ATM-mediated KDM2A phosphorylation is required for the DNA damage repair

Abstract

The ataxia-telangiectasia mutated (ATM) protein is a key signaling molecule that modulates the DNA damage response. However, the exact mechanism by which ATM regulates DNA damage repair has not yet been elucidated. Here, we report that ATM regulates the DNA damage response by phosphorylating lysine-specific demethylase 2A (KDM2A), a histone demethylase that acts at sites of H3K36 dimethylation. ATM interacts with KDM2A, and their interaction significantly increases in response to DNA double-stranded, but not single-stranded, breaks. ATM specifically phosphorylates KDM2A at threonine 632 (T632) following DNA damage, as demonstrated by a mutagenesis assay and mass spectrometric analysis. Although KDM2A phosphorylation does not alter its own demethylase activity, T632 phosphorylation of KDM2A largely abrogates its chromatin-binding capacity, and H3K36 dimethylation near DNA damage sites is significantly increased. Consequently, enriched H3K36 dimethylation serves as a platform to recruit the MRE11 complex to DNA damage sites by directly interacting with the BRCT2 domain of NBS1, which results in efficient DNA damage repair and enhanced cell survival. Collectively, our study reveals a novel mechanism for ATM in connecting histone modifications with the DNA damage response.

Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage

“…H3K36me2 is rapidly induced globally and locally after IR or etoposide treatment in a very rapid manner [47,76]. The increase of H3K36me2 at I-SceI-induced DSB site is mediated by recruiting Metnase (also SETMAR) and is required for NHEJ repair [47], which is in agreement with the role of Metnase in NHEJ [77,78].…”

“…The recruitment of Metnase relies on phosphorylation of Ser495 by Chk1, but not by ATM [79]. We also found that dissociation of H3K36me2-specific demethylase JHDM1a/KDM2A with chromatin is also critical for this process, and this dissociation between KDM2A and chromatin is a result of ATM-dependent phosphorylation on Thr632 [76]. PHRF1 (PHD and ring finger domains 1) recognizes H3K36me2 via its PHD domain, meanwhile binds to NBS1 through the SDTE motif [80] (Fig.…”

“…2C). More importantly and interestingly, H3K36me2 can improve the association of MRN complex with chromatin through direct interaction with the BRCT2 domain of NBS1 [76] (Fig. 2C).…”

Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage

“…Histone was extracted as previously described (34). Briefly, cell pellets were lysed in hypotonic buffer, re-suspended in 0.4 N sulfuric acid and precipitated by trichloroacetic acid.…”

G9a coordinates with the RPA complex to promote DNA damage repair and cell survival

“…The levels of histone H3K36 dimethylation (H3K36me2) increase following DSBs as a result of either the dissociation of the histone demethylase KDM2A from chromatin or the catalytic activity of the histone methyltransferase Metnase, and recruit either the MRN complex or Ku70 family proteins to DSBs, respectively (18,19). Suv39h1-mediated histone H3K9 trimethylation (H3K9me3) at DSBs directly binds to and activates Tip60-a histone acetylase that is essential for ataxia-telangiectasia-mutated (ATM) activation (20,21).…”