5.2.2 Gene Controllers

1. Purpose

Transcription factors do a good job of regulating the rate of transcription of a gene. They can speed up the transcription or slow it down to a stop. One important restriction for TF's though is that they have to be physically present at the time they are performing their regulation. They can not simply flip a gene on and then go away. But this is something that is definitely needed and it is something that occurs in nature. Nature has at least two simple ways to turn genes on and off. The first method to turn a gene off is to simply coil the DNA up so tightly on its histones that none of the polymeareses can physically get to it to read the instructions. If the instructions can not be read then no transcription can take place. To turn the gene back on the DNA is unwound into its loose form so that it can again be transcribed. Another method used by the cell is to methylate the bases on the DNA. A protein runs up the base pairs on the gene and on certain ones it adds a methyl group. This methyl group interferes with the polymeareses ability to attach to the DNA to read it and thus stops transcription. To turn the gene back on another protein comes along and strips the methyl groups back off. In both of these cases something similar happens. A protein comes along and alters the physical makeup of the gene so that it remains turned on or off even after the protein that performed the switch has long since degraded. This is a long term effect, whereas the TF's are short term effects. This is the purpose of the gene control elements. They are responsible for flipping genes on and off, and once flipped they remain in that state until another controller comes along to change that state. So once a gene is turned off it can have a huge quantity of TF's that up-regulate it, but that gene will still not be expressed because it is off. It can only be turned back on again if another controller comes along and flips it on. Now that we have an idea of what a gene controller does lets discuss how it does it.

Gene Controller Properties
Protein Type: All proteins have this property. It is used to determine the type of protein to load.
Binding ID: All proteins have this property. For GC's it matches up with control sites on genes to determine which genes that it can flip.
Degrade Rate: All proteins have this property. This determines the rate at which this protein is degraded in the cell.
Graph Type: This determines which type of graph to use for the expression function of this protein. The expression function determines how the protein will affect the regulation of genes with matching Binding ID's
A: This is one parameter of the expression function and its affect depends on the graph type.
B: This is one parameter of the expression function and its affect depends on the graph type.
C: This is one parameter of the expression function and its affect depends on the graph type.
D: This is one parameter of the expression function and its affect depends on the graph type.
Table 1.These are the different properties of a gene controller protein that are defined in the digital genes.

Gene Control Site Properties
Binding ID: This value matches up to the BindingID of the gene control protein.
Active: This determines whether this site will flip the gene on or off.
Threshold: This is the threshold value at which the controller/site will flip the gene.
Table 2.These are the different properties of a gene control site that are defined in the digital genes.

2. Flipping Genes

Gene controller proteins have the properties shown in table 1. It is essentially the same as that for the transcription factor. It is on the gene itself where these two begin to differ. The effects of a transcription factor are determined by the functionality of the factor itself. The only thing it needs from the gene is a place to dock. However, the functionality of the controllers is different. It is spread between the protein and the gene. The same GC protein might turn one gene on and turn another off. It is the site it binds to that determines this and not the protein itself. Table 2 shows the properties of a gene control site. Each gene has a list of these control sites so that multiple different GC proteins can compete to turn the gene on or off. The first element of the site is the binding ID. This ID matches up with the binding ID found in the protein and lets the system determine which protein and sites match up. The next parameter is the active flag. This tells the system whether this site is attempting to turn the gene on or off. Finally there is the threshold parameter. And it will require a bit more explanation.

There are actually two levels of competition to determine whether a gene is flipped or not. The first level is between different GC's attaching to the same site. The second is between different sites. Lets start with the simplest case and then work into something a little more complex. We have a gene that is turned off by default, a single control site that flips the gene on and a single GC protein that binds to that site. In this case at each time slice the quantity of GC available will be determined and this value will be fed into the expression function of the GC protein to get a new output value. This value will then be compared to the threshold of the site. If it is greater than or equal to the threshold then the gene is flipped on, otherwise the gene is left alone.
The next case has a gene that is turned off by default, a single control site that flips the gene on and two different GC proteins that bind to the site. The first protein up-regulates the site and the second down-regulates the site so that they are competing. The quantity of each protein is fed into their expression functions and the resulting values are added together. If the combined value still exceeds the threshold then the gene is flipped on, otherwise it is left alone. This is the competition within a site. If you have enough of the protein that down-regulates this site then it could effectively stop the gene from being flipped even if you have enough of the other protein that it would flip the gene if it were by itself.
The next level of competition is between the sites themselves. What happens if you have one site that says to flip the gene on and another site that says to flip it off? Which one is wins? To resolve this problem each site that is activated (flipped on or off during that time slice.) adds up the difference between its combined value and its threshold value. If it is flipping the gene on then it adds the difference to the total and if it is flipping it off it subtracts the total. Once all of the sites are checked it is this value that determines what happens to the gene. If it is greater than zero then the gene is flipped on, less than zero it is flipped off, and if it is zero then everything balanced out and nothing is done to the gene. So why add the difference value instead of just using the combined value for each site? Lets look at a simple example. We have two sites, one flips the gene on and the other flips it off. They have thresholds at 19,990 and 200, and their expression functions return 20,000 and 1000. The first GC is huge but barely over its threshold. The second one is small but is way over its threshold. If you were to simply add 20,000 - 1000 then you would get a positive number and the gene would stay on even though the first site is only 10 points over. But if you take the difference then you get 10-800=-790 and the gene is flipped off. The values produced by the expression functions can not be directly compared. It is the difference of that value from the threshold that is important. So now there is a simple way for the sites to compete to flip the gene.

3. Gene Control Examples

Gene Control Protein Competition
Figure 1. This graph shows the output of two GC proteins competing over the same site.
Click the image to view a chromosome analysis.

Gene Control Site Competition
Figure 2. This graph shows the output from two different GC sites competing to control the gene. Click the image to view a chromosome analysis.

Figure 1 shows a simple example of two GC proteins fighting for control of a given control site on a gene. If you look at the chromosome analysis for this example you can see that there are two different GC proteins that are each trying to turn the gene off. GC+ has an expression function with a positive slope, and GC- has an expression function with a negative slope. So while GC+ is trying to flip the gene off, GC- is fighting GC+ to keep the gene on. In figure 1 the two different GC proteins are injected after 5 time slices. If GC- not both there and competing then GC+ would immediately shut the gene off. But since it is there and since it degrades faster than GC+ then when it runs out of steam at around 3.5 seconds you can see that GC+ wins and the gene is flipped off.

Figure 2 on the other hand shows competition between two different control sites. There are two different GC proteins that have different binding ID's and thus bind to different sites on the gene. The gene in this case is off by default and GC+ is injected into the cell at time slice 5. When it is put into the cell it immediately switches the gene on and it begins producing GC- through basal transcription. But since GC+ is so much farther above its threshold GC- can not switch it off until it exceeds its threshold by the same amount. Once it does it again turns off the gene. This stops transcription of GC- and allows GC+ to turn the gene back on. This is a simple feedback loop, and it will continue to oscillate until GC+ has degraded enough that it can no longer turn the gene back on.

4. Gene Control Overview

The ability to shut a gene off or flip a gene on for extended periods of time without requiring that proteins like transcription factors are present is a very important part of any developmental system. It provides a kind of memory. At some point in the life of a liver cell the body is going to want to shut off a whole slew of cells that are not used in a liver cell, and at the same time turn on those that are used. This is the ability that gene control proteins and sites give to this system. And by having multiple levels of competition it provides a dynamic way for the controllers to interact and compete with each other to control who and when genes are flipped.


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