Reduction in replication‐independent endogenous DNA double‐strand breaks promotes genomic instability during chronological aging in yeast

ABSTRACT The mechanism that causes genomic instability in nondividing aging cells is unknown. Our previous study of mutant yeast suggested that 2 types of replication‐independent endogenous DNA double‐strand breaks (RIND‐EDSBs) exist and that they play opposing roles. The first type, known as physiologic RIND‐EDSBs, were ubiquitous in the G 0 phase of both yeast and human cells in certain genomic locations and may act as epigenetic markers. Low RIND‐EDSB levels were found in mutants that lacked chromatin‐condensing proteins, such as the high‐mobility group box (HMGB) proteins and Sir2. The second type is referred to as pathologic RIND‐EDSBs. High pathological RIND‐EDSB levels were found in DSB repair mutants. Under normal physiologic conditions, these excess RIND‐EDSBs are repaired in much the same way as DNA lesions. Here, chronological aging in yeast reduced physiological RIND‐EDSBs and cell viability. A strong correlation was observed between the reduction in RIND‐EDSBs and viability in aging yeast cells ( r = 0.94, P < 0.0001). We used galactose‐inducible HO endonuclease (HO) and nhp6aΔ, an HMGB protein mutant, to evaluate the consequences of reduced physiological RIND‐EDSB levels. The HO‐induced cells exhibited a sustained reduction in RIND‐EDSBs at various levels for several days. Interestingly, we found that lower physiologic RIND‐EDSB levels resulted in decreased cell viability ( r = 0.69, P < 0.0001). Treatment with caffeine, a DSB repair inhibitor, increased pathological RIND‐EDSBs, which were distin guished from physiologic RIND‐EDSBs by their lack of sequences prior to DSB in untreated cells [odds ratio (OR) ≤1]. Caffeine treatment in both the HO‐induced and nhp6a Δ cells markedly increased OR ≤1 breaks. Therefore, physiological RIND‐EDSBs play an epigenetic role in preventing pathological RIND‐EDSBs, a type of DNA damage. In summary, the reduction of physiological RIND‐EDSB level is a genomic instability mechanism in chronologically aging cells.—Thongsroy, J., Patchsung, M., Pongpanich, M., Settayanon, S., Mutirangura, A. Re duction in replication‐independent endogenous DNA double‐strand breaks promotes genomic instability during chronological aging in yeast. FASEB J. 32, 6252–6260 (2018). www.fasebj.org