Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair

Each day, approximately 20,000 oxidative lesions form in the DNA of every nucleated human cell. The base excision repair (BER) enzymes that repair these lesions must function in a chromatin milieu. We have determined that the DNA glycosylase hNTH1, apurinic endonuclease (APE), and DNA polymerase beta (Pol beta), which catalyze the first three steps in BER, are able to process their substrates in both 601- and 5S ribosomal DNA (rDNA)-based nucleosomes. hNTH1 formed a discrete ternary complex that was displaced by the addition of APE, suggesting an orderly handoff of substrates from one enzyme to the next. In contrast, DNA ligase III alpha-XRCC1, which completes BER, was appreciably active only at concentrations that led to nucleosome disruption. Ligase III alpha-XRCC1 was also able to bind and disrupt nucleosomes containing a single base gap and, because of this property, enhanced both its own activity and that of Pol beta on nucleosome substrates. Collectively, these findings provide insights into rate-limiting steps that govern BER in chromatin and reveal a unique role for ligase III alpha-XRCC1 in enhancing the efficiency of the final two steps in the BER of lesions in nucleosomes.