Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors

摘要: Activator proteins 1 (AP-1) comprise one of the largest families eukaryotic basic leucine zipper transcription factors. Despite advances in characterization AP-1 DNA-binding sites, our ability to predict new binding sites and explain how achieve different gene expression levels remains limited. Here we address role sequence-specific DNA dynamics for stability specific factors, using microseconds long molecular simulations. As a model system, employ yeast factor Yap1 three response elements from two genetic environments. Our data show that actively exploits plasticity within element form stable protein-DNA complexes. The also depends on four six flanking nucleotides, adjacent elements. sequences modulate conformational adaptability element, making it more shape-efficient contacts with protein. Bioinformatics analysis differential studied genes supports conclusions: Yap1-DNA complexes, modulated by environment, influences levels. results provide insights into mechanisms recognition biological regulation eukaryotes.