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. 2019 Nov 4;47(22):11609–11622. doi: 10.1093/nar/gkz979

Figure 3.

Figure 3.

DNA methylation is associated with Homology Directed Repair (A) Diagram showing the targeted region of C9orf72. Purple arrows indicate primers that amplify wild type DNA, whereas the red arrow indicates the primer that specifically amplifies a 12bp mutation that was included in the repair template. Figure drawn to scale. (B) Bisulfite PCR using the primers depicted in (A). Representative gel from two biological replicates. (C) Bisulfite amplicon sequencing from two biological replicates (Unmeth: n = 27 amplicons, Meth: n = 31 amplicons). Each row is an individual cloned and sequenced DNA molecule and columns are individual CpG dinucleotides. Grey boxes indicate unmethylated CpGs, black boxes indicate methylated CpGs and white boxes are undetermined due to poor conversion or poor sequencing quality. (D) Quantification of the percentage of methylated CpGs in (C). n = 2 biological replicates. Two-tailed t-test; P = 0.0109. (E) Quantification of the number of amplicons with less than or >20% methylation. Data are from two biological replicates. Fisher's exact test, P < 0.0001.