Fig. 5

DSB hotspot-associated R-loops are newly generated at the early stage of meiosis

(A) Plot shows the overlap rate of meiotic DSB overlapping R-loop peaks and de novo R-loop peaks at the early stage of yeast meiosis (2 h de novo R-loop: 0.5 h vs. 2 h; Pac de novo R-loop: 2 h vs. Pac). The number of 2 h de novo R-loop peaks was 165, and 14 peaks (8.48%) overlapped with meiotic DSB overlapping R-loops. The number of Pac de novo R-loop peaks was 715, and 249 peaks (34.83%) overlapped with meiotic DSB overlapping R-loops. Pac, pachytene.

(B) Venn plots showing the overlays of Spo11-oligo-seq peaks [7] and 2 h de novo R-loop peaks (0.5 h vs. 2 h) of yeast meiosis.

(C) Permutation test of colocalization between Spo11-oligo-seq peaks and 2 h de novo R-loop peaks. Evobs, evaluation observe; Evperm, evaluation permutation.

(D) Venn plots showing the overlays of Spo11-oligo-seq peaks [7] and Pac de novo R-loop peaks (2 h vs. Pac) of yeast meiosis. Pac, pachytene.

(E) Permutation test of colocalization between Spo11-oligo-seq peaks and Pac de novo R-loop peaks.  Pac, pachytene; Evobs, evaluation observe; Evperm, evaluation permutation.

(F) The signal intensity profiles of Spo11-oligo-seq [7] in regions ± 3 kb from the centre of Pac de novo  R-loops (2 h vs. Pac) detected in our ssDRIP-seq analysis. Pac, pachytene.

(G) The signal intensity profiles of H3K4me3 [65] in regions ± 3 kb from the centre of Pac de novo R-loops (2 h vs. Pac) detected in our ssDRIP-seq analysis. Pac, pachytene.

(H) A representative genomic region showing de novo R-loop signals (2 h vs. Pac) at the pachytene stage sharing overlap with meiotic DSBs detected in Spo11-oligo-seq and S1-seq analysis. The de novo wR-loop and cR-loop at the pachytene stage localized one side of the hotspot centres at the pachytene stage. Pac, pachytene.