA and TEs represent non-coding RNA and transposable elements, respectively. d, e Distribution of normalized ChIP-signal of RAD51 and RPA1A (normalized with reads of the internal control mitochondrial DNA) and H3K27me1 (RPKM) from Col-0 and atxr5 atxr6 over different categories. H3K27me1 ChIP-seq data were mined from published data (GSE111814). f IGV files of normalized ChIP signals (RPKM) of H3K9me2, H3K27me1, RAD51, RPA1A, H3K27ac, and H3K4me3 on a 45 S rDNA locus on chr2. H3K9me2 and H3K27me1, H3K4me3, and H3K27Ac ChIP-seq data were mined from published data GSE111814, GSE166897, and GSE146126, respectively. Scales for the distinct loci are shown on the left as solid lines. g IGV files of normalized ChIP signals (RPKM) of H3K27me1, H3K9me2, RAD51, and RPA1A over selected loci. The bottom panel displayed the IGV files of normalized transcript levels (RPKM) on selected loci from RNA-seq. Scales for the distinct loci are shown on the left as solid lines. h Violin plot shows transcript expression changes from the loci with reduced and unchanged RAD51 ChIP signal in mock-treated atxr5 atxr6 vs Col-0. Horizontal lines in the bar plots display the 75th, 50th and 25th percentiles, respectively. Whiskers represent the minimum and maximum values. P value is calculated by unpaired two-tailed Welch’s approximate t-test. Source data are provided in the Source Data File.
