Figure 1. Acetylation profiles over time.

A Histone acetylation profiles of Pou5f1/Oct4 and Klf4 before Nanog-knockdown (day 0) and on days 1, 3, and 5 afterwards. All plots are centered at the transcription start site (TSS; red dashed line). The gray area shows the background signal, circles indicate replicate measurements, dots averages. The blue heatmap underneath each plot shows quantitative data averaged over 5 kb intervals to make it comparable between genes with different numbers and positions of probes. B To test for evidence of location changes, we counted probes as ‘acetylated’ if they were above the noise (gray area in panel A). The smoothed scatterplot shows for each gene the percentages of probes staying acetylated (x-axis) or un-acetylated (y-axis) over time. The mass of the distribution lies in the upper right corner indicating high stability of acetylation islands. This is independent of particular gene sets of days as the inlay exemplifies by plotting only the changes between day 3 and 5 for genes differential on day 5. C We defined a peak in the acetylation profile as the smallest region covering 30% of the total signal. Peaks stay very stable over time. The plot shows that for example between days 3 and 5 ca. 70% of peaks are at exactly the same position and for almost 80% of peaks the location on day 5 overlapped the location on day 3 completely. If we allow one mismatch between peak locations the numbers go up to 80% and 95% respectively.