The functional consequences of alternative splicing on altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects of splicing on changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both cotranscriptional splicing and splicing efficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when cotranscriptional. Moreover, we demonstrate that altering the 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 optimize the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.

选择性剪接对改变转录率的功能后果一直是哺乳动物细胞深入研究的主题，但对剪接对改变酵母转录率的影响知之甚少。我们提出了几条证据，表明慢速 RNA 聚合酶 II 延伸增加了共转录剪接和剪接效率，而更快的延伸降低了出芽酵母中的共转录剪接和剪接效率，这表明在共转录时剪接效率更高。此外，我们证明在任一方向改变 RNA 聚合酶 II 延伸率会损害剪接保真度，并且我们揭示剪接保真度在很大程度上取决于内含子长度以及二级结构和剪接位点得分。对于高度表达的核糖体蛋白编码转录物，这些作用明显更强。我们建议调整 RNA 聚合酶 II 的转录以优化核糖体蛋白基因表达的效率和准确性，同时允许灵活地选择非核糖体蛋白转录物的剪接位点。