Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells
Figure 1
H3K9me2 covers large domains in pluripotent stem cells and derived neurons and is largely invariant between both states.
(A) H3K9me2 localization in ES cells and neurons at a representative chromosomal region. Bars above each track indicate H3K9me2 domains determined by HMM. The red boxes highlight two regions that lose and gain H3K9me2, respectively. (B) Pair-wise correlation of H3K9me2 signal among different samples and experiments. Biological replicates are indicated as 1 and 2. Pearson correlations of IP/Input ratios were calculated for 500 bp windows on chromosome 19 (white/yellow corresponds to higher correlations). (C) Quantification of genomic coverage of H3K9me2 in ES cells and neurons applying a two-state HMM (i.e. “high” or “low”). Shown is the percentage of chromosome 19 that is in an H3K9me2 “high” state (i.e. enriched for H3K9me2) in both biological replicates. The value was normalized to the total coverage of the tiled region on the array. (D) Western blot detection of H3K9me2 levels in ES cells and neurons (TN). (E) Venn diagram showing the overlap of H3K9me2 enriched regions between ES cells and neurons (TN).