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.
School of Informatics, University of Edinburgh, EH8 9AB, United Kingdom.|Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3BF, United Kingdom.
Edward W J
0000-0001-8025-6361
EWJ
Wallace
Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3BF, United Kingdom.
Jean D
0000-0002-8179-6519
JD
Beggs
D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D007700:Kinetics; D012319:RNA Polymerase II / Q000378:metabolism; D012326:RNA Splicing; D012335:RNA, Ribosomal / Q000096:biosynthesis / Q000378:metabolism; D004718:Saccharomycetales / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D061805:Transcription Elongation, Genetic; D014158:Transcription, Genetic
D012335:RNA, Ribosomal; D012319:RNA Polymerase II
CTD phosphorylation; introns; polymerase CTD; polymerase pausing; splicing kinetics