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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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Presentation Transcript
slide1

RNA folding during transcription

(Co-transcriptional folding)

taopan@uchicago.edu

October 29, 2007

slide2

RNA folds into cool tertiary structures

tRNA~25 KDa

P RNA~115 KDa

ribosome > 103 kDa

slide3

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

slide5

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

slide6

Folding of E. coli RNase P RNA

Cognate

non-cognate

(same speed, different pause)

Speed doesn’t matter.

Mg2+-initiated folding even slower.

slide7

Big-time Pausing

Its location: right after the 5’ portion of all long-range helices!

slide9

An extensive paused complex structure forms (structural mapping and phylogeny)

Core of the structure is phylogenetically conserved . . .

Structure of the paused complex matters ….

slide10

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.

slide11

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).

slide12

Thanks to

Terrence Wong

Discussions, insights, reagents:

Robert Landick (U. Wisconsin)

Sean Eddy (Janelia Farm, HHMI)

Tobin Sosnick

NIH