Figure 6. H3K27me3 Modifies Large Domains in MEF Cells.

(A) ChIP-PCR showing the distribution of H3K27me3, H3K9me2, and H3K9me3 in a 13 kb and 19 kb region containing the Slc22a2 (primer pairs 25–36) and Slc22a3 (primer pairs 37–48) promoters on the maternal and paternal allele in MEFB1 and MEFF cells. Details as in Figure 2A. Slc22a2 and Slc22a3 are silent on both parental chromosomes in MEF cells (gray lollipops).

(B and C) NimbleGen mouse chromosome 17 tiling arrays with one 50-mer per 100 bp of single-copy sequence showing the distribution of H3K27me3 over 600 kb containing Igf2r on the maternal (MEFB1) and paternal (MEFF) chromosome and a 450 kb region containing nonimprinted genes in MEFF cells. A transcript profile prepared from hybridizing total cell RNA to the tiling array shows that only some of the genes in this 450 kb region are expressed. Expressed genes are marked by dotted boxes that show expression correlates with H3K27me3 depletion. Nonexpressed genes in this region are marked by widespread H3K27me3, which covers the entire transcription unit and intergenic regions. Bars indicate the log₂ signal ratio (ChIP/Input enrichment) of each oligonucleotide on the array. Ensembl genes (http://genome.ucsc.edu) are shown below each array.