Fig. 3: SPLICER improves exon skipping through reduction of Both cryptic splicing and intron retention.

A Sashimi plot describing exon splicing following ABE editing of LMNA exon 11 with SPLICER, in which a cryptic SD site is recognized in the middle of the exon when editing the SD (left), leading to no exon skipping and partial retention of exon 11 (right). This aberrant splicing event is reduced 3-fold by ABE editing of both SA and SD sites. B Sashimi plot representing splicing of HSF1 exon 11 before and after ABE editing of splicing elements demonstrating a cryptic SA recognized in HSF1 exon 11 (left). This cryptic splicing leads to a frameshift mutation in a protein, which results in a premature termination codon in exon 11 (right). Cryptic splicing is reduced 10-fold when editing both sites (left). C Sashimi plot describing splicing of BAP1 exon 2 following editing with CBEs (left). Cryptic splicing and intron retention occur with SA and SD editing alone, leaving an in-frame, but mutated protein (right). Both events are minimized with SPLICER (left). All measurements of full and cryptic exon skipping were performed by NGS except for LMNA exon 11, in which full exon skipping was measured by RT-PCR densitometry. For sashimi plots, values represent the mean. All replicates are biological replicates originating from three independent transfections of each sgRNA set; n = 3 for all experiments; *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001; one-way ANOVA, Tukey’s post hoc comparing cryptic splicing events in SA or SD to the rate of that cryptic splicing event in simultaneous SA/SD editing. Source data are provided as a Source Data file.