Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles.
As mentioned above, of the 29 duplicated gene pairs harbouring miRNA binding sites, 12 pairs have miRNA binding sites on both paralogs, indicating that these genes most likely had been regulated by miRNAs or gained their miRNA binding sites before the WGD and that their miRNA binding sites were maintained after the WGD.
In support of this, H3K27 methylation introduced by targeting Ezh2 next to the Gal4 binding site was maintained 4 days post clearance of the targeting construct [ 108].
Nevertheless, molecular dynamics simulations identify transient water binding at sites that agree well with those observed by crystallography, indicating that the energy landscape of the binding site is maintained in solution.
Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture clusters of low affinity binding sites is maintained and required for enhancer function.
Here, these binding sites are not discussed one by one.
These binding sites are highly charged.
Noteworthy, these binding sites are juxtaposed to GATA3-binding sites.
Thus, the accessibility of their DNA binding sites is important in maintaining pluripotency.
