Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation (original) (raw)
Figure 6
Relationship between Replication Timing and Histone Modifications
(A and B) Correlation between replication timing and H3K4me3 of RefSeq gene promoters. The graphical format is the same as in Figure 5C and 5D, except that the heights of bins represent the percentages of H3K4me3-positive genes within each bin. Logistic regression (inner line) and 95% confidence intervals (outer lines) reveal a clear correlation in both ESCs (A) and NPCs (B) (p < 2 × 10−16 by the Likelihood Ratio test). H3K4me3 data were based on Mikkelsen et al [51].
(C) Relationship between replication timing and histone modifications at the level of replication domains. Densities of different histone modifications (total intensity/domain size) based on a ChIP-Seq study [51] were calculated for all replication domains in a given state (ESC or NPC) and Pearson _R_2 values between replication timing and different histone modification densities were obtained.
(D) Comparison of replication timing and different histone modifications in four exemplary 5-Mb genomic regions in ESCs and NPCs.
(E) Box plots showing the distribution of replication-timing changes of “bivalently” modified genes (i.e., K4K27) in ESCs that change to four different modification state (K4K27, K27, K4, or none) in NPCs. Genes that remained “bivalent” showed a distribution similar to the three other classes. The _p_-values were obtained from a two-tailed _t_-test for comparison of two unpaired groups.