Fig. 7: Influence of CpG C>T mutations. | Nature Communications

Fig. 7: Influence of CpG C>T mutations.

From: iPS cell generation-associated point mutations include many C > T substitutions via different cytosine modification mechanisms

Fig. 7

a CpG C > T mutations in CDS. Amino acid substitutions resulting from CpG C > T mutations in iPSCs are shown. b, c A differential methylation region found adjacent to a CpG C > T transition detected in sister clones analysis. Each dot indicates the methylation value (beta value) measured by Illumina 450 K methylation analysis (HipSci project). b The mutation (chr20: 17296063, nosn_6) was detected in a iPSC, clone nosn_6, which was not detected its sister iPSC, clone nosn_1. This C > T site is located in the intronic region of the PCSK2 gene. DNA methylation levels within the ~460 kb genomic region (PCSK2 gene region ±100 kb, chr20:17106752-17565222) between sister clones are plotted and that of another iPS set without mutations in this region (uiao_1 and uiao_2) is also shown as a control. The five hypomethylation sites in nosn_6, which were found to be around the C > T, are indicated by a dashed circle. c The methylation level of the PCSK2 genomic region gene±2Kb is shown on the Y-axis (chr20:17204815-17464832). The X-axis indicates the distance from the transcription start site (TSS, open arrow head). The position of the mutation detected only in nosn_6 is indicated by red arrowhead. The hypomethylated region of approximately 0.5 kb around the C > T mutation is indicated by the dashed line. d Frequency of CpG C > T mutations within the CpG island (CGI) and CGI shore. CpG C > T mutations within the CpG island (CGI) or CGI shore of iPSC lines (n = 75 biological replicates) and germline (n = 816) are shown. The Y-axis indicates the number of CpG C > Ts in the CGI and CGI shore regions (±5 kbp) per cell line (iPSC) or individual (germline). An error bar shows the SD of the mean. e Distance of CpG C > T mutations from the nearest transcription start site (TSS). The left Y-axis indicates the number of CpG C>Ts per cell line (iPSC) or individual (germline). The right Y-axis indicates the number of mutations per iPSC when the number of germline mutations is set to 1. Source data are provided as a Source Data file.

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