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RNA folding during transcription (Co-transcriptional folding)

RNA folding during transcription (Co-transcriptional folding). taopan@uchicago.edu October 29, 2007. RNA folds into cool tertiary structures. tRNA ~25 KDa. P RNA ~115 KDa. ribosome > 10 3 kDa. Mg 2+ -initiated. Transcription-initiated. RNA polymerase. RNA. 3’. RNA. 5’. 5’.

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RNA folding during transcription (Co-transcriptional folding)

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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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