Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

RNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that jointly quantify transcription and splicing in budding yeast. For many yeast transcripts, splicing is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3' splice site. Ribosomal protein transcripts are spliced particularly fast and cotranscriptionally. However, some transcripts are spliced inefficiently or mainly post-transcriptionally. Intron-mediated regulation of some genes is likely to be cotranscriptional. We suggest that intermediates of the splicing reaction, missing from current data sets, may hold key information about splicing kinetics.