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)

Outline Preliminary Introduction Model of Gene Transcription Experimental Results Conclusion

Preliminary Central dogma of molecular biology

Preliminary Gene Transcription: DNA->RNA

Initiation

Elongation

Termination

Introduction Regulation of Gene expression

DNA-binding Protein may facilitate or suppress the Transcription initiation

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

Model of Gene Transcription

Conventional Scheme:

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⋆

1 state:

Transcription Rate :

Model of Gene Transcription

Conventional Scheme + Diffusion:

Model of Gene Transcription

Conventional Scheme + Diffusion: probabilities of P⋆

1 , P*1, P*

2, P⋆2 state:

Steady-state

Model of Gene Transcription

Conventional Scheme + Diffusion: Transcription Rate :

With saturation Transcription rate:

Model of Gene Transcription

Conventional Scheme + Diffusion: Transcription Rate :

Model of Gene Transcription

Transcription Burst The probability that RNAP produces n RNA after

association is given by:

Model of Gene Transcription

Experimental Results

burst

Diffusion

Without Diffusion

Experimental Results

Experimental Results

diffusion jumps rate = 100 s-1

Experimental Results

diffusion jumps rate = 200 s-1

Experimental Results

diffusion jumps rate = 500 s-1

Experimental Results?

Conclusion Analyze the end of transcription cycle. Transcriptional burst might occur without

regulation of transcription by DNA-binding protein.