Nucleosome allostery in pioneer transcription factor binding

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  • Cheng Tan
    Department of Biophysics, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan
  • Shoji Takada
    Department of Biophysics, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan

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<jats:title>Significance</jats:title> <jats:p>Upon binding of effectors, allosteric molecules change their structures and responses to the downstream molecules, which can be viewed as the molecular if−then device. Simulating binding of two pioneer transcription factors (TFs), Sox2 and Oct4, to a nucleosome, which is the fundamental unit of genome folding, we found that a nucleosome acts as a new type of allosteric molecule. Free nucleosomes exhibited rotation-coupled sliding of their DNA among metastable positions. The Sox2 binding on them selected a specific rotational phase of its motif, inducing global sliding of nucleosomal DNA. Consequently, the repositioned DNA affected the accessibility of another TF, Oct4, or the second molecule of Sox2 at a distant region within the nucleosome, which thus is a long-distance allosteric effect.</jats:p>

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