Cryo-electron tomography reveals near-native archaeal chromatin architecture

Abstract Most archaea package their genomes using histones, the evolutionary ancestors of eukaryotic chromatin proteins. Yet how archaeal chromatin is organized in cells has remained unknown. Here we provide the first high-resolution view of archaeal chromatin in a near-native state. We combine cryo-electron tomography, subtomogram averaging and single-particle cryo-electron microscopy to study chromatin released from gently lysed cells of the model archaeon Thermococcus kodakarensis . We show that archaeal chromatin is built from closed hypernucleosomes of variable length and determine structures of multiple hypernucleosome species, revealing a variable-beads-on-a-string architecture with flexible local contact geometries. We further show that chromatin organization changes with cellular state: logarithmic-phase cells are enriched in short hypernucleosomes, whereas stationary-phase cells form longer assemblies. Histone HTkB deletion shifts chromatin towards shorter hypernucleosomes in both growth phases and reduces local contact order. These results establish archaeal chromatin as a dynamic and complex system, shaped by growth phase and histone composition.