Nucleosome Dynamics Studied by Single Pair FRET and Computer Simulations

DNA in nucleosomes is sterically occluded and nucleosomes must open to allow full DNA access. We studied this process by single pair FRET (spFRET), all-atom and coarse-grained molecular dynamics. spFRET shows evidence for a new structural intermediate preceding histone dissociation, in which the (H3-H4)2 tetramer/(H2A-H2B) dimer interface is split open. This is followed by H2A-H2B dimer release from the DNA and, lastly, (H3-H4)2 tetramer removal. This open intermediate state could be demonstrated in Xenopus and yeast nucleosomes; histone variants such as H2A.Z change the mechanism of opening. We estimate that the open state is populated at 0.2 - 3 % under physiological conditions, and could have significant in vivo implications for factor-mediated histone exchange and for DNA accessibility.To look for subpopulations and changes in FRET distances during the salt-induced transition for the various FRET pairs, we used photon distribution analysis (PDA). We observed two to three populations for all the FRET pairs, their calculated distance corresponding to the values expected from the dye positions in the crystal structure. Histone tail acetylation increased these distances and shifted the midpoint of the opening transition to lower salt concentrations.The effect of histone tail modification was studied by all-atom MD simulations with 100 ns trajectories of the full nucleosome. We find evidence for an internal allosteric transition at the H2A-H3 interface induced by the removal of either the H3 or the H2A N-terminal tail. DNA dynamics on the histone core are studied by a new coarse-grained model; these simulations show a strong influence of the presence of the histone tails on DNA unwrapping, and an open state that can be stabilized by the displacement of the H3 tail into the gap between the DNA and the histone core.