Figure 5.

Old nucleosomes are recycled to the daughter chromatid that replicated first. (A) Box plot distributions of lagging/leading ChIP-NChAP ratios for H3, H3K36me3, H3K4me3, H3K56ac, and RNAPII from early (column 1) and mid-early S phase (column 2) for early genes from the same WT culture (biological replicate 1). The histograms in the header show the distribution of genome read densities for each NChAP (replicated DNA) fraction at indicated time points in S phase, as in Figure 2B. (Rows A and B) Genes have been sorted by decreasing lagging/leading ratios of H3K4me3 in early S phase (row A) and mid-early S phase (row B) (yellow background), and divided into seven bins (y-axis on the left), as in Figure 2B. Box plot distributions of lagging/leading ratios (x-axis) for the chromatin features indicated in the headers have been determined for each bin. Average lagging/leading H3K4me3 ratios in early S phase for each bin are shown on the y-axis on the left. The bar graphs on the left show the “same” gene enrichment for gene bins indicated in the y-axis of each row on the right. Column 3 shows box plot distributions for the difference in replication timing (ΔRT) between the lagging and the leading strand for each gene (RT for each gene is the median RT of all 50-bp segments in the CDS of any given gene, averaged from two replicate time courses in Supplemental Fig. S10) (left) and ΔDNA synthesis rate (average difference between lagging and leading DNA synthesis rates for each gene in the bin) (right). Synthesis rates were calculated as in Supplemental Figure S11 using replication timing from Supplemental Figure S10 and ROADs (replication origin-associated domains) determined from NChAP fractions of the 20- and 25-min time points of two biological replicates (replicate 1 from Fig. 5A and replicate 2 from Supplemental Fig. S7A). (B) Average TSS (transcription start site)-centered metagene profiles of ChIP-NChAP fractions indicated in the header, from WT cells (replicate 1) from gene bins from A sorted according to the average log₂ (lagging/leading) ratios for H3K4me3 in early S phase. Only the two bottom (bins 1–2) and top (bins 6–7) bins are shown. The value of the average ratio for each bin is indicated in the blue strip on the left. (C) Distribution of the differences in replication timing between sister gene copies (ΔRT, lagging-leading and leading-lagging) in WT cells for all early and mid-early genes. The yellow surface shows 95% of early and mid-early genes whose ΔRT is between 0.5 and 6.5 min. “avgΔRT = 2.4 min” is the average of the 95% of the gene population represented under the yellow surface (n = 0.95 × 2548 = 2421). (D) As in C, for mid-late and late genes with RT ≥ 55 min. (E) Cumulative distribution of differences in replication timing between the lagging and the leading sister gene copy (ΔRT) for the top bin 7 (orange) and bottom bin 1 (blue) from field A3 (ordered by H3K4me3 log₂[lagging/leading] in early S phase, left panel) and field B3 (ordered by H3K4me3 log₂[lagging/leading] in mid-early S phase, right panel).