Nucleosome Mediated Transcription Regulation
Top panelFast Update / Animation: The button in the top right corner, gives the option to either gather statistics fast or to view the recruitment and nucleosome updates as a little sequence of events. The feeder is located on the left site and the promotor is on the right site. When the Nucleosome the promotor sits on is either methylated or unmodified, the promotor will have a black X over it, indicating that its inactive.
Bottom panelThe Applet continues to run through a sequence of σ gathering statistics.
The left plot shows the probability distribution for each of theses σ's, with the distribution for the current value highlighted in red.
The right plot shows the average number of A's for each σ. The simulation for any σ can be accessed by pressing the corresponding square in this plot. (Not active before the first round of σ's is completed).
The control buttons gives the possibility to change the system size N, the recruitment to noise ratio F and the asymmetry μ. The asymmetry can either work on the recruitment mechanism or the noise, an option thats given by the last button.
In the applet we investigate how a transcription factor that recruit
histone modyfying enzymes may use these to influence the overall
state of nucleosomes in the region where the gene is embedded.
With varying strength of the TF mediated recruitment, one easily
obtain a sharp response on the average nucleosome state,
and thereby for the activity of the promoter in region regulated by
the transcription factor.
The basic Algorithm is similar to that introduced in , with an added asymmetry μ and the regulation by TF σ. The steps are shown in the figure below.
 I. B. Dodd, M. A. Micheelsen, K. Sneppen and G. Thon. (2007)
 K. Sneppen, M. A. Micheelsen, I. B. Dodd. (2008)