This movie shows a 3D version of the stochastic reaction-diffusion
model of transcription, mRNA export, translation, protein import,
and gene regulation model in Isaacson, Peskin SISC 2006. Gene
regulation involves dimerization of the protein being expressed,
which then can bind and inhibit transcription of its own gene. The
movie shows an oscillation in protein number as the gene flips
between being repressed from bound dimer, and free to transcribe.
Notice also the "burstiness" of transcription.
Movie Key:
The inner blue sphere is the nuclear membrane, the outer the cellular
membrane.
The movie shows:
Light blue marker in center = gene of interest when nothing
is bound (polymerase or repressor).
Slightly lighter blue marker = gene of interest when
repressor is bound
(so can undergo
transcription).
Green marker
=
mRNA bound to nuclear export factors.
Red
marker
= Protein Monomers
Dark Blue
marker
= Protein Dimers, these can act as
repressors.
Other
markers
= Various export factors and protein or mRNA
complexes.
When the gene disappears it is undergoing transcription. It is
always constrained to lie in the center mesh cell in the
simulation, however, its position within this mesh cell is chosen
randomly. mRNAs are not shown when undergoing translation, and so
may disappear due to either translation or degradation.
Movie:
[here]