Extended Data Fig. 2: In-silico off-target analysis for CAG repeat-targeting strategy. | Nature Genetics

Extended Data Fig. 2: In-silico off-target analysis for CAG repeat-targeting strategy.

From: Base editing of trinucleotide repeats that cause Huntington’s disease and Friedreich’s ataxia reduces somatic repeat expansions in patient cells and in mice

Extended Data Fig. 2

(a-b) CRISPRitz-predicted off-target candidate sites in the (a) macaque (Macaca mulatta) and (b) human genomes organized based on the position of mismatches between the genomic site and sgCTG spacer sequence. Mismatch category A includes the five nucleotides most proximal to the PAM (positions 1-5), category B represents positions 6-10, and category C spans the last ten, PAM-distal nucleotides (positions 11-20) of the protospacer. A0-A5, B0-B5 and C0-C10 indicate the number of mismatches (0-5) between the sgCTG and a target site in categories A, B or C. Each square shows the number of loci in each mismatch subgroup. (c) Predicted in cellulo base editing off-target activity of our CBE strategy in the macaque genome, based on in silico CRISPRitz predictions of off-target edits and a subsequent WGS-transformation using the ratio of off-targets edited in HEK293T cells ( > 0.5% editing by WGS) versus predicted by CRISPRitz in the human genome. Heatmap colors represent predicted in cellulo editing per mismatch bin, based on corresponding editing frequencies per bin observed in WGS analysis of edited HEK293T cells.

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