Nucleosome core particle-catalyzed strand scission at abasic sites

The reactivity of apurinic/apyrimidinic (AP) sites at different locations within nucleosome core particles was examined. AP sites are greatly destabilized in nucleosome core particles compared to free DNA. Their reactivity varied ~5-fold with respect to the location within the nucleosome core particles but followed a common mechanism involving formation of a Schiff base between histone proteins and the lesion. The identity of the histone protein(s) involved in the reaction and the reactivity of the corresponding DNA-protein cross-links varied with the location of the abasic site, indicating that while the relative rate constants for individual steps varied in a complex manner, the overall mechanism remained the same. The source of the accelerated reactivity was probed using nucleosomes containing AP89 and histone H3 and H4 variants. Mutating the five lysine residues in the amino tail region of histone H4 to arginines reduced the rate constant for disappearance almost 15-fold. Replacing histidine 18 with an alanine reduced AP reactivity more than 3-fold. AP89 in a nucleosome core particle composed of the H4 variant containing both sets of mutations reacted only <4-fold faster than it did in naked DNA. These experiments reveal that nucleosome-catalyzed reaction at AP89 is a general phenomenon and that the lysine rich histone tails, whose modification is integrally involved in epigenetics, are primarily responsible for this chemistry.