Abstract
In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.
Highlights
The nucleus of all eukaryotic cells contains meters of DNA organized by histone proteins into a hierarchical architecture: the chromatin [1,2]
Linkers are aligned next to each other allowing this very high fiber compaction. This arrangement is reminiscent of DNA cholesteric liquid crystals
The pitch of the cholesteric phase depends on the number of starts of the chromatin fiber helix and ranges from 35 to 100 nm
Summary
The nucleus of all eukaryotic cells contains meters of DNA organized by histone proteins into a hierarchical architecture: the chromatin [1,2]. A fifth histone type (H1/H5) helps this folding by interacting with DNA at the entry-exit of each nucleosome [3]. This interaction has been observed at the molecular level in vitro [4] and induces the wrapping of 20 additional DNA bp to complete the second full turn around each nucleosome. Semi-compact fibers can be obtained by the apposition of entry and exit DNA linkers [5]. This zigzag folding pattern is not compact enough to explain the high density of chromatin as measured in vivo in metaphasic chromosomes [6] (6 nucleosomes/11 nm compared to 11 nucleosomes/11 nm)
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