Chromatin Structure Regulation By An Epigenetic Switch Tuning The Flexibility Of The H1 C-Terminal Domain

Inside Eukaryotic Cells, DNA is complexed with histone proteins forming chromatin - an array of nucleosomes separated by protein-free linker DNA. H1 Linker Histones (LH) are an essential component of chromatin where they bind to the surface of nucleosomes, transforming the conformation of nucleosomes with respect to one another. H1 proteins are formed by a structured globular domain (GD) and unstructured N- and C-terminal domains (CTD). While high-resolution structural studies have characterized the binding of the H1 GD to nucleosomes, truncation mutant experiments demonstrate a dependence of chromatin compaction on the unstructured terminal domains. These intrinsically disordered terminal domains are also the sites of multiple post-translational modifications that can further regulate chromatin structure and thereby gene expression. Here we determine the influence of the terminal domains on chromatin structure through a novel multiscale strategy that combines nucleosome-scale multi-microsecond atomistic enhanced-sampling Molecular Dynamics simulations with coarse-grained Monte-Carlo simulations of 100 nucleosome arrays. In the atomistic scale, we use a Biased-exchange Metadynamics setup biasing the CTD's secondary structure and its interactions with DNA. These results are used to develop LH parameters for integration into the successful NYU chromatin coarse-grained model. Our results suggest that the CTD bridges DNA through flexible loops and abets the formation of an asymmetric chromatosome with curved linker DNA arms - a result challenging the canonical view that LHs induce a rigid and symmetric DNA stem but more consistent with the emerging view of chromatin polymorphism. The chromatosome asymmetry allows the formation of polymorphic structures remarkably similar to those from recent Chrom-EMT images. Extending the multiscale strategy to investigate H1 CTD phosphorylation, we demonstrate that this epigenetic modification's cyclical effect on chromatin compaction is tied to its influence on the disordered CTD's flexibility.