Early replication is associated with actively transcribed genes and active enhancers. (A) Replication timing of transcription start sites (TSSs) versus all genomic regions (Genome). (B) Replication timing of genes in three expression level bins: not detectable (0 FPKM), low (1–10 FPKM), and moderate-to-high (>10 FPKM): (FPKM) fragments per kilobase of transcript per million mapped reads (Pauli et al. 2012). (C) Replication timing of H3K4me3+ and H3K4me3− TSSs (Aday et al. 2011). (D) Actively transcribed genes (H3K36me3 marked) replicate significantly earlier with increasing H3K36me3 (Vastenhouw et al. 2010). (E) All genomic regions marked by H3K4me3, H3K4me1, and H3K27ac peaks replicate early, and enhancers defined by either PDREs or DMRs replicate even earlier (Bogdanović et al. 2012; Lee et al. 2015). t-test with Bonferroni corrected P-values: (*) P < 10−8; (#) P < 10−8 compared to H3K4me3, H3K4me1, and H3K27ac peaks. Box plots show the median (line), 95% confidence interval (notch), 25th–75th percentile (box), and 10th–90th percentile (whiskers).
