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. 2022 Feb;32(2):337–356. doi: 10.1101/gr.275387.121

Figure 4.

Figure 4.

RNAPII is distributed asymmetrically in the absence of H3K56ac in rtt109Δ cells. (A) Heat map of median RNAPII occupancies in coding regions of yeast genes not regulated by the cell cycle, as in Figure 2A. (Columns, from left) Early-mid S phase after release from G1 arrest in rtt109Δ (early S phase [rep.1] and early-mid S phase [rep. 2]) and WT (10% unreplicated, from Fig. 2B), from total RNAPII (ChIP), replicated RNAPII (ChIP-NChAP), and replicated DNA (NChAP) fractions. Even though both rtt109Δ time points have 10% of their genome still unreplicated, replicate1 is at an earlier stage of genome replication than replicate 2 because a greater number of genes have been replicated in more cells in replicate 2 than in replicate 1 (mid-early genes are more “red” and “yellow” in the NChAP fraction of replicate 2 compared with replicate 1; also compare the distributions of percentage replicated genome fractions between replicate 1 and 2 in B). (B) Box plot distributions of replicated RNAPII lagging/leading ratios from early S phase (WT) to early-mid S phase (WT and rtt109Δ, columns 1–4) for early (rows A–C) and mid-early genes (rows D–F). (Header) Distribution of genome read densities as in Figure 2B. (Rows A and D) Genes have been sorted by increasing lagging/leading RNAPII occupancy in early S phase (WT, Fig. 2B) and divided into seven bins, as in Figure 2B (y-axis), and box plot distributions of replicated RNAPII lagging/leading ratios (x-axis) have been determined for each bin at indicated time points. (Rows B, E and C, F) As rows A and C except that genes have been ordered by increasing lagging/leading RNAPII ratios from rtt109Δ (early S phase, replicate 1) or early-mid S phase (WT) (Fig. 2B), respectively. The bar graphs on the left show “same” gene enrichments calculated as in Figure 2B for gene bins indicated in the y-axis of each row on the right. The RNAPII distribution pattern between leading and lagging strand gene copies in rtt109Δ cells from replicate 2 (fields C3 and F3) correlates with WT (fields C4 and F4), indicating that the asymmetric distribution of RNAPII on replicated DNA is independent of the distribution of H3K56ac.