If you don't see a picture above with DNA and various
regulatory buttons, please install newest version of Java.
This applet allows one to simulate stocastic transcription initiation.
In the middle, there are three redio buttons:
"Standard", "Recruit", and "Dead-end".
"Standard" is the standard 3-step model for the initiation:
RNAP bind to DNA to form a closed complex (which can fall off),
then changed into an open complex,
and finally start to elongate.
"Recruit" is a model to make correlation in
successive transcription initiation, by
taking into account the possibility that an elongating complex
may recruit new RNAP to form open complex directly
by changing the supercoiling of the DNA.
"Dead-end" is a model to consider the pathway that
an open complex fails to elongate but go into
dead-end complex, which occlude next RNAP
until it is removed after some time.
In the "Standard" model,
there is the total strength of the promoter, ``Strength",
quantified by the average time in seconds between two subsequent
transcription initiation events. E.coli promoters can here have widely
different strengths, from about 1 second for some Ribosomal promoters
to for example 360 second for the lysogeny maintenance
gene in the P2 phage. The promoter strength, or its reciprok namely
the time between two subsequent RNAP's is:
1/Strength = time(off)+time(closed)+time(open)+time(self-occlusion)
Second there is the aspect ratio, which is the ratio of effective rate for
forming an open complex formation all the way from free RNAP, to the rate
of initiating an elongating complex from an already formed open complex:
Aspect ratio = rate(off->Open)/rate(Open->Elongation)
A low aspect ratio means a slow on-rate, and a relatively
fast elongation initiation.
Thus a low aspect ratio imply that the RNAP
spend a short time on the promoter. A low aspect ratio also means that
the promoter activity is limited by the rate of open complex formation.
The aspect ratio have large implications for transcriptional interference
(Sneppen et al. (2005)), as well as for the most efficient ways that
the promoter can be regulated by transcription factors.
P2 lysogeny maintenance promoter have aspect ratio 0.04
whereas 186 lysogeny maintenance promoter have aspect ration of 1.
[Off--> Closed] and [Closed-->off] are equilibrium rates of forming and dissociating from
the closed complex. The ratio between these rates sets the average
time spent in the closed state.
If one choose "Recruit",
the applet also incorporates the possibility for correlations between
subsequent transcription initiations events. This is done by
assigning a non zero probability P that an elongating complex
recruit an open complex when it leaves the promoter.
When P approaches 1, each elongating complex will tend to recruit an
open complex and subsequent transcription initiations will have
exponentially distributed waiting times with mean set
by the rate at which open complexes becomes elongating.
When P is small or P=0, subsequent firings will be governed by the statistics
of the full 3 step process.
If one choose "Dead-end", an open complex can elongate
normally with a probability Q (given in a
box "Q(Succeed elongation)", or go into a dead-end complex with
a probability (1-Q) which cannot elongate any more but
prevent new RNAPs to comes in: The dead-end complex
is removed stocastically with a given average decay time
(In the box "Decay time (sec)").
The dead-end complex will be shown by Black and grey.
The applet allows you to change parameter.
One can change the equilibrium rates and recruitment rate.
To control the transition between the close complex to the open complex
and the open complex to the elongating complex,
one can choose to
(i) give the strength of the promotor and the aspect ratio,
and then the transition rates are calculated,
(ii) controle the transition rates,
and then the strength of the promotor and the aspect ratio is
(i) is applied when one choose the buttom "Control Strength",
while (ii) is applied when
the button "Control rates" is chosen.
The background of the parameters that one is controling appears
light blue, while the one that is calculated (and cannot be changed)
In the rectuitment model or the dead-end model,
there is some restriction in possible combinations
of parameters. For example, in the dead-end model,
if one gives very long decay time of the dead-end complex
with high probability to go into the dead-end complex,
it is impossible to get high strength.
If one chose "Control Strength" but gave impossible
strength, the value of the strength is refused
and go back to the previous value.
Finally the applet opens the possibility for viewing the whole process
at a large scale. Change the scroll bar with "Small" and "Large";
"Small" means you see smally regision (but magnified),
while "Large" means you see large scale structure of DNA,
and thus get a better view of separation between subsequent RNAP.
With the scroll bar with "Slow" and "Fast",
one regulate the speed of the simulation.
Transcription initiation modeled as a 3 step process (McClure 1985):
Of these processes, step 1 is an equilibrium process with an on- and an off-
rate that sets the affinity of the RNAP to the promoter.
Step 2 and 3 are considered one way reactions,
and each is therefore characterized by one one-way reaction rate.
- A closed complex (C) formation.
- An open complex (O) formation.
- RNA polymerase (RNAP) which elongate (E) without its sigma factor.
In the applet we visualize the 3-step process with transitions between
3 representations of the same piece of DNA.
The ``1-position" of the promoter is illustrated with the arrow,
whereas the -10 and -35 positions are indicated with green bars
across the double stranded DNA.
We quantify the promoter in terms of 4 numbers,
ordered after decreasing practical implications.
In addition the applet incorporates the possibility for correlations between
subsequent transcription initiations.
This modification is inspired by the bunched activity
that have been observed for some promoters (Golding et al.).
H. Buc, W.R. McClure. "Kinetics of open complex formation between
Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence
for a sequential mechanism involving three steps."
Biochemistry. 1985 24(11): 2712–2723.
W.R. McClure. "Mechanism and control of transcription initiation in
prokaryotes." Annu Rev Biochem. 1985;54:171–204.
Sneppen K, Dodd IB, Shearwin KE, Palmer AC, Schubert RA, Callen BP, Egan JB.
"A mathematical model for transcription interference"
J. Mol. Biol. 346 399 (2005).
I. Golding, J. Paulsson, S.M.Zawilski and E.C. Cox,
"Real time kinetics of gene activity in individual bacteria"
Cell 123, 1025 (2005)