Fig. 2

Altered splicing after PRPF8 depletion affects only a subset of human transcripts. a Intronic expression levels across the genome are increased in PRPF8-depleted cells. Normalized intron expression was calculated following analysis of the transcriptome of PRPF8-depleted Cal51 cells using RNA sequencing (left; “Materials and methods”). Statistically significant pairwise comparison is indicated (***p < 0.001). The number of mapped reads, the percentage of reads that map to exons, exon–intron boundaries, and intron bodies are shown in tabular form (right). b RNA sequencing experiments demonstrate that PRPF8 depletion results in altered splicing in only a subset of human transcripts. DEXSeq (“Materials and methods”) identifies a set of 2086 protein-coding genes that contain at least one retained intron [false discovery rate (FDR) < 0.01] and a set of 1921 protein-coding genes that display significant differences in exon usage (FDR < 0.01) following PRPF8 depletion; 637 genes display both retained introns and alternative exon usage (p < 2.2e-16). Transcripts with altered splicing patterns constitute only a subset of all expressed protein-coding genes (n = 3388 out of 13,216; expression threshold = 1 FPKM (Fragments per kilobase of exon per million reads mapped); “Materials and methods”). c Functional enrichment analysis using DAVID and WebGestalt (“Materials and methods”) shows that this subset is enriched for transcripts that participate in mitosis, ubiquitin conjugation, or RNA processing. GO Gene Ontology