The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects
Fig 3
Seed and non-seed region-dependent off-target effect analyses for siVIM-270 and siVIM-805.
(A, B) Expression profiles of off-target genes with 3’UTR sequences that perfectly match the corresponding siRNA seed region (i.e. off-targets) were compared to genes without such sequence. (C, D) The correlation between GC content in all the subsections within mRNA targets of siRNA non-seed region (8–21) and fold change of off-target effect was calculated in a similar manner to that shown in Fig 2. The correlation coefficient was grouped using quantiles as boundary values and target position corresponds to the numbering shown in Fig 1. GC contents in the non-seed regions at positions 8–15 showed the highest correlation with off-target effect (Fig 3C; siVIM-270, r = 0.22, p-value = 1.13E-12, Fig 3D; siVIM-805, r = 0.15, p-value = 1.57E-05). (E, F) Off-target transcripts for siVIM-270 and siVIM-805 were divided into four groups defined by the number of GC nucleotides in their non-seed regions (positions 8–15). Quantiles were used as the boundary values for classification; ‘Low’ (GC content < 3), ‘Medium’ (GC content = 3), ‘High’ (GC content = 4) and ‘Very High’ (GC content ≥ 5)(out of a total of 8). The number of off-target genes was 1065 for siVIM-270 (E) and 823 for siVIM-805 (F).