Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates.

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