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RNA Folding During Transcription: Maximizing Efficiency and Accuracy

Explore the intricate process of RNA folding during transcription, focusing on key aspects like speed, pausing, and structural considerations. Understand the importance of timing, interaction with RNA polymerase, and the role of Mg2+-initiated folding. Discover how pausing at critical points influences the formation of native structures and prevents non-native structures. Dive into the complex interplay between RNA sequence, RNA polymerase properties, and evolutionary conservation. This study sheds light on the dynamic mechanisms behind efficient RNA folding.

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RNA Folding During Transcription: Maximizing Efficiency and Accuracy

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  1. RNA folding during transcription (Co-transcriptional folding) taopan@uchicago.edu October 29, 2007

  2. RNA folds into cool tertiary structures tRNA~25 KDa P RNA~115 KDa ribosome > 103 kDa

  3. Mg2+-initiated Transcription-initiated RNA polymerase RNA 3’ RNA 5’ 5’ DNA template Native structure Native structure (Biophysics) Mg2+-initiated RNA folding versus (Biology) transcription-initiated RNA folding

  4. The obvious problem spots: Long-range helices Short-range Long-range

  5. Things that matter in folding during transcription Speed Pausing 2 1 Interstate 3 Lake Shore Lake Shore Take CR County road County road • Location. • Timing. • Interaction with RNA polymerase? Timing is everything. 5’ Polarity RNA polymerase

  6. Folding of E. coli RNase P RNA Cognate non-cognate (same speed, different pause) Speed doesn’t matter. Mg2+-initiated folding even slower.

  7. Big-time Pausing Its location: right after the 5’ portion of all long-range helices!

  8. Pausing at 119 matters to folding

  9. An extensive paused complex structure forms (structural mapping and phylogeny) Core of the structure is phylogenetically conserved . . . Structure of the paused complex matters ….

  10. Why should this non-native structure help folding? Prevents super-stable non-native structure from forming. It’s labile, easy to undo for native structure when downstream partners are transcribed. Provides a topological benefit for the order of strand invasions.

  11. Recap Long-range helix: cool for native structure, not cool for folding….. Non-native structure in folding: can be good, can be bad; devils are in the details ….. Pausing matters: location, location, location ….. (Poster) Two other non-coding RNAs need pausing, too. (Poster) Pause sites are conserved in related bacteria species. Evolutionary cross-talk? Non-coding RNA sequence/structure co-evolves with the properties of their transcribing RNA polymerase? Wong, Sosnick, Pan: PNAS, in press (2007).

  12. Thanks to Terrence Wong Discussions, insights, reagents: Robert Landick (U. Wisconsin) Sean Eddy (Janelia Farm, HHMI) Tobin Sosnick NIH

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