Fig. 3: Oligonucleotides preferentially target transcripts that are not protected by the splicing machinery. | Nature Communications

Fig. 3: Oligonucleotides preferentially target transcripts that are not protected by the splicing machinery.

From: Variant-selective stereopure oligonucleotides protect against pathologies associated with C9orf72-repeat expansion in preclinical models

Fig. 3

a Schematic illustration of selectivity model. When the splicing machinery binds to SS1b (Splicing), the resulting transcription produces V2. An RNase H-active oligonucleotide (RNase H-mediated degradation) will selectively bind non-V2 variants and promote their degradation. An RNase H-inactive oligonucleotide with high Tm (Intron retention) will displace the splicing machinery yet leave the unspliced RNA intact, resulting in the accumulation of intron 1-containing transcripts. b Relative expression of V3 (top) and ratio of V3: all variants (bottom) with respect to HPRT in human ALS iPSC-derived motor neurons treated with 10 μM of the indicated oligonucleotide. The coral star marks the location of SS1b. Data are presented as mean ± SD, n = 3. One-way ANOVA with Dunnett’s multiple comparison test. ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05. c Relative expression of intron-1-containing transcripts (left) and all variants (right) with respect to HRPT in human ALS motor neurons treated with 10 μM of the indicated oligonucleotide. Note that the y axes for the two graphs are different. Data are presented as mean ± SD, n = 3. One-way ANOVA with Dunnett’s multiple comparisons test with comparison to NTC ****P < 0.0001, **P < 0.01 (Intron 1 C9-756 P = 0.002), *P < 0.05 (All V C9-756 P = 0.0135). d Percentage of full-length surrogate RNA remaining after heteroduplex formation with oligonucleotide–RNA pre-mix (V3), U1 RNA mimic-RNA pre-mix (V2), or oligonucleotide, U1 RNA mimic and surrogate pre-mix and treatment with RNase H in vitro with respect to time. Data are presented as mean ± SEM, n = 3. Lines depict 2-phase decay for least-squares fit. The substrate (S) to enzyme (E) ratio for each panel is shown. Source data, including exact P values for panel b, are provided as a Source Data file. snRNP small nuclear ribonuclearprotein, ASO antisense oligonucleotide, V variant.

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