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Regulatory evolution of the genes in the eyespot network (losing or gaining binding sites for genes such as Spalt, as well as for other wing sector-restricted genes, activators or repressors) may have produced the pattern of successive eyespot origins uncovered in this study.
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And so, populations of pathways that tend to gain binding sites over losing them — that is to say, populations with genomes that harbor large ncDNA regions — would have access to more innovative phenotypes over populations with shorter ncDNA regions.
The presence of the target may induce a deformation of the ligand that, in order to gain binding energy, shifts the binding sites to new positions.
If selection favours a change in the way a group of genes are regulated, then each of the target genes must independently gain novel binding sites and/or lose existing ones [ 8, 9, 11, 12].
Binding is specific, that is a binding site of the ligand can gain binding energy ε only by fastening to its complementary binding site on the target.
This analysis identified 170 genes associated with HARs that display a significant loss or gain of binding sites in human compared with chimpanzee (TFBS divergence) (File S1).
Since the annotation of fast or slow characters emitted by the root is conserved in the descendent sequences, the model cannot detect the loss or gain of binding sites.
miR156 and miR535 are all conserved in dicots and were predicted to target only one member of their respective target gene families (Additional file 6), suggesting potential gains of binding sites after the WGD.
Over time, however, phosphorylated Stat1 could accumulate as Stat1 slowly gains access to binding sites on EGFR.
This is consistent with our observation that HIF-1 binding sites gaining 5-hmC in our hMe-Seal experiments exhibit an increase in the amount of unmodified cytosine at the HRE in TAB-seq experiments, which facilitates gene induction.
Figure 7 displays further transcription factor binding sites gained by primates (green), as well as transcription factor binding sites gained by rodents (cyan).
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