Nucleosomes are complexes of DNA and histone proteins that form the basis of eukaryotic chromatin. Eukaryotic histones are descended from Archaean homologs; however, how this occurred remains unclear. Our previous genetic analysis on the budding yeast nucleosome identified 26 histone residues conserved between S. cerevisiae and T. brucei; 15 that are lethal when mutated and 11 that are synthetically lethal with deletion of the FEN1 nuclease. These residues are partially conserved in nucleosomes of a variety of giant viruses, allowing us to follow the route by which they were established in the LECA (Last Eukaryote Common Ancestor). We analyzed yeast nucleosome genetic data to generate a model for the emergence of the eukaryotic nucleosome. In our model, histone H2B-H2A and H4-H3 doublets found in giant virus nucleosomes facilitated the formation of the acidic patch surface and nucleosome entry sites of the eukaryotic nucleosome, respectively. Splitting of the H2B-H2A doublet resulted in the H2A variant, H2A.Z., and subsequent splitting of the H4-H3 doublet led to a eukaryotic specific domain required for chromatin binding of H2A.Z. We propose that the LECA emerged when the newly-split H3 N-terminal horizontally acquired a common N-tail found in extinct pre-LECA lineages and some extant giant viruses. This hypothesis predicts that the emergence of the H3 variant CENP-A and establishment of CENP-A-dependent chromosome segregation occurred after the emergence of the LECA, implying that the root of all eukaryotes is assigned within Euglenida.
Keywords: CENP-A; H2A.Z; LECA; evolution; giant virus; histone; nucleosome.