Quantitative single-cell splicing analysis reveals an ‘economy of scale’ filter for gene expression

In eukaryotic cells, splicing affects the fate of each pre-mRNA transcript, helping to determine whether it is ultimately processed into an mRNA, or degraded. The efficiency of splicing plays a key role in gene expression. However, because it depends on the levels of multiple isoforms at the same transcriptional active site (TAS) in the same cell, splicing efficiency has been challenging to measure. Here, we introduce a quantitative single-molecule FISH-based method that enables determination of the absolute abundances of distinct RNA isoforms at individual TASs. Using this method, we discovered that splicing efficiency behaves in an unexpected economy of scale manner, increasing, rather than decreasing, with gene expression levels, opposite to a standard enzymatic process. This behavior could result from an observed correlation between splicing efficiency and spatial proximity to nuclear speckles. Economy of scale splicing represents a non-linear filter that amplifies the expression of genes when they are more strongly transcribed. This method will help to reveal the roles of splicing in the quantitative control of gene expression.