Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines
Figure 3
Analysis of chromatin marks along U-domains.
Over representation of open chromatin markers (Material and Methods) at replication timing U-domain borders relative to the corresponding genome-wide value. (A) Mean coverage by DNase I hypersensitive zones, as a function of the distance to the closest U-domain border in BG02 using DNase H1-hESC data (green, genome-wide mean value = 0.0073), K562 using DNase K562 data (red, genome-wide mean value = 0.0138), GM06990 using DNase GM06990 data (blue, genome-wide mean value = 0.0107). (B) Proportion of clones presenting a ratio of “open” over input chromatin greater than 1.5 versus the distance to the closest U-domain border in GM06990 for four U-domain size categories: L0.8 Mb, 0.8 Mb
L
1.2 Mb, 1.2 Mb
L
1.8 Mb and 1.8 Mb
L
3 Mb from light to dark blue curves (genome-wide mean value = 0.20). (C) Mean coverage by 1 kb-enlarged CpG islands as a function of the distance to the closest U-domain border in BG02 for the four U-domain size categories defined in (B) from light to dark green curves (genome-wide mean value = 0.0254). (D) Mean coverage by Pol II peaks as a function of the distance to the closest U-domain border in BG02 (green: Pol II in H1 ESC, genome-wide mean value = 0.0026), K562 (red: Pol II in K562, genome-wide mean value = 0.0024), GM06990 (blue: Pol II in GM12878, genome-wide mean value = 0.0097).