Extended Data Fig. 8: Cohesin represses dormant origin firing in the middle of chromatin loops.
From: Cohesin maintains replication timing to suppress DNA damage on cancer genes
a Model of loop formation. b Top: CTCF degron system in K562 cells. Bottom: Western blotting of the CTCF-mAC K562 cell line (clone 5C9). Two independent replicates. c Violin plots showing distances between ERIZ centers and the nearest loop anchor in K562 cells. P-values from two-sided Mann–Whitney test are labeled on top. Red lines and numbers indicate median distances. d Distributions of distances between the neighbor loop anchor to the center of ERIZs in mES cells. Loop list of mES cells were from GSE8082065. Anchors and adjacent 100-kb regions within each loop are aligned at the center of anchors with loop regions on the right. ERIZs outside loops were excluded for analysis. Dashed lines and numbers mark median distances. e Violin plots for statistics of the distances between ERIZ centers and the nearest loop anchor in mES cells. P-values from the two-sided Mann–Whitney test are labeled on the top. Red lines and numbers indicate the median. f Knockout strategy (left) and PCR validation (right) indicating the CBE heterozygous knockout cell line. Two independent replicates. g Number of PEM-seq-captured translocations within or out of new ERIZ regions. New, new ERIZs; Ctrl., random genomic regions locate outside of ERIZs but harboring equal widths to new ERIZ regions. Mean ± SD, three biological replicates; two-sided paired t-test; *, p < 0.05; ***, p < 0.001. h Distribution of MCM5 ChIP-seq signals in the treatment (blue) or control (black) of α-amanitin within loop domains. The fold-change of MCM5 is defined as the ratio of ChIP-ed over input signals and normalized to z-scores. P-value is calculated by the two-sided Kolmogorov-Smirnov test. i Working model of cohesin-mediated loop extrusion in preserving early replication initiation near loop anchors. Distribution of MCM double hexamers undergoes regulation mediated by cohesin-driven loop extrusion, transcription, and stalls at loop boundaries, resulting in early replication adjacent to loop boundaries. Loss of cohesin induces dormant origin firing away from loop boundaries in the early S phase and results in elevated DNA damage and cancer-related gene vulnerability.
