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A subpopulation of Archaea possesses histones, which are similar to eukaryotic histones H3 and H4. However, archaeal histones are smaller than H3 and H4, and are not post-translationally modified. In addition, the fundamental unit of archaeal histones might be a dimer. The organization of archaeal nucleosomes, therefore, differs from that of eukaryotic nucleosomes. The base compositions of archaeal genome are much more diversified than those of eukaryote and the archaeal histones have more diversified amino acid sequences, which are reflected by their varied isoelectric points. We hypothesized that the highly diversified archaeal genomic DNA base composition may cause the archaeal histone variation. Phylogenetic analysis revealed that the distribution of archaeal histones is associated with their genomic DNA base composition. This result strongly suggests that archaeal histones have evolved concomitantly with their genomic DNA base composition. Eukaryotic histones are one of the most evolutionarily conserved proteins and would limit the diversification of genomic DNA base composition. In contrast, archaeal histones have diversified and would permit the great diversification of genomic DNA base composition.

Archaeal histone distribution is associated with archaeal genome base composition