Histone H2A Variants Enhance the Initiation of Base Excision Repair in Nucleosomes

Substituting histone variants for their canonical counterparts can profoundly alter chromatin structure, thereby impacting multiple biological processes. Here, we investigate the influence of histone variants from the H2A family on the excision of uracil (U) by the base excision repair (BER) enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase. Using a DNA population with globally distributed U:G base pairs, enhanced excision is observed in H2A.Z and macroH2A-containing nucleosome core particles (NCPs). The U with reduced solution accessibility exhibit limited UDG activity in canonical NCPs but are more readily excised in variant NCPs, reflecting the ability of these variants to facilitate excision at sites that are otherwise poorly repaired. We also find that U with the largest increase in the level of excision in variant NCPs are clustered in regions with differential structural features between the variants and canonical H2A. Within 35-40 bp of the DNA terminus in macroH2A NCPs, the activities of both glycosylases are comparable to that on the free duplex. We show that this high level of activity results from two distinct species within the macroH2A NCP ensemble: octasomes and hexasomes. These observations reveal potential functions for H2A variants in promoting BER and preventing mutagenesis within the context of chromatin.