Research Article

Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data

Figure 2

Splicing efficiency in the prp45(1-169) mutant. Splicing efficiencies for all known introns (for 5′ and 3′ splice sites separately) were calculated using the pipeline described in Figure 1. (a, b) Results for two pooled biological replicates of the prp45(1-169) mutant and its corresponding wild-type strain. Higher values correspond to more efficient splicing. Full circles represent values for introns with sufficient coverage (≥5 transreads and ≥5 reads covering intron end base); open circles represent low-confidence values for introns with low sequencing read coverage. (c, d) Relative splicing efficiencies (prp45(1-169) normalized to wild type) at the 5′ and 3′ splice sites were calculated for each biological replicate separately. Only introns with sufficient read coverage were considered. Pearson’s values for the two replicates are indicated. (e) Comparison of relative splicing efficiencies at the 5′ and 3′ splice sites of selected genes calculated from the pooled RNA-seq data with relative splicing efficiencies determined by RT-qPCR (means of 4–6 independent RT-qPCR experiments ± SD).
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