Figure 5

Decreased H3K4me3 and H3K9ac influence transcriptional accuracy upon induction. (A) Schematic representation of the qPCR strategy used to quantify various Cdkn1a mRNA splicing products. Total RNA is detected using primers on 3’ UTRs (shown in red). (B) RT-qPCR analysis of Cdkn1a splicing products. P-values were calculated using two-tailed Student’s t-tests: *P < 0.05, **P < 0.01, P > 0.05 is not significant (ns). (C) Average profile showing sense RNA-Seq normalized read count at TSSs of genes induced by doxorubicin treatment in WT ES cells (n = 755). Signal is displayed from -3 kb to +3 kb surrounding each annotated TSS. (D) Same as (C) for antisense RNA-Seq normalized read count (note that sense and antisense transcripts are plotted on a different scale). (E) Average profile showing sense RNA-Seq normalized read count at transcription end sites (TESs) of genes induced by doxorubicin treatment in WT ES cells (n = 755). Signal is displayed from -3 kb to +3 kb surrounding each annotated TES. (F) Same as (E) for antisense RNA-Seq normalized read count (note that sense and antisense transcripts are plotted on a different scale). (G) Comparison of sense or antisense RNA-Seq normalized read density at TSSs of upregulated genes (n = 755), from 3 kb upstream to 3 kb downstream, in WT or Cfp1^-/- ES cells, treated or not with doxorubicin as indicated. Box plots show the central 50% of the data (filled box), the median (central bisecting line) and 1.5× the interquartile range (whiskers). P-values were calculated using two-tailed unpaired Wilcoxon tests: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. (H) Same as (G) for TESs of upregulated genes (n = 755).