Figure 2
The hPTM dynamics of histone H3 and H4 during the conversion of primed to naive hESCs. (a) PCA of the differential histone peptidoforms used to calculate the RA of single hPTMs throughout the conversion. Differential histone peptidoform abundances cluster P0 markedly away from other time points in PC1. P6, P9 and P12 clusters overlap, implying that histones stabilize faster than the protein expression profile. Prediction ellipses are such that with a probability of 0.95, a new observation from the same group will fall inside the ellipse. See also Supplementary Table S3 for the normalized histone peptide abundanes. (b) A comprehensive map of the relative abundance (RA) of hPTMs (in the Y-axis) on 12 residues of histone H3 variants and 11 residues of histone H4 over 12 passages, i.e. a 37 day transition experiment from primed to naive hESCs. The X-axis representing the different passages (P0-P3-P6-P9-P12) was omitted for clarity. Individual RA measurements are depicted by dots and their averages over four biological replicates are connected by a line. Each graph represents a location and the coloured lines depict the different hPTMs that were quantified on that residue. hPTMs that are significantly changing over time, i.e. with an ANOVA P-value < 0.05, are depicted by dotted lines, while full lines are statistically stable. The RA of the unmodified peptides are not depicted, but simply accounted for by the remaining RA (adding up to 100%). (c) A zoom with scaled Y-axis for H31K27 and H33K27, to highlight the significant changes seen in the low RA region, i.e. <5% RA. See also Supplementary Table S4 for the pairwise P-values between all time points. (d) cH3K27: RA of the histone clipping event at H3K27 (depicted by the scissors icon in (b)).
