Association of replication origins with ORC1 (in HeLa cells) and with G-quadruplex motifs (in K562 cells).

<p>A: ORC1-chIP signal with respect to the number of reads in detected origins in HeLa cells (on a log scale). ORC1-chIP signal (y-axis) corresponds to the log-ratio of the number of reads in ORC1 peaks between the IP and the Input data. B: Percentage of replication origins (K562) associated with G-quadruplexes with a loop size of 1-07 according to the association with CGIs and timing categories (from early to late origins, as explained in the Methods Section). Notation G₄1-07 in the figures corresponds to G-quadruplex motifs with loop sizes shorter than 7 nucleotides (G₄N_1–7G₄N_1–7G₄N_1–7G₄). Black lines correspond to the expected percentage association of random segments with G-quadruplexes, and stars correspond to exceptional enrichment, with . C: Impact of the density of G-quadruplexes of given loop sizes on the efficiency of replication origins. G-quadruplex motifs are detected with Quadparser <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004282#pgen.1004282-Huppert1" target="_blank">[43]</a>, and origins are considered associated with a G-quadruplex if they overlap any G-quadruplex motif of a given loop size (from 7 to 30). Origin efficiency is defined as the of the number of reads within the origin interval divided by the length of the origin. D: Percentage of CGIs associated with a G-quadruplex of loop size 1-07 or 1-15, according to the association of CGIs with constitutive replication origins, or with no replication origin (CGIs-nonOri are CGIs that are not associated with replication origins in any of the 5 cell lines investigated).