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 ID: 266398
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Slide1
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)Slide2
OutlinePreliminary
Introduction
Model
of Gene
Transcription
Experimental Results
ConclusionSlide3
PreliminaryCentral dogma of molecular biologySlide4
PreliminaryGene Transcription:
DNA->RNA
Initiation
Elongation
TerminationSlide5
IntroductionRegulation of Gene expressionDNA-binding Protein may increase or suppress the Transcription initiation rateSlide6
IntroductionWhat happens at end of transcriptional cycle?
RNAP d
iffuse 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 Slide7
Model of Gene TranscriptionConventional Scheme:Slide8
Model of Gene TranscriptionConventional 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 :Slide9
Model of Gene TranscriptionConventional 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 :Slide10
Model of Gene TranscriptionDefinition
k
a
: associate rate (P
o
->P
⋆
1
)kd : disassociate rate (
Po <-P ⋆ 1) c : RNAP concentrationk
0 : 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
*
: elongatedSlide11
Model of Gene TranscriptionConventional Scheme + Diffusion:
probabilities of P
⋆
1
,
P
*
1,
P*2, P⋆
2 state:
Steady-stateSlide12
Model of Gene TranscriptionConventional Scheme + Diffusion:Transcription Rate :
With saturation Transcription rate:Slide13
Model of Gene TranscriptionConventional Scheme + Diffusion:Transcription Rate :
Slide14
Model of Gene TranscriptionTranscription BurstThe probability that RNAP produces
n
RNA after
association is
given
by:Slide15
Model of Gene TranscriptionSlide16
Experimental Results
burst
Diffusion
Without DiffusionSlide17
Experimental ResultsSlide18
Experimental Results
diffusion
jumps rate
= 100 s
-1Slide19
Experimental Results
diffusion jumps rate
=
200
s
-1Slide20
Experimental Results
diffusion jumps rate
=
500
s
-1Slide21
Experimental Results?Slide22
ConclusionAnalyze the end of transcription cycle.
Transcriptional burst might occur without regulation of transcription by DNA-binding protein.