Abstract
Nucleosomes are important for chromatin compaction and gene regulation; their integrity depends crucially on the structural properties of the histone tails. Recent all-atom molecular dynamics simulations revealed that removal of the N-terminal tails of histone H3, known to destabilize nucleosomes, causes a rearrangement of two arginines of histone H2A, namely R81 and R88 by altering the electrostatic environment of the H2A α3 domain. Whether this rearrangement is the cause or the effect of decreased stability, is unclear. Here, we emulate the altered electrostatic environment that was found after H3 tail clipping through charge-modifying mutations to decouple its impact on intranucleosomal interactions from that of the histone tails. Förster resonance energy transfer experiments on recombinant nucleosomes and all-atom molecular dynamics simulations reveal a compensatory role of those amino acids in nucleosome stability. The simulations indicate a weakened interface between H2A-H2B dimers and the (H3-H4)2 tetramer, as well as between dimers and DNA. These findings agree with the experimental observations of position and charge dependent decreased nucleosome stability induced by the introduced mutations. This work highlights the importance of the H2A α3 domain and suggests allosteric effects between this domain and the outer DNA gyre as well as the H3 N-terminal tail.
Highlights
The nucleosome, the basic unit of chromatin compaction, is central to gene regulation[1,2]
Previous molecular dynamics (MD) simulations on wild type and H3 tail-less nucleosomes suggested that the electrostatic potential of the H2A α3 domain could play an important role for nucleosome stability[8]
We designed a total of six recombinant H2A mutants, where arginine was replaced with alanine (RA) or glutamic acid (RE) either at position 81 (R81A, R81E), at position 88 (R88A, R88E) or at both loci simultaneously
Summary
The nucleosome, the basic unit of chromatin compaction, is central to gene regulation[1,2]. To understand the impact of H3 tail removal on nucleosome structure our laboratory recently performed molecular dynamics (MD) simulations based on the crystal structure 1KX5 of the nucleosome core particle[8] Those analyses suggest an active role of two histone arginines within the H2A α3 domain in structural alterations. A state, with higher FRET, which was already observed in[16,17] and is assumed to be connected with histone octamer opening, was promoted during nucleosome disassembly in the H2A α3 mutants. We conclude that these mutations weaken the interactions between H2A-H2B dimer and (H3-H4)[2] tetramer and thereby lead to a decrease in nucleosome stability
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