Figure 6.—

ChIP assays using antibodies against histone H3, monomethylated H3K4, monomethylated H3K9, and acetylated H3K9/14. Solid bars and Shaded bars indicate relative amounts of the PCR fragments amplified from immunoprecipitated chromatins of strongly silenced RNAi-37 subclones and weakly silenced subclones, respectively. (A) The PCR-amplified regions of the inverted repeat silencer are indicated as horizontal bars under the illustration. Specific primers are listed in supplemental Table 6. (B) H3 occupancy levels normalized with respect to the input DNA level in the TOC1 LTR, the RPS3 promoter, the IR promoter, and the aadA IR regions were determined by immunoprecipitation with a modification-insensitive anti-histone H3 antibody. (C) H3K9me1 levels normalized with respect to histone H3 levels in the same regions were determined by immunoprecipitation with an anti-H3K9me1 antibody. (D) H3K4me1 levels normalized with respect to histone H3 levels in the same regions were determined by immunoprecipitation with an anti-H3K4me1 antibody. (E) Acetyl histone H3 levels normalized with respect to histone H3 levels in the same regions were determined by immunoprecipitation with an anti-acetyl histone H3 antibody.