Chromatin Structure and Dynamics: Histone Variants and Remodeling Complexes

Abstract

The organization of DNA into nucleosome can be seen as a barrier for the transcription factors binding to their target DNA sequences and interferes with several basic cellular processes. ATP-remodeling machines and the incorporation of histone variants into chromatin are used by the cell to overcome the nucleosomal barrier and modulate DNA accessibility by the control of nucleosome dynamics. In this work, we use a single molecule technique (Atomic Force Microscopy, AFM) to visualize isolated mono- and oligo-nucleosomes and quantify their structure and dynamics at thermodynamical equilibrium and out of equilibrium.We have studied the impact of H2A.Bbd histone variant incorporation at the mono-nucleosome and oligo-nucleosome level, and we have shown that this variant modifies both the structure and the dynamics of the nucleosome altering the ability to form a higher structure organization of the chromatin. Using a polymer physics model, we demonstrated that the behavior of variant chromatin can be quantitatively explained by the mono-nucleosome flexibility [1].We are also interested in the mechanism of nucleosome remodeling by SWI/SNF and RSC on mono- and di-nucleosomes. Focusing on the di-nucleosomes, AFM imaging showed only a limited set of distinct configurational states for the remodeling products. No stepwise or preferred directionality of the nucleosome motion was observed [2]. Analysis of the corresponding reaction pathways allows deciphering the mechanistic features of RSC-induced nucleosome relocation. The final outcome of RSC remodeling of oligosomal templates is the packing of the nucleosomes at the edge of the template, providing large stretches of nucleosome depleted DNA.[1] F. Montel, H. Menoni, M. Castelnovo, J. Bednar, S. Dimitrov, D. Angelov & C. Faivre-Moskalenko; Biophys. J. 97, 544-553 (2009).[2] F. Montel, M. Castelnovo, H. Menoni, D. Angelov, S. Dimitrov & C. Faivre-Moskalenko; Nucleic Acids Res. 39, 2571-9 (2011).