Co-localization between genes and transcription factors.

<p>(<b>A</b>) Experimental results with immuno-RNA FISH reveal co-localization between transcription factors and factories (RNAPII), genes and transcription factors, and gene pairs and transcription factors. This is the contour plot from original experimental data. (Aa) Immune-fluorescence detection of Klf1 (red) and RNAPII-S5P (green) in definitive erythroid cells, with a scale bar of 2 µm. This shows the co-localization between Klf1 and transcription factories RNAPII. This Klf1 background association rate (level) is estimated to be 20%. (Ab) The co-localization between transcription factor Klf1 and Hbb gene. (Ac) The co-localization between factor Klf1 and genes pairs (Hbb and Hist1). (<b>B</b>) Simulation results when we hold the Klf1 background association level as 20%, while the translocation of transcription units (genes, factors and factories) are following sub-diffusion process (<i>H</i> = 0.4). (Ba) Gene-factor association level (numbers indicated behind the stars) with various factors and binding time, both for 2D and 3D cases. The number of genes (for each family) is fixed to be 5 and the Klf1 (X factor) background association level is fixed to be 20% (the stars indicate the parameter values when this condition is satisfied). The detailed Klf1 association level for each X gene and Y gene are presented in the figure below, revealing the fact that the simulation results for 3D case (gene-factor association level = 0.6) match the experimental result (gene-factor association level = 0.64) quite well for a specific set of parameters (5 genes, 2 factors and 130 sec binding time). (Bb) Gene-factor association level (numbers besides the stars) with various genes and binding time for 2D and 3D cases. The number of factors is fixed to be 2 and the Klf1 background association level is fixed to be 20%. (Bc) The association rate of Klf1 (X factor) with Z gene and paired X-Z genes when there is a negative correlation between X and Z gene, or X and Z factors, under 3D case. The parameter used here are 5 genes, 2 factors, and 130 sec binding time. Preventing probability means the chance for stopping another gene (factor) to enter the factory when there is already one gene (factor) in that factory. When <i>p</i> = 0, it represents the independent situation of X factor (gene) and Y factor (gene).