Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
J Biol Chem. 2023 Aug;299(8):105037. doi: 10.1016/j.jbc.2023.105037. Epub 2023 Jul 11.
The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4) tetramer. The strong yet flexible DNA-histone interactions are the physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions also implies that nucleosomes dissociate DNA-histone contacts both transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At high nucleosome concentrations, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely event, where nucleosomes could act as their own histone chaperone. This spontaneous histone exchange could serve as a mechanism for maintaining overall chromatin stability, although it has never been reported. Here we employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes on a time scale of a few tens of seconds at a physiological nucleosome concentration. We show that the rate of histone exchange increases at a higher monovalent salt concentration, with histone-acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support the notion of histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.
核小体是真核生物中基本的基因包装单元。核小体由约 147bp 的 DNA 包裹在一个由两个 H2A-H2B 二聚体和一个（H3-H4）四聚体组成的八聚体组蛋白核心上。DNA-组蛋白的强而灵活的相互作用是染色质中包装的基因动态调控的物理基础。DNA-组蛋白相互作用的动态性质也意味着核小体瞬时且反复地解离 DNA-组蛋白的接触。这种动力学不稳定性可能导致自发的核小体解体或核小体之间的组蛋白交换。在高核小体浓度下，核小体-核小体碰撞和随后的组蛋白交换更有可能发生，其中核小体可以作为自身的组蛋白伴侣。这种自发的组蛋白交换可以作为维持整体染色质稳定性的一种机制，尽管它从未被报道过。在这里，我们采用三色单分子 FRET（smFRET）来证明在生理核小体浓度下，H2A-H2B 二聚体在几十秒的时间尺度上在核小体之间自发交换。我们表明，在更高的单价盐浓度、组蛋白乙酰化核小体和组蛋白伴侣 Nap1 的存在下，组蛋白交换的速率增加，而在更高的温度下不变，并且在 DNA 甲基化时降低。这些结果支持通过核小体的瞬时和重复部分解组装来进行组蛋白交换的观点，并证实了在紧凑染色质环境中组蛋白扩散的自发性，从而调节组蛋白修饰和变体的局部浓度。
