The ratio of InDels to precise sequence edits is unaffected by heterochromatin.

(A) The relative frequency of mutations arising from NHEJ versus HDR in cells collected at 96 hours post transfection for five sgRNAs with target sites within imprinted heterochromatin (S1A, S2A and S3A Figs). The percentage of hypermethylated (>80%) strands in mock-transfected cells is indicated above the plot. Asterisk denotes Bonferroni-corrected p t tests of difference between HDR frequencies on maternal versus paternal alleles. (B) The size and frequency of the top five most common InDels 96 hours following transfection with sgKVDMR#1 (S1A Fig), broken down by parental allele. The horizontal red line denotes the predicted cleavage site. Deletion sizes are depicted against the scale bar at the top, and for insertions, the number of inserted bases is indicated next to the blue rectangle. Note that different +1 nucleotide insertions were observed and are represented as blue rectangles on opposite sides of the cleavage site. The fraction of Indels was calculated as the number of reads corresponding to each specific mutation expressed as a proportion of all InDel-containing reads. Quantitative data underlying both panels are provided in S1 Data, and details of MiSeq libraries including SRA accessions are provided in S2 Data. HDR, homology-directed repair; InDel, Insertion or deletion; mat, maternal; NHEJ, nonhomologous end joining; PAM, protospacer adjacent motif; pat, paternal; sgRNA, single guide RNA; SRA, Sequence Read Archive.