Transcription elongation rates influence RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S. cerevisiae. Mapping RNAPI by Miller chromatin spreads or UV crosslinking revealed 5′ enrichment and strikingly uneven local polymerase occupancy along the rDNA, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution: folding energy and GC content in the transcription bubble. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high GC in the transcription bubble slows elongation. A mathematical model for RNAPI elongation confirmed the importance of nascent RNA folding in transcription. RNAPI from S. pombe was similarly sensitive to transcript folding, as were S. cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use, indicating regulatory significance for transcript folding.

转录延伸率影响RNA加工，但对序列特异性的调控了解甚少。我们解决了这个问题，分析酿酒酵母中的RNAPI 。通过Miller染色质扩散或UV交联对RNAPI进行图谱分析显示，沿rDNA的5'富集和局部聚合酶占有率显着不均匀，表明转录速度存在明显差异。新生转录本的两个特征与RNAPI分布有关：折叠泡中的折叠能量和GC含量。体外实验证实，靠近聚合酶的强大RNA结构可促进正向转运并限制回溯，而转录气泡中的高GC则可延缓延伸。RNAPI延伸的数学模型证实了新生RNA折叠在转录中的重要性。来自粟酒裂殖酵母的RNAPI对转录物折叠也同样敏感，酿酒酵母RNAPII和RNAPIII也是如此。对于RNAPII，有利于延长延伸的非结构化RNA与更快的共转录剪接和近端剪接位点使用有关，这表明转录折叠具有调控意义。