Genetic Rearrangements Modify Nearby Chromatin Figure 4. Sequence rearrangements change chromatin features. (A) Methylation analysis in three week-old seedlings of the cis-mutants. Genomic DNA was treated with HpaII not cutting mCmCGG, blotted and hybridized to a probe spanning the P1 promoter and the HPT gene. (B,C) DNA methylation in sequence-specific context (black: total mC, red: mCG, blue: mCHG, green: mCHH) at promoter P1 in the cis-mutants analyzed by bisulfite sequencing. Methylation at individual sites (B), summary of methylation across P1 (C). (D,E) Analysis of histone H3 at promoter P1 (amplicon 133 bp) and the HPT gene (amplicon 137 bp; primers see Table S4) in selected cis-mutants by chromatin immunoprecipitation. (D) Association with H3K4me3 and H3K9me2; nd: not detectable; (E) modification-independent precipitation. Inactive (S) and active (R) epiallele, resistant cis-mutants derived from line S (RD1-6). doi:10.1371/journal.pgen.1002331.g004 active and the silenced version to be authentic epialleles. Their occurrence in Arabidopsis, the best studied model for epigenetic research in plants, and the easy assay for the selectable hygromycin resistance conferred by the active state, made this pair of epialleles convenient tools for studying maintenance and switching of epigenetic states. PLoS Genetics | www.plosgenetics.org 7 October 2011 | Volume 7 | Issue 10 | e1002331