Diverse Forms of RPS9 Splicing Are Part of an Evolving Autoregulatory Circuit
Figure 2
RPG intron deletions reveal gene-specific effects on steady-state mRNA levels.
A–C) Microarray expression data for 16 RPG Δi mutants compared to a common wild-type strain. In each panel, the change in expression due to intron deletion is shown for either the intronless gene (red lines) or its paralogous gene copy (blue lines) compared to all other changes detected by microarray (boxplots). The effect of intron deletion is shown for each Δi mutant on A) the expression of the intronless gene copy, B) the expression of the paralogous gene copy, and C) the Intron Accumulation Index of the paralogous gene copy. Microarray data are expressed as the normalized log2 transformed probe intensity for exon features averaged from at least two replicate microarrays. Whiskers represent 1.5 times the interquartile range. D) RT-qPCR quantification of RPS9A (red circles) and RPS9B (blue triangles) expression changes for each Δi mutant relative to wild-type (columns). RPS9A and RPS9B values were divided by SCR1 values to obtain ratios controlled for variations in cDNA quantity. Log2 transformed ratios are plotted relative to wild-type (based on the mean of three biological replicates). Each of three biological replicates is shown as a point and the mean as a dash. E) The effect of intron deletion on the total number of transcripts encoding S9. Stacked barplots illustrate the percent of RPS9A (red bars) and RPS9B (blue bars) transcripts calculated for each Δi mutant. For a wild-type strain (first column), the percent of RPS9A and RPS9B transcripts encoding S9 were estimated from published RNA-seq data [19]. Changes in RPS9A and RPS9B transcript numbers for each Δi mutant (columns) were calculated by multiplying wild-type percentages by relative expression changes determined by qPCR.