Nucleosome Dynamics : Atomic Force Microscopy Reveals Its Intimity

Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet, in living cells, this organization of nucleosomes also results from the action of various external factors like DNA binding proteins and chromatin remodelers. To decipher the code for intrinsic chromatin organization and dynamics, there is thus a need for in vitro experiments to bridge the gap between computational models of nucleosome sequence preferences and in vivo nucleosome occupancy data. Here we first combine atomic force microscopy (AFM) in liquid and theoretical modeling to demonstrate that the main sequence signaling in vivo are high energy barriers that locally inhibit nucleosome formation rather than favourable positioning motifs. We show that these excluding genomic energy barriers condition the collective assembly of neighboring nucleosomes consistently with equilibrium statistical ordering principles. The analysis of two gene promoter regions in S.cerevisiae and the human genome indicates that these genomic barriers direct the intrinsic nucleosome occupancy of regulatory sites, thereby contributing to gene regulation. We further apply time-lapse AFM imaging to directly visualize the dynamics of a single nucleosome nearby a genomic excluding energy barrier. The observation, in the absence of remodelers, of the unwrapping and/or ejection of this nucleosome suggests that the sequence-dependent intrinsic nucleosome dynamics can contribute to chromatin remodeling. These results provide novel hypotheses about chromatin dynamics and its contribution to gene regulation.