. PRPF40A knockdown causes global loss of microexon and small exon splicing. (A) Protein domain structure of PRP-40 homologs, modeled after TreeFam database (Ruan et al. 2008). (B) Volcano plot showing changes in gene expression as determined by DESeq2 upon PRPF40A siRNA knockdown. (C) The effect of PRPF40A knockdown on alternative splicing is largely restricted to changes in cassette exon inclusion (67%). (D) Effects of PRPF40A knockdown on cassette exon inclusion binned by exon size, including microexons (1–30 nt). ΔPSI = change in percent spliced in from control to PRPF40A conditions. (E) Same as in D, except for C. elegans prp-40 loss-of-function mutants. (F,G) Sashimi plots showing that PRPF40A knockdown results in dramatic decreases in microexon inclusion, but does not affect splicing of upstream or downstream exons, or lead to increased retention of the flanking introns. Numbers in parentheses represent PSI values for the replicate in question; numbers over splice junctions indicate number of reads for that splice junction in the replicate in question.
