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Vladimir P. Zhdanov* PHYSICAL REVIEW E 80, 051925 (2009)

Model of gene transcription including the return of a RNA polymerase to the beginning of a transcriptional cycle. Vladimir P. Zhdanov* PHYSICAL REVIEW E 80, 051925 (2009). Outline. Preliminary Introduction Model of Gene Transcription Experimental Results Conclusion. Preliminary.

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Vladimir P. Zhdanov* PHYSICAL REVIEW E 80, 051925 (2009)

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  1. Model of gene transcription including the return of a RNA polymeraseto the beginning of a transcriptional cycle Vladimir P. Zhdanov* PHYSICAL REVIEW E 80, 051925 (2009)

  2. Outline • Preliminary • Introduction • Model of Gene Transcription • Experimental Results • Conclusion

  3. Preliminary • Central dogma of molecular biology

  4. Preliminary • Gene Transcription: DNA->RNA Initiation Elongation Termination

  5. Introduction • Regulation of Gene expression • DNA-binding Protein may increase or suppress the Transcription initiation rate

  6. Introduction • What happens at end of transcriptional cycle? • RNAP diffuse along DNA • RNAP disassociate from DNA • RNAP start Transcription cycle again • A kinetic model of gene transcription • Include the return of RNAP to a transcription cycle • Show transcriptional burst

  7. Model of Gene Transcription • Conventional Scheme:

  8. Model of Gene Transcription • Conventional Scheme: • probability that the gene is in the P⋆1 state: • Steady-state probability that the gene is in the P⋆1state: • Transcription Rate :

  9. Model of Gene Transcription • Conventional Scheme: • probability that the gene is in the P⋆1 state: • Steady-state probability that the gene is in the P⋆1state: • Transcription Rate :

  10. Model of Gene Transcription • Definition • ka : associate rate (Po->P⋆ 1) • kd : disassociate rate (Po<-P ⋆ 1) • c : RNAP concentration • k0: disassociate rate (P ⋆ ->P*) • k1: transition rate (P*1->P*2) • k2: transition rate (P * 2 -> P⋆1) • : diffusion jumps rate (P ⋆1 <->P ⋆2) • P : states for RNAP ,p :probability … ⋆ : associated o : unbound * : elongated

  11. Model of Gene Transcription • Conventional Scheme + Diffusion: • probabilities of P⋆1 ,P*1,P*2, P⋆2 state: Steady-state

  12. Model of Gene Transcription • Conventional Scheme + Diffusion: • Transcription Rate : • With saturation Transcription rate:

  13. Model of Gene Transcription • Conventional Scheme + Diffusion: • Transcription Rate :

  14. Model of Gene Transcription • Transcription Burst • The probability that RNAP produces n RNA after association is given by:

  15. Model of Gene Transcription

  16. Experimental Results Diffusion burst Without Diffusion

  17. Experimental Results

  18. Experimental Results diffusion jumps rate  = 100 s-1

  19. Experimental Results diffusion jumps rate  = 200 s-1

  20. Experimental Results diffusion jumps rate  = 500 s-1

  21. Experimental Results?

  22. Conclusion • Analyze the end of transcription cycle. • Transcriptional burst might occur without regulation of transcription by DNA-binding protein.

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