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. 2023 Jul 19;12:RP87714. doi: 10.7554/eLife.87714

Figure 4. Impact of expression on chromatin states over TE genes in ddm1.

(A) Enrichment profiles of H2A.W.6 and H2A.Z.9 over TE genes in ddm1. TE genes were grouped by expression in ddm1 mutant. Out of the 3901 TE genes in the Arabidopsis genome annotation, 497 were excluded because they showed expression in wild-type, 2116 TE genes showed no expression in ddm1 (non-expressed TE genes) while 1288 TE genes were expressed. Because many of these TE genes showed very low expression levels, we divided the expressed TEs into 4 quartiles (322 TE genes each) based on their expression values where the 1st quartile contains TE genes with the lowest expression and the 4th quartile contains TE genes with the highest expression. Given that the TE genes in 1st and 2nd quartile showed nominal expression values, we placed only TE genes in 3rd and 4th quartile (644 TE genes) in the category of expressed TEs. n represents the number of TE genes in each group. (B) Stacked bar plots of the proportion of states in wild-type (top panel) and in ddm1 (bottom panel) overlapping TE genes grouped by expression in ddm1. (C) Box plot showing the expression of TE genes overlapping the 16 concatenated model states in ddm1.

Figure 4.

Figure 4—figure supplement 1. Analyses of the parameters that could correlate with the chromatin states with TE expression in ddm1.

Figure 4—figure supplement 1.

Enrichment profiles of histone variants (A) and H3 modifications (B) plotted over groups of TE genes based on their expression in decreased in DNA methylation (ddm1) as defined in the legend for Figure 4A and Methods.
Figure 4—figure supplement 2. Analyses of the parameters that could correlate with the chromatin states with TE expression in decreased in DNA Methylation (ddm1).

Figure 4—figure supplement 2.

(A) Box plot showing the expression of the TE genes grouped by the state overlapping the TSS in ddm1. See also Figure 4C. (B) Box plot showing the TE gene length distributions across the five different TE gene expression groups. (C) Box plots showing state statistics for TE genes per expression group in ddm1 and wild-type (WT). ‘# state types’ (top) is the number of different kinds of states present over the TE genes. ‘# state changes’ (middle) is the number of times there is a transition from one state to another and the bottom shows the length of the states overlapping the TE genes. No trend can be seen across expression groups, whereas all TE genes tend to have a larger diversity of states, more frequent transitions between states and hence shorter stretches of each state.