Figure 4

Effect of ASOs targeting APOB exon 27 sequences. (a) ESEfinder output for APOB exon 27, using version 2.0 matrices and thresholds [21]. Y-axis shows ESEfinder above-threshold scores for identified matches; X-axis corresponds to the exon 27 sequence. Red = SF2/ASF, blue = SC35, green = SRp40, yellow = SRp55. The light grey horizontal lines indicate the matches that were found by RESCUE-ESE [22]. The dark grey lines indicate the ESE candidates identified by PESXs server [23, 24]. ASOs were designed to bind to locations corresponding to ESE clusters, and these locations are represented below the X-axis by the arrows, which run from the 5' to 3' direction. (b) RT-PCR assay for exon 27 skipping with RNA from cells transfected with ASOs at 250 nM. Exonic ASOs 6–25, 31–50, 61–80, 88–107 weakly promote exon 27 skipping, whereas scrambled versions of these ASOs had no effect on exon 27 skipping. (c) Quantitative data from three independent experiments. Error bars show S.E.M. Overall repeated measures one-way ANOVA showed p < 0.0001, indicating significant differences between compared groups. Dunnett's multiple comparison test showed a significant difference between skip 27-3B and 3B scram (p < 0.01), but no statistically significant differences were seen between skip 27-3B scram and other skip 27 ASOs.