Chromatin condensation and decondensation play critical roles in regulating biological processes such as transcription and replication. Recent studies have demonstrated that molecular crowding can induce chromatin condensation both in vitro and in vivo. However, the underlying molecular mechanisms—particularly regarding nucleosome-nucleosome interactions—remain poorly understood. In this study, we investigated how molecular crowding affects chromatin structure using single-molecule force spectroscopy with optical tweezers. We conducted pulling experiments on 12-mer polynucleosomes in the presence of polyethylene glycol (PEG, 0–15% w/v, and MW, 62–8000) as a molecular crowding agent. At low-PEG concentrations (5%) and molecular weights (e.g., 10% EG or 5% PEG 400), polynucleosome compaction was minimal, although modest inhibition of individual nucleosomal DNA unwrapping was observed. In contrast, significant compaction occurred at high-PEG concentrations and molecular weights (e.g., ≥10% PEG 4000 or PEG 8000). This substantial compaction was not observed in bare DNA under identical crowding conditions. Analysis of the force-distance curves revealed that inter-nucleosomal interactions contribute to polynucleosome compaction, with more distal interactions favored under higher crowding conditions. Under these conditions, a force of approximately 30 pN was required to disrupt these inter-nucleosomal interactions and release DNA, compared to only 22 pN in the absence of PEG. These findings suggest that the extent of molecular crowding strongly influences cellular function by affecting chromatin structure and DNA accessibility through modulation of both histone-DNA interactions and nucleosome-nucleosome associations.
Sunami et al. (2026) studied this question.