Histone demethylase KDM5B is a key regulator of genome stability

Maintenance of genomic stability is essential for normal organismal development and is vital to prevent diseases such as cancer. As genetic information is packaged into chromatin, it has become increasingly clear that the chromatin environment plays an important role in DNA damage response. However, how DNA repair is controlled by epigenetic mechanisms is not fully understood. Here we report the identification and characterization of lysine-specific histone demethylase 5B (KDM5B), a member of the JmjC domain-containing histone demethylases, as an important player in multiple aspects of DNA double-strand break (DSB) response in human cells. We found that KDM5B becomes enriched in DNA-damage sites after ironizing radiation and endonuclease treatment in a poly(ADP ribose) polymerase 1- and histone variant macroH2A1.1-dependent manner. We showed that KDM5B is required for efficient DSB repair and for the recruitment of Ku70 and BRCA1, the essential component of nonhomologous end-joining and homologous recombination, respectively. Significantly, KDM5B deficiency disengages the DNA repair process, promotes spontaneous DNA damage, activates p53 signaling, and sensitizes cells to genotoxic insults. Our results suggest that KDM5B is a bona fide DNA damage response protein and indicate that KDM5B is an important genome caretaker and a critical regulator of genome stability, adding to the understanding of the roles of epigenetics in the maintenance of genetic fidelity.The ability of cells to maintain genome integrity is vital for cellular homeostasis. Defects in the maintenance of genome stability underlie a number of developmental disorders and human diseases including cancer (1–3). Compared with other types of DNA lesions, DNA double-strand breaks (DSBs) are particularly dangerous to cells because failure to repair these kinds of damage in an appropriate manner can cause cell death, and aberrant repair can lead to gross chromosomal abnormalities that may eventually lead to tumorigenesis (1, 2, 4).Upon detection of DSBs, cells activate local and global DNA damage response (DDR) events that promote cell-cycle checkpoint activation and DNA repair signaling (5, 6). For example, in response to DSBs, phosphorylation of the histone variant H2AX (γH2AX) by DDR protein kinases such as ataxia telangiectasia mutated (ATM) (7) creates an extensive modified chromatin environment that allows spatiotemporal redistribution and accumulation of checkpoint and repair factors, including DNA-damage check point-1 (MDC1) and breast cancer susceptibility gene 1 (BRCA1), into repair centers, forming microscopically visible nuclear aggregates known as foci (4, 8). The two extensively studied DSB repair pathways are homologous recombination (HR) and nonhomologous end-joining (NHEJ) (2, 9). In NHEJ, the DSB ends are blocked from 5′ end resection and held in a close proximity by DSB end-binding protein complex, the Ku70–Ku80 heterodimer (10). NHEJ promotes direct ligation of the DSB ends in an error-prone manner (2, 8). In contrast, HR is largely error free and is initiated when the DSB is resected by nucleases and helicases, generating ssDNA overhangs. This structure can invade homologous duplex DNA, which is used as a template for DNA synthesis to restore the original genetic information (11, 12). Meanwhile, ssDNA generates a structural platform for another signaling module triggered by assembly and activation of the ataxia telangiectasia and Rad3-related (ATR) kinase (10). Eventually, ATM and ATR amplify the signals generated at DSBs by phosphorylating several regulatory proteins, including CHK1, CHK2, and p53, that coordinate cell cycle progression or induce cell apoptosis (5). All of these occurrences are essential for timely initiation, amplification, and transmission of the DNA damage signaling.Because nuclear DNA is packaged into chromatin, accumulating evidence suggests that DNA repair occur both temporally and spatially in the context of highly structured chromatin surrounding the breaks (6, 10), an environment that enables repair factors to detect DNA lesions, assemble, and function properly and promptly. Consistent with this notion, a number of epigenetic regulators that physically or chemically modify chromatin structures have been linked to DSB repair (13), the outcome of which is predominantly determined by chromatin remodeling events as well as histone modification profiles around the breaks (6, 14). These modifications include but are not limited to phosphorylation, acetylation, ubiquitination, and methylation. DSBs might not only induce the formation of specific histone modifications, but also entail alterations of the constitutive modification patterns in a dynamic manner. For example, similar to histone acetylation, recent reports suggest that deacetylation also plays a critical role in DSB response and processing (15, 16). Although histone methylation, another reversible modification, has been linked to the initial phase of repair (17, 18), whether and how histone demethylation contributes to DSB repair are currently unknown.Here we report on the identification and characterization of lysine-specific histone demethylase 5B (KDM5B), a member of the JmjC domain-containing histone demethylases (19), as an important contributor to DNA repair and signaling pathway in human cells.