Extended Data Fig. 5: Chromosomal translocation profiles.
From: C-to-G editing generates double-strand breaks causing deletion, transversion and translocation
a, Circos plots of genome-wide translocation junctions in cells treated with nCas9 or the indicated BEs. Translocation junctions were binned into 5-Mb regions (black bars) and plotted on a log scale; the orange line connects the on-target bait site with a Cas-OT prey hotspot, the green line connects the on-target bait site with a deaminase-OT prey hotspot. The middle number indicates unique translocation junctions from 3.6 million edited cells. b, Distribution of translocation junctions at Cas-OT hotspots of an sgEMX1 on-target bait in cells edited with the indicated BE. c, Translocation, H3K27Ac and transcription profiles at an AID deaminase-OT hotspot. Top: Translocation junctions are indicated by black bars from cells transfected with AID-CGBE or CGBE1. Middle (H3K27Ac and SE): The H3K27Ac ChIP-seq profile is shown in orange, and identified SEs are depicted below with orange bars. Bottom (PRO-seq): PRO-seq detected sense and antisense transcription are shown in blue and red, respectively. d, Enrichment of scattered translocation junctions at genomic regions associated with the indicated histone markers, open chromatin and transcription in cells transfected with AID-CGBE from the 4 baits. Each dot indicates average number of two biological replicates at the indicated locus. Mean ± SD of 4 sgRNA loci is shown. e, Relative motif enrichment in AID-CGBE-edited samples compared to that of random sampling of the human genome. Each dot indicates average number of two biological replicates at the indicated locus. Mean ± SD of 4 sgRNA loci is shown. f, Substitution frequency (left) and C > G purity (right) of indicated pairs of synthetic sequences with and without palindromic deamination motif. The editing assay was performed in a 48-well plate format. Four independent replicates are shown. For boxplot, centre line indicates the median; box limits represent the upper and lower quartiles, and the whiskers represent minimum to maximum values. g, Substitution (upper) and deletion (lower) profile of CGBE1 on 5 pairs of synthetic sequences as shown in Fig. 1f. “TCAA” was applied as a control for “TCGA”. h, Percentage of sgRNAs containing palindromic motifs in the editing window. A total of 3040 potential CGBE-correcting loci were analysed. For Panels d and e, two-tailed one-sample t-test was performed. For Panel f, two-tailed Student’s paired t-test was applied. Source numerical data are available in source data.
