Fig. 3

DDAF peaks at replication origins and termination zones in S. cerevisiae. a A DDAF heatmap in 50 bp bins for one kilobase on either side of 289 replication origins (green bars in Figs. 1d and S2). Origin motifs (ACS motifs) on the plus (top) strand are grouped as “plus strand ACS” and minus (bottom) strand oriented origins are gouped as “minus strand ACS”. Origins are ranked by efficiency. Blue indicates a high DDAF value (less Pol ε usage), red denotes the opposite. b Averaged DDAF value at inefficient origins (efficiency < 0.5). Orange curves are for plus strand origins and purple curves are for minus strand origins. The number of origins used is indicated. c Averaged DDAF value at efficient origins (efficiency > 0.9). d DDAF peak areas (after baseline subtraction) increase linearly with origin efficiency (R² = 0.986). The negative value at origin efficiency of zero is due to aggressive background subtraction (see the “Methods” section). e As per a but in 1000 bp bins for 20 kb on either side of predicted collision points (red bars in Figs. 1d and S2) for forks proceeding from 259 well-separated adjacent origins (distance ≥ 20 kb). The heatmap is ranked by the efficiency of the lesser ones of the pairs of adjacent origins. On average, origin pairs with a lesser member of both f moderate and g high efficiency have broad DDAF peaks centered at predicted termination zones, both if the data is truncated at the member origins (orange curves; heatmap in Fig. S4) or not (brown dotted curves). h The areas under truncated curves are independent of flanking origin efficiency. Slight negative areas for some inefficient origins suggest that true baselines are somewhat lower