Genome-Wide H3K9m2 Profiling Figure 7. H3K9m2 of various repeat elements in the Arabidopsis genome. (a) Percent of H3K9m2 methylated (purple) and unmethylated repeats (white). The majority of unmethylated repeats are present in euchromatic arms (green), while the majority of methylated repeats are located in pericentromeric regions (red). (b) Average H3K9m2 levels across tandem, inverted and interspersed repeats present in different genome compartments. All three kinds of repeats are more frequently methylated and have higher average H3K9m2 levels when they reside in pericentromeric regions. X axis represents the average H3K9m2 level (Z-score) for the element and Y axis represents the percentage of elements falling into each category. doi:10.1371/journal.pone.0003156.g007 TE buffer, without incubation and immunocomplexes were eluted with 500 ul of 0.1% SDS and 0.1 M NaHCO3 at 65uC for 10 min. DNA was then purified using conventional phenol- chlorophorm extraction and ethanol/salt precipitation. DNA amplification was performed using the GenomePlexH Whole Genome Amplification Kit (Sigma). Four amplification reactions were performed in parallel for each sample to minimize spurious amplification artifacts and purified using QlAquick spin columns (Qiagen) and the products were combined. 4–6 ug of DNA was obtained and Roche Nimblegen performed array hybridization, PLoS ONE | www.plosone.org 9 September 2008 | Volume 3 | Issue 9 | e3156