Figure 1

Cfp1 is crucial for H3K4me3 deposition at promoters of genes regulated upon DNA damage. (A) Heatmap representing gene expression changes induced by doxorubicin treatment (P-value <0.05, fold change ≥ 2.5). Genes highlighted were identified in previous studies [33],[34]. Untr, untreated. (B) Genome browser screenshots representing RNA-Seq normalized read count in WT ES cells at the Cdkn1a locus. Positions for quantitative PCR (qPCR) primers used during the study are also represented. TSS, transcription start site. (C) Heatmap showing H3K4me3 normalized read count 3 kb upstream and downstream of the TSS of genes induced by doxorubicin in WT ES cells (n = 755). Unmethylated CpGs are represented by CAP-Seq enrichment in WT ES cells [28]. (D) ChIP-qPCR analysis of H3K4me3 enrichment at the Cdkn1a locus for untreated or doxorubicin-treated WT and Cfp1^-/- ES cells. Results are expressed as fold enrichment relative to input DNA and a control intergenic region on chromosome 15. Control corresponds to an intergenic region on chromosome 5. Gapdh and Actb promoters are also shown. Data are represented as mean ± standard deviation, n = 3. P-values were calculated using two-tailed Student’s t-tests: *P < 0.05, **P < 0.01; P > 0.05 is not significant (ns). (E) Same as (C) for Cfp1^-/- ES cells. (F) Genome browser screenshots representing H3K4me3 ChIP-Seq normalized read count in WT (untreated in blue, treated in black) and Cfp1^-/- (untreated in pink, treated in red) ES cells at the Cdkn1a locus. (G) Average profile showing H3K4me3 normalized read count at TSSs of genes induced by doxorubicin treatment in WT ES cells. Input DNA is shown as a control. Signal is displayed from -3 kb to +3 kb surrounding each annotated TSS. (H) Comparison of H3K4me3 normalized read density at TSSs of upregulated genes, from 3 kb upstream to 3 kb downstream. P-values were calculated using two-tailed unpaired Wilcoxon tests: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.