In eukaryotes, genomic DNA is compacted in chromatin, which generally suppresses transcription, replication, repair, and recombination. The fundamental unit of chromatin is the nucleosome, whose structure was first determined at atomic resolution in 1997. However, recent findings have revealed that the nucleosome is not a structurally homogenous entity. Nucleosomes containing histone variants often have subtle but clear differences in their structural and functional characteristics, as compared to the canonical nucleosome. In addition to the conventional nucleosome structure, the structure of the overlapping dinucleosome, a new structural unit of chromatin, has been determined. Although archaeal chromatin adopts a unique polymer architecture, its structural unit is very similar to that of the eukaryotic nucleosome, suggesting that the archaeal histone-like protein is orthologous to the eukaryotic histones. In this article, we review the diversity of the nucleosome structures, which plays key roles in their specific functions in the epigenetic regulation of chromatin.
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