NHEJ-mediated DSB repair and chromatin dynamics at the PHO5 locus. (A) Cutting/rejoining kinetics of the ectopic 117-bp HO recognition site that was engineered upstream of the PHO5 gene. Suppression of HO (starts at the time denoted by the dotted red line) facilitates repair by NHEJ, a Dnl4-dependent repair process, in this donorless system. (B,C). Bulk MNase coverage over the cut/repair time course in the WT strain (B) and the dnl4Δ mutant (C). The red line denotes the HO cut site. Time pre-induction (−1 h after HO induction [0 h]), and after repression of HO expression (1 h, 2 h, etc.) are shown in darker shades of blue. (D,E) Chromatin occupancy profiles of the WT (D) and dnl4Δ (E) strains. As in Figures 2 and 3, the black trace represents the 2D cross-correlation score and the blue shaded regions represent 0.5 standard deviations of nucleosome positions from the center of each identified nucleosome.
