Figure 7.

CELF1 overexpression results in extensive alternative splicing changes in adult skeletal muscle. RNA-sequencing was performed on RNA isolated from the gastrocnemius muscle of female hCELF1par, hCELF1nuc, hCELF1cyt, TRECUGBP1 (positive control), MDAF and WT mice at the time points indicated in Table 1. Animals with comparable mCherry-CELF1 protein expression and similar minimal histological defects were chosen for sequencing. Data was analyzed for alternative splicing (AS) changes. (A) Types of AS events responsive to CELF1 overexpression as compared to MDAF (+dox) negative controls in the hCELF1par, hCELF1nuc and TRECUGBP1 lines induced to overexpress CELF1 for 5 days; and the hCELF1cyt line induced to overexpress CELF1 for 21 days. The total number of alternative splicing changes with ∆PSI values ≥15%, a FDR ≤ 0.05 and a count cutoff >20 reads is also listed. CE, cassette exon; AS 5′SS, alternative 5′ splice site; AS 3′SS, alternative 3′ splice site; and MXE, mutually exclusive exons. (B) Analysis shows correlation between ΔPSI values [PSI (CELF1 overexpression—PSI (MDAF)] obtained by RNA-seq and RT-PCR for 5 splicing events tested at each time point of hCELF1par, hCELF1nuc and hCELF1cyt overexpression. (C–E) AS transitions were intersected between CELF1 overexpression (as compared with MDAF negative controls); (C) in the hCELF1par and hCELF1nuc lines induced for 5 or 7 days; (D) in the hCELF1par, hCELF1nuc and TRECUGBP1 lines induced for 5 or 7 days, with GO analysis; or in the (E) hCELF1par, hCELF1nuc and hCELF1cyt lines induced for 5, 7 or 21 days, respectively. P, Fisher’s exact test. Red line = P-value of ≤0.032. CC, cellular compartment; BP, biological process; MF, molecular function.