Supplementary Figure 8: Product purity and indel formation yielded by hA3A-BE3-Y130F and hA3A-BE3-Y132D.
From: Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion
(a) Comparison of product purity yielded by BE3, hA3A-BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in genomic DNA regions with natively high levels of DNA methylation. Fractions of cytosine substitutions induced by BE3 and hA3A-BE3s were individually determined at indicated cytosines. (b) Statistical analysis of C-to-T fractions of base editing products induced by BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D shown in (a). n = 12 samples from three independent experiments. (c) Comparison of indel formation induced by BE3, hA3A-BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in genomic DNA regions with natively high levels of DNA methylation. Indel frequencies were individually determined at indicated genomic loci under different conditions. (d) Statistical analysis of normalized indel frequencies induced by BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in regions with natively high levels of DNA methylation shown in (c), setting the ones induced by BE3 as 100%. n = 9 samples from three independent experiments. (e) Base editing efficiencies induced by BE3, hA3A-BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in genomic regions with natively low levels of DNA methylation. C-to-T editing frequencies of indicated cytosine were individually determined. Target site sequences are shown with the overlapped editing window (position 4-7, setting the base distal to the PAM as position 1) in lavender, PAM in cyan and CpG site in capital. (f) Comparison of product purity yielded by BE3, hA3A-BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in genomic DNA regions with natively low levels of DNA methylation. Fractions of cytosine substitutions induced by BE3 and hA3A-BE3s were individually determined at indicated cytosines. (g) Statistical analysis of C-to-T fractions of base editing products induced by BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D shown in (f). n = 9 samples from three independent experiments. (h) Comparison of indel formation induced by BE3, hA3A-BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in genomic DNA regions with natively low levels of DNA methylation. Indel frequencies were individually determined at indicated genomic loci under different conditions. Asterisk denotes an unusually high basal indel frequency (or amplification, sequencing or alignment artifact) at examined VEGFA-M-c site in NT. (i) Statistical analysis of normalized indel frequencies induced by BE3, hA3A-BE3-Y130F and hA3A-BE3-Y132D in regions with natively low levels of DNA methylation shown in (h), setting the ones induced by BE3 as 100%. n = 6 samples from three independent experiments.
(b,d,g,i) P value, one-tailed Student’s t test. The median and IQR are shown.
(c,e,h) Means ± s.d. were from three independent experiments.
