Fig. 8

Chromatin states of h2a.x DMRs. (a) Comparison of the chromatin states comprising each group of DMRs from Fig. 6a. Chromatin state distribution, and the total length they covered, within WT unique, WT-h2a.x shared, and h2a.x unique Endosperm-Embryo DMRs. States 1 to 7 correspond to euchromatin, and states 8 and 9 correspond to AT- and GC-rich heterochromatin, respectively. The chromatin states most increased (as a fraction of their total) in h2a.x embryo-endosperm DMRs are 4, 8 and 9. (b and c) Kernel density plots showing the fractional methylation difference for h2a.x mutant endosperm (EN) minus embryo (EM), plotted according to chromatin state, demonstrating that the largest shift to endosperm hypomethylation (i.e. to the left) lies in State 4 (yellow in b) and State 8 (green in c). (d) Ends analysis plot showing distribution frequency of DMRs with respect to coding genes. Genes were aligned at the 5’- or the 3’-end, and the proportion of genes with DMRs in each 100-bp interval is plotted. DMR distribution is shown with respect to all WT DMRs (orange trace), WT unique DMRs (red trace), all h2a.x DMRs (cyan trace), and h2a.x unique DMRs (blue trace). (e) Arabidopsis chromosome view of genome-wide methylation levels for h2a.x mutant DMRs between endosperm (EN) and embryo (EM), and WT DMRs between endosperm (EN) and embryo (EM), represented by the distribution frequency of DMRs along the 5 chromosomes. Dark blocks represent centromere and peri-centromeric regions of each chromosome. (f) IGV browser view of methylome data and DMR calls for H2A.X segregating wild-type endosperm and embryo (Green), h2a.x mutant endosperm and embryo (Red), as well as DMRs identified between dme-2 /wt endosperm (Black) [8]