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. 2023 Apr 7;51(12):5948–5980. doi: 10.1093/nar/gkad259

Figure 5.

Figure 5.

Risdiplam and branaplam affect usage of alternative 5′ss and 3′ss. (A) Table summarizing splicing-relevant information regarding the top candidate exons with altered 5′ss usage after HiR treatment only, both treatments or after HiB treatment only. Sequences represent 12 bases upstream and downstream of the two 5′ss with increased (left) and decreased usage (right) after small compound treatment. Intronic and exonic sequences are indicated; exonic sequences are boxed. The 5′ss score of each splice site is indicated to the right of each sequence. ΔShort indicates the change in proportion of total transcript with the shorter form of the exon due to the usage of the upstream 5′ss. The sizes of the long and short forms of the exon in question are indicated. (B–D) Genomic views of RNA-Seq reads (upper panels) and RT–PCR results (lower panels) examining A5S events that are triggered by HiR alone (B), both HiR and HiB (C) and HiB alone (D) in GM03813 fibroblasts. For genomic views, green arrows indicate the location of the 5′ss with increased usage, red arrows the 5′ss with decreased usage. ‘L’ indicates a longer isoform of an exon due to usage of the downstream 5′ss; ‘S’, a shorter one due to usage of the upstream 5′ss. An asterisk marks a non-specific PCR product. Other labeling and coloring are the same as in Figure 3B–D. (E) Table summarizing splicing-relevant information regarding the top candidate exons with altered 3′ss usage after HiR treatment only, both treatments or after HiB treatment only. Table content is similar to (A), except that the 3′ss were analyzed. (F–H) Genomic views of RNA-Seq reads (upper panels) and RT–PCR results (lower panels) examining A3S events that are triggered by HiR only (F), both HiR and HiB (G) and HiB only (H). For genomic views, in the case of >2 alternative 3′ss, the intermediate sized region is indicated with a pink box. Green arrows indicate the location of the 3′ss with increased usage, red arrows the 3′ss with decreased usage. ‘L’ indicates a longer isoform of an exon due to usage of the upstream 3′ss; ‘S’, a shorter one due to usage of the downstream 3′ss. Other coloring and labeling are the same as in (B–D).