Deciphering the functional significance and physico-chemical mechanisms of histone post-translational modification cross-talk

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In eukaryotic cells DNA is packed in chromatin. Nucleosomes represent subunits of chromatin and hubs in epigenetic signalling. They are comprised of a histone octamer of four types of core histones, two copies each, with ~147 base pairs of DNA wrapped around them. All histones are flanked by the intrinsically disordered tails that carry multiple post-translational modifications (PTMs - methylation, acetylation and others). Through their PTMs, histones can disrupt or mediate the interactions with other chromatin factors, thereby coordinating pathways in time and space. It requires a switch that can be achieved by a cross-talk between multiple histone modifications. Histone tails can extensively interact with the nucleosomal and linker DNA and these interactions can drastically change the DNA and histone site accessibility to readers, writers and erasers. However, there are very few studies on histone tails and their binding to DNA in the context of nucleosomes, which is explained by the difficulty in their experimental and in silico characterization. We propose to initiate a new collaboration to identify the molecular basis for regulation via histone tail modifications and their cross-talk. We test the main hypothesis according to which the dynamics of histone tails and their interactions with DNA in nucleosomes is an important factor explaining the cross-talk of histone tail modifications. We will perform in silico, in vitro and in vivo experiments. The sampling of tail conformations in nucleosomes and in a free peptide with and without PTMs will be done using enhanced sampling methods and all-atom molecular dynamics simulations. The effects of PTMs on tail flexibility and interactions with DNA will be verified by NMR spectroscopy and unbiased mass spectrometry analyses. Outcomes of this project will provide insights into physico-chemical mechanisms of engagement of chromatin factors in transcription and replication. The study will link certain combinations of histone modifications with distinct chromatin states and will provide liaisons to bridge experimental and in silico approaches, basic and applied science.