Cell-specific replication timing regimes correlate with cell-specific histone enrichment. (A) For GSC-like cells, the log₂FE values for H3K4me3, H3K27me3, and H3K9me3 are shown for genomic locations ordered from early to late by their replication timing value. The expression level for genes (categorized and colored by their CPM group as in Fig. 3) is also shown, indicating genes with the highest expression are replicated earlier in S phase. (B) The log₂FE values for H3K4me3, H3K27me3, and H3K9me3 are shown for CySC-like cells within genomic locations ordered by their replication timing (from early to late). Gene expression level (categorized and colored by CPM group) is also shown, indicating genes with the highest expression are replicated earlier in S phase. (C) The enrichment levels of H3K27me3 are plotted according to replication timing for the GSC-like, CySC-like, Kc167, and S2 cells, demonstrating increased H3K27me3 enrichment at regions that replicate early in CySC-like cells compared with the other three cell types. (D) Percentage of chromatin within in each indicated chromosomal domain was calculated and categorized as enriched in either GSC-like or CySC-like cells. Cell-specific enriched regions are considered as having log₂FE values >0.2 in one cell type and <−0.2 in the other. (E–H) Box and whisker plots of log₂FE for histone modifications in GSC-like (green) and CySC-like (magenta) cells on the indicated chromosomes. The values here are a subset of enrichment scores found in genomic regions that replicate earlier in the indicated cell type. (PC) Pericentromeric region, (*) statistical significance as measured by a paired sample t-test (Supplemental Table S5).