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. 2022 Jan 13;119(3):e2115570119. doi: 10.1073/pnas.2115570119

Fig. 4.

Fig. 4.

Distinct mechanisms of atxr5/6 (W) suppression. (A) Boxplot of average expression of TEs up-regulated in atxr5/6 (W) cotyledons for the indicated mutants and replicates. Center lines indicate the median, upper and lower bounds represent the 75th and 25th percentiles, respectively, whiskers indicate the minimum and the maximum, and outliers are not plotted. (B) Overlap between significantly (log2 fold change ≥ 1, false discovery rate ≤ 0.05) up-regulated and down-regulated genes for each mutant vs. wild type in cotyledons. (C) Bar chart of RNA-seq FPKM values for ATXR6 expression in wild-type, atxr5/6 (W), stubl2-3 atxr5/6 (W), mbd9-3 atxr5/6 (W), and sac3b-3 atxr5/6 (W) flowers. Bars represent mean and whiskers represent ±SE (SEM) from n = 3 biological replicates. (D) Immunofluorescence and quantification of chromocenter appearance in H3K27me1-stained leaf nuclei from wild type, atxr5/6 (W), stubl2-3 atxr5/6 (W), mbd9-3 atxr5/6 (W), and sac3b-3 atxr5/6 (W). (E) Genome-wide H3K27me1 ChIP-seq signal normalized by input for the indicated samples in leaves. Smoothed log2 ratio of normalized (RPM) ChIP-seq signal over 100-kb windows is shown. (F) Boxplot of log2(H3K27me1/input) ChIP-seq signal over TEs up-regulated in the atxr5/6 (W) mutant in leaves of the indicated genotypes.