Figure 3: Genome-wide colocalization of RepID with replication-initiation sites.

(a) A screenshot of a sample genomic region showing replication-initiation profiles (NS-Seq) and protein-binding (ChIP-Seq) data. Top track, below the RepSeq genes: nascent-strand patterns from cells with WT RepID (Replication: WT NS). Middle track: ChIP-Seq patterns in WT cells (RepID ChIP). Lowest track: nascent-strand patterns from cells depleted of RepID (Replication: RepID KO NS). The shaded region delineates a RepID-binding origin adjacent to an origin that does not bind RepID. An expanded screenshot of the same region is shown in Supplementary Fig. 4d. (b) The distribution of replication-initiation events in RepID KO cells (overall, 58,656 NS-Seq peaks) that colocalized with initiation events in WT cells, plotted as a function of the distance from the centre of WT origins (overall, 78,859 NS-Seq peaks). (c) A screenshot of a sample genomic region showing replication-initiation profiles as in a. The shaded region delineates a replication origin that binds RepID in WT cells and does not initiate replication in KO cells. An expanded screenshot of the same region is shown in Supplementary Fig. 4e. (d) The distribution of replication-initiation events in KO cells plotted as a function of the distance from the centre of origins that were bound by RepID in WT cells (14,716 NS-Seq peaks). (e) A screenshot of a sample genomic region showing replication-initiation profiles as in a. The shaded region delineates a replication origin that does not bind RepID in WT cells and initiates replication in both WT and KO cells. An expanded screenshot of the same region is shown in Supplementary Fig. 4f. (f) The distribution of replication-initiation events in KO cells along genomic regions flanking replication origins that initiated replication but did not bind RepID in WT cells (64,143 peaks). (g) Consensus sequence for RepID binding identified using a subset of RepID-bound regions. Consensus is aligned with a 12-bp motif, which matches the AG1 site. Data showing the abundance of the motif in RepID-bound regions or randomized files are presented in Supplementary Table 4.