An advantage of multiple gene regulatory proteins over single ones is that many different genes can be controlled with a handful of proteins. Consider the opposite situation, in which every gene would need a unique regulatory protein. The gene for each of those proteins would also need its own protein, and so on. Instead, a smaller set of proteins combines in different ways to make a large set of regulatory possibilities. Imagine that any regulatory element must be composed of two proteins. Four proteins (a, b, c, and d) can combine in pairs in ten different ways (aa, ab, ac, ad, bb, bc, etc.), and could thus, theoretically, control ten different genes. In reality, the situation is more complex, with literally thousands of regulatory proteins combining in ways researchers have not even begun to calculate.
With combinatorial control, therefore, a regulatory protein does not necessarily regulate a particular battery of genes or specify a particular cell type. Instead it might serve many purposes, and those purposes might overlap with those of other regulatory proteins. A regulatory protein might be switched on in many cell types, at different locations in the animal, and several times during development. Thus, combinatorial gene control makes it possible to generate a great deal of biological complexity with relatively few gene regulatory proteins.
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