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Remarkably, we found a direct association between sequence divergence and CTCF binding divergence.
Is there a direct (or perhaps causal) relationship between genetic divergence and TF binding divergence?
We show broad conservation of Dichaete and SoxN regulatory networks coupled with widespread binding divergence at a rate that is consistent with studies of other TFs in Drosophila.
Thus, the data demonstrate a relationship between CTCF binding divergence and divergence of local insulation structure and therefore point to a role for CTCF in driving structural change in the genome.
In agreement with previous studies, the rates of binding divergence for both Dichaete and SoxN between Drosophila species are lower than those for TFs in vertebrate species at comparable evolutionary distances [ 20, 81].
In agreement with the PCA plot, 8880 differentially bound intervals were identified between D. melanogaster and D. yakuba at FDR1, while only 5044 were identified between D. melanogaster and D. simulans, indicating a greater amount of quantitative binding divergence between D. melanogaster and D. yakuba.
Similar(52)
In fact, as might be expected, CTCF-binding divergence generally corresponded with evolutionary distance.
The reason could be the presence of novel arsenite oxidase gene within them (Sultana et al. 2012) or mutation in primer binding sites (divergence in its conserved catalytic domain) of the isolates.
Rates of binding site divergence are elevated in noncoding sequences of duplicated loci with accelerated substitution rates.
If the 21st aa performed a binding function, such divergence could have reflected ligand binding specificity between PFWs and NPFWs.
The conservation of the secondary binding mode despite divergence of the primary specificity indicates that the binding modes can in some cases evolve independently of each other.
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