Columnar Nucleosome Stacking Dictates NCP and (Telomeric) Chromatin Condensation
Lars Nordenskiöld et al.
School of Biological Sciences, Nanyang Technological University, Singapore
A decisive factor that governs the compaction of mono-nucleosomes and chromatin is the close stacking the neighbouring flat surface of the wedge-like cylindrical nucleosomes, which is generally observed both in vitro and in vivo. Isolated nucleosome core particles (NCPs), in the presence of multivalent cations (Mg2+, CoHex3+, Spermine3+, Spermine4+) form stacked columns, usually arranged in hexagonal packing and mediated by histone tail interactions. NCP phase separation can be modelled by multi-scale coarse-grained bottom-up simulations (Sun et al, Biophys. J., 2023, 10.1016/j.bpj.2023.10.030). Chromatin higher order structure displays nucleosome stacking in solenoid, zig-zag and in interdigitated fibres. Using Cryo-EM, we determined the columnar structure formed by chromatin with telomeric DNA (comprised of TTAGGG repeats in mammals) where the nucleosomes stack tightly on top of each other mediated by histone tail interactions (Soman et al, Nature, 2022, 609, 10048). More recently, using EM and single molecule force spectroscopy, we discovered that the protein TRF2 (telomere repeat binding factor 2), which is a component of the six-protein shelterin complex that provides the protective capping at the ends of the linear chromosomes, alone (in the absence of Mg2+) induces the columnar architecture of telomeric chromatin (Wong et al, EMBO J., 2024, 43(1), 87). The columnar fibres resulting from binding of TRF2 results in stiffer and thermodynamically more stable fibres compared to those formed in the presence of Mg2+. Here, we discuss the modelling of the ion-mediated phase separation of NCPs to ordered columnar phases and we review the recent columnar structure of telomeric chromatin with emphasis on the importance of telomere maintenance and interactions with shelterin components.