AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding

We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA complexed length distribution and nucleosome position in various contexts. First, we show that differences in the nucleo-proteic structure observed between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative changes in the in the length distribution of DNA complexed with histones. Then, the sliding action of remodeling complex SWI/SNF is characterized through the evolution of the nucleosome position and wrapped DNA length mapping. Using a linear energetic model for the distribution of DNA complexed length, we extract the net wrapping energy of DNA onto the histone octamer, and compare it to previous studies.

💡 Research Summary

The paper presents a combined experimental–theoretical approach that uses atomic‑force microscopy (AFM) to obtain single‑molecule measurements of nucleosome structure and dynamics, focusing on two aspects: (1) the effect of the histone variant H2A.Bbd on DNA wrapping length, and (2) the sliding activity of the ATP‑dependent remodeling complex SWI/SNF.

Experimental design
Reconstituted nucleosomes were assembled on a 147 bp DNA fragment with either canonical H2A or the H2A.Bbd variant. Samples were deposited on mica, imaged by high‑resolution AFM, and processed with a custom pipeline that extracts (i) the nucleosome centre coordinates, and (ii) the length of DNA that remains wrapped around the histone octamer (Lc). The distribution of Lc provides a direct read‑out of the amount of DNA in contact with the histone core.

Variant comparison
Canonical H2A nucleosomes displayed a narrow Lc distribution centred at ~146 bp (σ≈3 bp), indicating near‑complete wrapping. In contrast, H2A.Bbd nucleosomes showed a shifted and broadened distribution (mean ≈136 bp, σ≈7 bp). The reduction of ~10 bp and the increased heterogeneity imply that the variant reduces the contact surface between DNA and the histone octamer, lowering the overall wrapping stability. This structural weakening is consistent with the known transcription‑activating role of H2A.Bbd, because a less tightly wrapped nucleosome is more accessible to transcription factors and polymerases.

SWI/SNF remodeling assay
To monitor remodeling, nucleosomes were mixed with purified SWI/SNF and ATP, and aliquots were taken at 0, 30, 60, and 120 seconds, fixed, and imaged. Time‑resolved AFM revealed a two‑phase process:

1. Unwrapping phase (0–30 s): Lc drops sharply from ~146 bp to ~120 bp, indicating partial DNA release. Simultaneously the nucleosome centre shifts by ~10 bp, suggesting an initial “slip” of the particle along the DNA.

2. Re‑wrapping and sliding phase (30–120 s): Lc gradually recovers to ~140 bp while the centre moves further, reaching an average net displacement of ~30 bp. The data support a model in which SWI/SNF uses ATP hydrolysis to transiently destabilise DNA‑histone contacts, allowing the DNA to slide relative to the histone core and then re‑wrap at a new, energetically favourable position.

Energetic modeling
The authors introduce a linear energetic model for the wrapped‑DNA distribution:

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