Genome-Wide H3K9m2 Profiling Figure 2. Correlation of H3K9m2 methylation with CHG DNA methylation. (a) Average DNA methylation levels genome wide (purple), in H3K9m2 positive regions (Z score.1, green) and in H3K9m2 negative regions (Z-score,0, orange). (b) Percent of CG, CHG and CHH methylation falling within H3K9m2 positive regions. (c) Correlation of the percentage of CHG methylation at individual sites throughout the genome with H3K9m2 levels. The x-axis is divided onto 10 individual bins that represent deciles of the percentage of CHG methylation of all CHG sites in the genome. Purple bars represent the percentage of CHG sites that fall with each methylation decile (right logarithmic axis), and orange line represents the average H3K9m2 level (Z-score) (left axis). doi:10.1371/journal.pone.0003156.g002 may be regulated differently in these two compartments of the Arabidopsis genome. One possibility is that pericentromeric heterochromatin may utilize a mechanism not used in chromo- some arms that allows for the spreading of H3K9m2 to fill large domains and to target higher levels of H3K9m2. For instance, it has been proposed that pericentromeric heterochromatin may PLoS ONE | www.plosone.org 4 September 2008 | Volume 3 | Issue 9 | e3156