Figure 7. Knockdown of CstF-77 leads to widespread APA events.

(A) Analysis of effect of CstF-77 knockdown in proliferating C2C12 cells by 3′READS. Left, IB of CstF-77 knockdown; right, regulation of alternative pAs in the 3′-most exon after CstF-77 knockdown. Genes with significantly upregulated distal (red) and proximal (blue) pA isoforms are indicated in each graph along with total numbers. Significantly regulated isoforms are those with P<0.05 (Fisher's exact test) and abundance change >5%. Only the two most abundant isoforms for each gene were analyzed. (B) Comparison of genes with 3′UTR changes between CstF-77 knockdown and C1C12 differentiation. The number of consistently regulated genes is significantly greater (P = 4.1×10⁻⁹, Chi-squared test) than the number of oppositely regulated ones. (C) Pentamers enriched for pAs of downregulated isoforms (top) and of upregulated isoforms (bottom). (D) CstF-64 binding around the pAs of upregulated isoforms (UP) and downregulated isoforms (DN). Left, binding profiles representing the number of CstF-64 CLIP-seq reads per thousand pAs per million mapped reads; right, aggregated reads in the −10 nt to +40 nt region around the pA. The difference between UP and DN groups is significant (P<0.05, bootstrap analysis).