@article{TEXTUAL,
      recid = {10208},
      author = {Ni, Xiaochun and Zhang, Yong E. and Nègre, Nicolas and  Chen, Sidi and Long, Manyuan and White, Kevin P.},
      title = {Adaptive Evolution and the Birth of CTCF Binding Sites in  the &amp;lt;i&amp;gt;Drosophila&amp;lt;/i&amp;gt; Genome},
      journal = {PLOS Biology},
      address = {2012-11-06},
      number = {TEXTUAL},
      abstract = {&lt;p&gt;Changes in the physical interaction between  &lt;em&gt;cis&lt;/em&gt;-regulatory DNA sequences and proteins drive  the evolution of gene expression. However, it has proven  difficult to accurately quantify evolutionary rates of such  binding change or to estimate the relative effects of  selection and drift in shaping the binding evolution. Here  we examine the genome-wide binding of CTCF in four species  of &lt;em&gt;Drosophila&lt;/em&gt; separated by between ∼2.5 and 25  million years. CTCF is a highly conserved protein known to  be associated with insulator sequences in the genomes of  human and &lt;em&gt;Drosophila&lt;/em&gt;. Although the binding  preference for CTCF is highly conserved, we find that CTCF  binding itself is highly evolutionarily dynamic and has  adaptively evolved. Between species, binding divergence  increased linearly with evolutionary distance, and CTCF  binding profiles are diverging rapidly at the rate of 2.22%  per million years (Myr). At least 89 new CTCF binding sites  have originated in the &lt;em&gt;Drosophila melanogaster&lt;/em&gt;  genome since the most recent common ancestor with  &lt;em&gt;Drosophila simulans&lt;/em&gt;. Comparing these data to  genome sequence data from 37 different strains of  &lt;em&gt;Drosophila melanogaster&lt;/em&gt;, we detected signatures of  selection in both newly gained and evolutionarily conserved  binding sites. Newly evolved CTCF binding sites show a  significantly stronger signature for positive selection  than older sites. Comparative gene expression profiling  revealed that expression divergence of genes adjacent to  CTCF binding site is significantly associated with the gain  and loss of CTCF binding. Further, the birth of new genes  is associated with the birth of new CTCF binding sites. Our  data indicate that binding of &lt;em&gt;Drosophila&lt;/em&gt; CTCF  protein has evolved under natural selection, and CTCF  binding evolution has shaped both the evolution of gene  expression and genome evolution during the birth of new  genes.&lt;/p&gt;},
      url = {http://knowledge.uchicago.edu/record/10208},
}