Functional Analyses of an Evolutionarily Conserved Acidic Patch on the Nucleosome

The eukaryotic canonical nucleosome has an acidic patch on each H2A/H2B dimer. This acidic patch is also detected in histone variants, such as the H2A.Z (yeast Htz1)/H2B dimer. Here, we screened a comprehensive histone point mutant library and identified 11 histone residues located in four distinct nucleosome domains (Homologous Recombination (HR) Domain I-IV (HRD-I-IV)) with a potential role in HR. H2A-L66, -E93, and -L94 residues in HRD-I are located in the acidic patch region. Equivalent residues (H2A-L66 and Htz1-L73) partly compensate the function of each dimer. A common residue H2B-L109, which is located underneath of the acidic patch in both dimers, also partly compensates the function of each dimer. Upon exposure to DNA double-strand break (DSB)-inducing agents, the fragmented chromosomes of H2AL66A mutant cells exhibited slow and limited recovery into intact chromosomes, suggesting that the H2AL66A mutant is partly deficient in DSB repair. Furthermore, strand invasion, one of critical steps of HR, could be less efficient in H2A-L66A cells. All 11 HRD residues, including H2A-L66, are highly conserved in extant eukaryotic cells; therefore, our screening reported in this study will provide a foundation for future studies about the mechanisms underlying eukaryotic HR based on chromatin.