Fig. 2: DNA break end orientation of “inward-moving” RDC and their association with the timing transition regions. | Nature Communications

Fig. 2: DNA break end orientation of “inward-moving” RDC and their association with the timing transition regions.

From: Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters

Fig. 2

A The figure illustrates single-ended DNA breaks at rightward- (left) and leftward-moving forks (right). The light blue DSB end at the rightward-moving fork is linked with centromeres, maintaining its centromeric orientation (Dcen) when joined with the “bait” DSB end. Conversely, pink DSB ends at the leftward-moving forks are linked with telomeric sequences, preserving their telomeric orientation (Dtel) upon joining with the “bait” DSB end. B Illustration of inward-moving fork direction at RDC with two timing transition regions (TTRs), shaded in gray. The arrow above each fork annotates the replication direction. Light blue represents rightward movement, and pink indicates leftward movement. Initiation zones correspond to the dashed red line, and the blue line indicates the termination zone. TTRs were shaded in gray rectangular. C Multiomics figures provide information regarding genomic loci containing two “inward-moving”, TTR-containing RDCs at the Npas3 and Cdk14 gene loci. The top panel shows a high-resolution Repli-seq normalized heatmap using aphidicolin (APH)-treated ES cell-derived NPCs, as described in Fig. 1B. Pink and blue arrows indicate the replication directions of the genome beneath RDC. The middle panel displays DNA break density, with the Y-axis representing extended interchromosomal Dcen or Dtel density per 25 kilobases kernel. The bottom panel includes annotations indicating Dcen and Dtel island positions, RDC range (purple line), and actively transcribed gene orientation (+: light green, -: dark green). Additional annotations associated with this figure are depicted on the right. D, F Illustrations of inward-moving fork direction at RDCs with (D) or without (F) TTR flanking an extended late constant timing region (CTR), which is shaded in yellow. E, G Multiomics figures describe the genomic loci containing two “inward-moving,” CTR-containing RDC at Prkg1 (E) and Cadm2 (G). Figures are shown as described in (C).

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