Conformational Dynamics of Chromatin Fiber: Comparative Analysis of Force-Extension Spectroscopy with Monte Carlo Simulations

Force spectroscopy experiments are ideally suited to unveil conformational dynamics of chromatin fiber. However, to extract structural information at the subnucleosomal level it is necessary to combine the experimental data with a detailed mechanical fiber model. We used a coarse-grained Monte Carlo (MC) approach to simulate nucleosome arrays under external force (F), for variable nucleosome repeat length (NRL = 167 and 197 bp), stacking energy (E = 0 to 12 kT), and DNA unwrapping at the nucleosome ends (U = 0 to 72 bp). We found that different regions of the experimental force-extension curves correspond to the MC-simulated curves with different degrees of DNA unwrapping and the inter-nucleosome stacking interaction E = 8 kT can account for the experimental observations. Our comparative analysis reveals that the DNA ends in nucleosomes breathe by 9 – 12 bp even at small forces, F < 3 pN, corresponding to a linear force-extension regime. Importantly, under these conditions the fiber is highly dynamic with continuous unstacking-restacking transitions. The simulated structures are mostly two-start zig-zag fibers with rare occurrences of 3- to 5-start morphologies. At the so-called plateau force, F ≈ 3.5 pN, fiber undergoes an abrupt extension accompanied by unwrapping of 15 – 25 bp at the nucleosome ends. Nucleosomes unwrap further up to ~45 bp from both ends at force F ≈ 8 pN. Our results have implications regarding accessibility of DNA to transcription factors in chromatin fiber and are vital for understanding the fiber unfolding pathways induced by RNA polymerase and nucleosome remodelers.