Skip to main content
. Author manuscript; available in PMC: 2021 Aug 17.
Published in final edited form as: Nature. 2021 Feb 17;590(7847):660–665. doi: 10.1038/s41586-021-03193-z

Figure 4. DSBs trigger modifications of cohesin biology at a genome-wide scale and accentuated in damaged TADs.

Figure 4

(a) Boxplot showing the quantification of SCC1 recruitment on loop anchors before (grey) and after (red) DSB induction, within damaged (n=1456) or undamaged TADs (n=7804). Center line: median; Box limits: 1st and 3rd quartiles; Whiskers: Maximum and minimum without outliers; Points: outliers. P values are indicated (two-sided Wilcoxon test). The increased SCC1 enrichment on loop anchors following DSB is significantly higher in damaged TADs as compared to undamaged TADs (two-sided Wilcoxon test). (b) Genomics tracks showing the γH2AX ChIP-seq signal (50kb smoothed), SCC1 and phosphorylated SMC3 (pSMC3 S1083) ChIP-seq signal expressed as the log2 ratio (+DSB/-DSB) (20kb smoothed). (c) Model: Cohesin-mediated loop extrusion ensures γH2AX establishment on the entire damaged TAD. (i) Loop extrusion constantly occurs on the genome. (ii) The occurrence of a DSB creates a roadblock for cohesin-mediated loop extrusion leading to accumulation of cohesin at the site of damage. (iii) Cohesin blocked at DSB continues to mediate loop extrusion in a unidirectional manner (i.e. one-sided loop extrusion, arrows). ATM, recruited at the immediate vicinity of the break, phosphorylates H2AX-containing nucleosomes as they are extruded. Meanwhile, cohesin are also phosphorylated by ATM. (iv) The same process takes place on both sides of the DSB, leading to divergent one-sided loop extrusion at either side of the break ensuring a bidirectional spreading of γH2AX. (v) Loop extrusion triggers enlargement of γH2AX modified chromatin and halt at boundary elements such as CTCF-bound loci, that demarcate TAD borders. The speed of loop extrusion (measured in vitro as 0.5-2kb/s) ensures that the entire damaged TAD is phosphorylated in 10-30 minutes, giving rise to a DDR focus. NB: here the cohesin is shown as a ring encircling DNA for graphical reasons, but it is not known yet, whether and how cohesin ring entraps DNA during the loop extrusion process.