Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro

Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, the assembly dynamics of H2A.Z-containing nucleosomes remain elusive. Here, we demonstrate that our previous chemical kinetic model for nucleosome assembly can be extended to H2A.Z-containing nucleosome assembly processes. The efficiency of H2A.Z-containing nucleosome assembly, like that of canonical nucleosome assembly, was also positively correlated with the total histone octamer concentration, reaction rate constant, and reaction time. We expanded the kinetic model to represent the competitive dynamics of H2A and H2A.Z in nucleosome assembly, thus providing a novel method through which to assess the competitive ability of histones to assemble nucleosomes. Based on this model, we confirmed that histone H2A has a higher competitive ability to assemble nucleosomes in vitro than histone H2A.Z. Our competitive kinetic model and experimental results also confirmed that in vitro H2A.Z-containing nucleosome assembly is governed by chemical kinetic principles.

Automated summary

Nucleosomes are important for eukaryotic chromatin structure and regulate various biological processes. The histone variant H2A.Z can be dynamically incorporated into nucleosomes to modulate gene expression. Researchers have extended a chemical kinetic model to study the assembly dynamics of H2A.Z-containing nucleosomes. They found that the assembly efficiency of H2A.Z-containing nucleosomes is positively correlated with histone octamer concentration, reaction rate constant, and reaction time. Furthermore, they developed a competitive kinetic model to assess the competitive ability of histones in nucleosome assembly and confirmed that H2A has a higher competitive ability than H2A.Z in vitro. This study demonstrates that the assembly of H2A.Z-containing nucleosomes follows chemical kinetic principles.