Widespread transcriptional readthrough caused by Nab2 depletion leads to chimeric transcripts with retained introns

Precision RNA-sequencing methods have been recently developed to analyze the occurrence of pre-mRNA splicing during transcription by RNA polymerase II (Pol II). Here we apply these globally in budding yeast to identify a cohort of co-transcriptional splicing regulators by machine learning. One candidate, Nab2, displayed reduced splicing of a fraction of the genes tested by Single Molecule Intron Tracking (SMIT). These splicing defects were attributable to readthrough transcription revealed by long read sequencing of nascent RNA; transcripts extended both upstream and downstream of intronless and intron-containing genes after Nab2 depletion, with individual transcripts sometimes spanning many genes. Thus, Nab2 regulation of splicing is indirect. We conclude that coordination between Pol II and pre-mRNA processing operates at the level of individual transcripts to determine gene expression. The data deposited here are agarose gels of PCR products which validate the findings from our sequencing experiments. The sequencing datasets are deposited in the GEO database under accession number GSE156133.