Figure 2. Origin recognition complex/minichromosome maintenance complex (ORC/MCM) enrichment within ascending segments (ASs) depends on active transcription.

(a) Top panel: example of an replication fork direction (RFD) profile on chr1: 178,400,000–182,800,000, covering 4 Mb. Detected ASs are labeled by green rectangles (irrespective of length and RFD shift). Middle and bottom panels: representative Mcm3 (blue) and Orc2 (red) chromatin immunoprecipitation followed by sequencing (ChIP-seq) profiles after binning for the same region. (b–e) Average input-normalized relative ChIP read frequencies of Orc2, Orc3, Mcm3, and Mcm7 at AS borders of (b) all AS (L > 20 kb and ΔRFD >0.5; n = 2957), (c) type 1 ASs with transcribed genes at both AS borders (n = 673), (d) type 2 ASs oriented with their AS border associated to transcribed genes at the right (n = 1026), and (e) non-genic ASs in gene-deprived regions (n = 506). The mean of ORC and MCM relative read frequencies is shown ±2 × SEM (lighter shadows). The dashed grey horizontal line indicates relative read frequency 1.0 for reference. For type 1 and 2 ASs, yellow bars mark the AS borders associated to transcribed genes. Refer to Figure 2—figure supplement 2 for analysis without input division.

Figure 2—figure supplement 1. Characterization of different ascending segment (AS) types.

(a) Average replication fork direction profiles (±2 × SEM; lighter shadows) for different AS types (Table 1) aligned at AS borders. (b) Replication timing ratio log₂(Early/Late) was assigned to type 1, type 2, and non-genic AS and represented as boxplot. Each boxplot represents the mean (circle), median (thick line), first and third quartile (box), and first and ninth decile (whiskers) of the relative read frequencies, without representing outliers. Statistics were performed by one-way ANOVA followed by Tukey’s post-hoc test. ***p<0.001.

Figure 2—figure supplement 2. Origin recognition complex/minichromosome maintenance complex (ORC/MCM) enrichments within ascending segments (ASs) without input normalization.

(a–d) Average chromatin immunoprecipitation-normalized read frequencies of Orc2, Orc3, Mcm3, Mcm7, and input at AS borders of (a) all ASs (n = 2957), (b) type 1 ASs with transcribed genes at both ASs borders (n = 673), (c) type 2 ASs with transcribed genes oriented at their right ASs border (n = 1026), and (d) non-genic ASs in gene-deprived regions (n = 506). The mean of normalized read frequencies is shown ±2 × SEM (lighter shadows). The dashed grey horizontal line indicates read frequency 1.0 for reference. Yellow bars mark the AS borders associated to transcribed genes.