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The dotted trace in Figure 1b shows the distribution of ΔS for binding sites evolving in the absence of constraint.

Substitution into the general formulas for the expectation gives for the case of binding sites evolving in the absence of selection (case 1).

For example, I can show (see Methods) that for binding sites evolving in the absence of selection, A similar, albeit more complicated expression is available for the variance (see Methods).

It seems that the authors have the ability to investigate what is evolving, either: 1) CRM TFBS composition (binding sites evolving in our out), 2) TFBS linear arrangement (binding sites reordered), or 3) CRM-gene association (entire CRMs relocating and losing synteny).

Similar(56)

Emergence in genomes of Modern Humans of 794 regulatory sequences during 370,000 years implies that 2.15 novel NANOG-binding sites evolved in hESC genome every 1,000 years or one novel NANOG-binding site per 466 years of evolution (table 4; fig. 6).

It has been shown that TF binding sites evolve rapidly in order to adapt to metabolic control and detoxification in the liver [ 56].

In each case there are significantly fewer substitutions (p < 0.05, 1000 bootstraps) in the characterized binding sites than in the promoters in which they lie (figure 1B), suggesting that, in general, characterized transcription factor binding sites evolve more slowly than the surrounding intergenic sequences.

This is generally observed in the proteins studied and supports a hypothesis that protein protein binding sites evolve more rapidly than protein small ligand binding sites.

Many Zn extant binding sites evolved after that transition.

The expected value of ΔS for binding sites that evolve in the absence of selection is ΣΔ S iab p(a → b at i|one subs).

Furthermore, as we are interested in specific interactions of cognate ligands with binding sites that evolved to bind such molecules, the most common molecules found in crystallization buffers are also excluded from our analysis.

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