Figure 2

Decreased H3K4me3 at regulated promoters mildly affects transcriptional output. (A) Heatmap comparing gene expression changes (as log2 fold change) induced by doxorubicin treatment in WT and Cfp1^-/- ES cells as determined by RNA-Seq. (B) Dot plot comparing gene expression differences in WT and Cfp1^-/- ES cells. Genes were sorted on the basis of their log2 fold change upon doxorubicin treatment in WT ES cells (most upregulated gene on the far left, most downregulated gene on the far right). The log2 fold changes (untreated (untr) versus doxorubicin treatment (Doxo)) are plotted for WT (blue) and Cfp1^-/- ES cells (red). (C) Genome browser screenshots representing RNA-Seq signal (as normalized read count) in WT ES cells (untreated in blue, treated in black) and Cfp1^-/- (untreated in pink, treated in red) ES cells at the Cdkn1a locus. (D) Same as (C) for the Nanog locus. (E) Absolute quantification of Cdkn1a and Mdm2 mRNA levels in WT (untreated in blue, doxorubicin-treated in black) and Cfp1^-/- ES cells (untreated in pink, doxorubicin-treated in red) by RT-qPCR. Expression levels are normalized using an RNA spike-in standard (ERCC-00074) and then expressed as fold induction compared with the untreated value. The ERCC-00130 standard is shown as control. Data are represented as mean ± standard deviation, n = 4. P-values were calculated using two-tailed Student’s t-tests: *P < 0.05, **P < 0.01; P > 0.05 is not significant (ns). (F) Same as (E) for Nanog, Sox2, Pou5f1, Gapdh, and Actb mRNA levels. Lmna and ERCC-00096 are shown as controls.