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)