High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale

Abstract

Nucleosome dynamics, such as nucleosome sliding and DNA unwrapping, are important for gene regulation in eukaryotic chromatin. H2A.Z, a variant of histone H2A that is highly evolutionarily conserved, participates in gene regulation by forming unstable multipositioned nucleosomes in vivo and in vitro. However, the subsecond dynamics of this unstable nucleosome have not been directly visualized under physiological conditions. Here, we used high-speed atomic force microscopy (HS-AFM) to directly visualize the subsecond dynamics of human H2A.Z.1-nucleosomes. HS-AFM videos show nucleosome sliding along 4 nm of DNA within 0.3 s in any direction. This sliding was also visualized in an H2A.Z.1 mutant, in which the C-terminal half was replaced by the corresponding canonical H2A amino acids, indicating that the interaction between the N-terminal region of H2A.Z.1 and the DNA is responsible for nucleosome sliding. These results may reveal the relationship between nucleosome dynamics and gene regulation by histone H2A.Z.

Epigenetic Modulation via the C-Terminal Tail of H2A.Z

“…It is also possible that H2A.Z can stabilize the histone octamer in a tail-dependent fashion as measured in our assay, while simultaneously weakening the histone-DNA interactions at the DNA entry and exit points as detected by cryo-EM. However, recent AFM studies suggest that the N-terminal part of the histone, not the C-terminal, controls nucleosome-DNA binding strength 34 .…”

“…4F). The N-terminal part of H2A.Z has a marked effect on the sliding of the nucleosome on the DNA 34 , while the C-terminal tag is expected to directly interfere with interactions involving the tail. Tagged H2A.Z also appears to be localized in a scattered rather than dominantly peripheral manner in the nucleus, compared with ZAbA-detected native H2A.Z (Suppl.…”

“…Through the spectacles of mobility features of nucleosomal DNA termini, cryo-EM studies 21 support the notion of a destabilizing role of H2A.Z which depends on its C-terminal tail; however, the same study has also demonstrated the formation of more condensed chromatin fibers in the presence of H2A.Z (recently reviewed in 33 ). In a recent high-speed atomic microscopic (AFM) study 34 , interaction between the N-terminal region of H2A.Z.1 and the DNA was found to be responsible for nucleosome sliding, at variance with 21 . In summary, the different approaches addressing the relationships between the stability features of H2A.Z-containing nucleosomes and their other characteristics, including isoform composition, post-translational modifications (PTMs) and their roles in euchromatin vs. heterochromatin, have not yet led to a fully coherent picture 2,29 .…”

High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes

“…32,33 Previously, we visualized spontaneous nucleosome sliding events in nucleosomes containing H2A.Z.1, an H2A variant, with a temporal resolution of 0.3 s through optimization of the AFM substrate. 34 Building on this methodology, we employed HS-AFM to observe the dynamics of tail-less nucleosomes. Our results showed that the absence of histone tails causes a 10-fold increase in the frequency of nucleosome sliding and DNA unwrapping/wrapping events.…”

Role of Nucleosome Sliding in the Protein Target Search for Covered DNA Sites

“…Experimental studies indicate that the sliding rates depend on the DNA sequence and length of the DNA fragment between the neighboring nucleosomes. − It has been also suggested that the inherent mobility of nucleosomes can be altered by the deletion of histone tails and/or mutations in histone proteins . Recent high-speed atomic force microscopy investigations , have successfully captured spontaneous reversible sliding of mononucleosomes on a subsecond time scale with high temporal resolution. Another single-molecule study probed the diffusion of nucleosomes with a base-pair scale resolution on natural, biologically relevant sequences.…”