Transcription Rate Strongly Affects Splicing Fidelity and Co-transcriptionality in Budding Yeast

The functional consequences for alternative splicing of altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects on splicing of changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both co-transcriptional splicing and splicing efficiency and faster elongation reduces co transcriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when co-transcriptional. Moreover, we demonstrate that altering RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimise the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.改变转录速率（transcription rate）对可变剪接（alternative splicing）的功能影响，已在哺乳动物细胞中得到广泛深入的研究，但目前学界对酵母中转录速率变化对剪接的影响仍知之甚少。本研究通过多项实验证据表明，在出芽酵母中，减慢RNA聚合酶II（RNA polymerase II）的延伸速率可同时提升共转录剪接（co-transcriptional splicing）水平与剪接效率（splicing efficiency），而加快延伸速率则会降低共转录剪接水平与剪接效率，这提示共转录状态下的剪接过程效率更高。此外，我们证实，无论向哪个方向调整RNA聚合酶II的延伸速率，都会损害剪接保真度（splicing fidelity）；同时揭示剪接保真度主要取决于内含子长度（intron length）、二级结构（secondary structure）以及剪接位点评分（splice site score）。这类效应在高表达的核糖体蛋白编码转录本（ribosomal protein coding transcripts）中尤为显著。我们提出，RNA聚合酶II的转录过程经过精准调控，以最大化核糖体蛋白基因表达的效率与准确性，同时允许非核糖体蛋白编码转录本（nonribosomal protein transcripts）在剪接位点选择上具备一定灵活性。