Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility

Sub-nucleosomal complexes have been identified as intermediates in nucleosome assembly and disassembly. Their formation is promoted by certain histone chaperones and ATP-dependent remodelers, as well as through transcription by RNA polymerase II. They in turn regulate the activity of these factors. Nucleosome composition has been found to affect the structure and accessibility of the nucleosomal DNA, however the effect on the histone tails is largely unknown. Here, we investigate the conformational dynamics of the H3 tail in the hexasome and tetrasome sub-nucleosomal complexes. Using a combination of NMR spectroscopy, MD simulations, and trypsin proteolysis, we find that the conformational ensemble of the H3 tail is regulated by nucleosome composition. Similar to what we previously found for the nucleosome, the H3 tails bind robustly to DNA within the hexasome and tetrasome, but upon loss of the H2A/H2B dimer, we observe a change in the conformational ensemble and an increase in the dynamics and accessibility of the adjacent H3 tail. Similar to observations of DNA dynamics, this is seen to be asymmetric in the hexasome. Our results indicate that nucleosome composition has the potential to regulate chromatin signaling at the histone tails and ultimately help shape the chromatin landscape.