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Fig. 4 | Cell & Bioscience

Fig. 4

From: Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis

Fig. 4

R-loops co-localize with meiotic DSB hotspots in pachytene cells. (A) Heatmap of ssDRIP-seq signals (R-loop, wR-loop and cR-loop) in regions ± 3 kb from previously confirmed meiotic DSB distribution on the genomes of pachytene cells from Spo11-oligo sequencing from Pan et al. data during yeast meiosis [7]. (B) Venn plots showing the overlap of Spo11-oligo-seq peaks [7] and R-loop peaks at the pachytene stage. Pac, pachytene. (C) Permutation test of colocalization between Spo11-oligo-seq peaks and R-loop peaks at the pachytene stage. Pac, pachytene; Evobs, evaluation observe; Evperm, evaluation permutation. (D) R-loop profile relative to some meiotic DSB sites. The signal intensity profiles of ssDRIP-seq at the pachytene stage and RNase H-treated ssDRIP-seq in regions ± 3 kb from the centre of the colocalized Spo11-oligo-seq signal region in (B). (E) Pachytene stage R-loops are enriched in some meiotic DSB sites. Heatmap of the ssDRIP-seq signals at the pachytene stage and RNase H-treated ssDRIP-seq signals at regions ± 3 kb from the centre of the colocalized Spo11-oligo-seq signal region in (B). (F) The signal intensity profiles of Spo11-oligo-seq in regions ± 3 kb from the centre of meiotic DSB overlapping R-loops detected in our ssDRIP-seq analysis at the pachytene stage. (G) DNA:RNA hybrids could form at ssDNA ends of meiotic DSBs. Heatmap of S1-seq signals [9] in regions ± 3 kb from meiotic DSB overlapping R-loops. (H) The signal intensity profiles of MNase-seq [65] in regions ± 3 kb from the centre of meiotic DSB overlapping R-loops detected in our ssDRIP-seq at the pachytene stage. (I) The signal intensity profiles of H3K4me3 [65] in regions ± 3 kb from the centre of meiotic DSB overlapping R-loops detected in our ssDRIP-seq analysis at the pachytene stage. (J) The signal intensity profiles of H4K44ac [65] in regions ± 3 kb from the centre of meiotic DSB overlapping R-loops detected in our ssDRIP-seq analysis at the pachytene stage. (K) A representative genomic region showing R-loop signals sharing overlap with meiotic DSBs detected in Spo11-oligo-seq and S1-seq analysis. The wR-loop and cR-loop asymmetrically localized one side of the hotspot centres at the pachytene stage.

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