This Java applet (If
you don't see anything above, please install Java 1.4) models
between two promoters, through RNA polymerase (RNAP) traffic.
Each polymerase occupies 70bp when sitting on the promoter, and 35 bp
when elongating. The interference imply that each of the promoters will
less active due to effect from the opposing promoter. This reduced
is due to a number of effects associated to collisions between moving
RNAP's, occlusion of one promoter by the passage of an RNAP from the
as well as ejecting of RNAP on one promoter due to collision with a
RNAP. Finally the applet also opens for simulation of road block
where a sitting duck also eject a elongating RNAP (with probability set
The interference (I-factor) measure activity of promoter without
opposing promoter, divided with activity in current setting.
The approximate I-factor is based on an analytic estimate, which will
correct when opposing promoter is much stronger, or if both promoters
weak. It basically counts reduction of activity of given promoter,
the opposing promoter is not perturbed.
Realistic strength of
promoters covers a wide interval. For the very
promoter PL in lambda phage 1/K=4.5sec correspond to one firing per 4.5
second. Other typical numbers are 1/K=18sec for PR in phage 186,
the lysogen maintenance promoter promoter PL in 186 which have
1/K=180sec. The interference increases when as a promoter is
exposed to a
promoter (i.e. K(opposing)/K(observed) increases ). The aspect ratio
the ratio between the on rate (kon) and the firing rate (kf) of an
promoter. For aspect ratio>>1, the on rate is high, and the
loads easily, but stays occupied for a long time. For aspect ratio
the promoter loads rarely, but fire instantly when it has loaded. PL in
have aspect ratio close to 1. pC from phage P2 on the contrary have
ratio of about 0.1. One will see that an aspect ratio of about 1
the interference (try the applet).
The overall system
parameter also include distance N between
promoters, that could be varied fro -120 to 3000, with N<40
corresponding to overlapping or partially overlapping promoters. The
velocity is the assumed
velocity of elongating RNAP that experimentally (see paper
to JMB) is fitted to be between 40 and 50 bp/sec.
The applet also opens
for toying with the system, as clicking below or
above the DNA line in middle of screen, artificially initiate a
RNAP of corresponding
type on the DNA. Also one may view interference between distant
promoters by adjusting the distance button. For strong promoters with
one then observe a system with possibility for very strong fluctuations.
Transcriptional Interference Model
Dodd, K.E. Shearwin, A. Palmer,
R.A. Shubert, B. Callen
and J.B. Egan.
(A mathematical model
for transcriptional interference by RNA
traffic in Escherichia coli)
model deals with the interference
the two promoters pA and pS as shown in the applet. The RNAPs are
onto the DNA through binding and formation of sitting duck complexes at
respective promoters, followed by subsequent formation of elongating
The traffic is simulated by a stochastic model that is adjusted to take
account all known details of the dynamics. The stochastic dynamics are
by updating at any time step [t,t+dt]= [t,t+1bp/v] the presence of any
according to the basic processes (v is the velocity). That is, in time
step dt, a promoter forms an open complex with probability
kon dt unless it is occupied or occluded by other RNAPs. In
the promoter is occupied, it initiates elongation with a probability
dt except when an RNAP from the opposing promoter is positioned
that it will collide with the sitting duck in the time step dt. kon and
kf together defines the strength of the promoter, that is firing (going
from "sitting duck complex" to elongation) with a total
rate K which approximately is equal to kon *kf/(kon+kf).
Any elongating RNAP is
moved vdt step in the direction of elongation,
when it collides with an RNAP moving in opposite direction. When such a
occurs the RNAP's are removed from the system. The transcription
of any of the promoters is counted by the number of RNAPs which pass
opposing promoter. The interference is found by comparing this number
the number obtained when the opposing promoter is assumed to be silent.
The model, together
with carefull analysis and comparison to experiment
submitted to JMB.
Measurements of up to
30 fold interference between tandem promoters:
S. Adhya and M.
Gottesman (1982), Cell 29, 939-944.
Measurements 2-10 fold
interference for various
B. P. Callen, I. Dodd,
K.E. Shearwin and J.B. Egan (2004), Mol. Cell