Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions

Abstract

The histone demethylase KDM5A erases histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDRs). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a noncanonical poly(ADP-ribose) (PAR)–binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi’s) blocks KDM5A–PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and function at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR binding and macroH2A1.2 in KDM5A recognition of DNA lesion sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity.

Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?)

“…Recently, our work uncovered new regulatory elements controlling KDM5A functions in the DDR and damage‐proximal transcriptional responses, which includes the involvement of PARP1 in promoting the recruitment of KDM5A to DSBs. [ 55 ] PAR mediated signaling has emerged as a diverse and essential mode of regulation for multiple cellular processes, including the DDR and transcription [ 57,58 ] . Cells express multiple PARPs that can deposit PAR chains of various lengths and structures under different cellular conditions.…”

DNA Double-Strand Break Repair: All Roads Lead to HeterochROMAtin Marks

“…In human cells lacking the chromatin remodeler Alpha thalassemia/mental retardation syndrome X-linked (ATRX), macroH2A1.2 is also highly enriched at telomeres and contributes to ALT, a HR-mediated process ( Kim et al, 2019 ). Mechanistically, macroH2A1.2 collaborates with the histone demethylase KDM5A to promote both DSB repair by HR and transcriptional silencing at breaks ( Kumbhar et al, 2021 ). MacroH2A1.1 in contrast supports MMEJ, a mutagenic DSB repair pathway ( Sebastian et al, 2020 ).…”

“…H3K9 dimethylation is deposited by PR/SET domain 2 (PRDM2), recruited to DSBs in a manner dependent on the histone variant macroH2A1.2 ( Khurana et al, 2014 ). This histone variant also inhibits transcription at DSBs by stimulating H3K4me3 demethylation by KDM5A ( Kumbhar et al, 2021 ). Further studies will be needed to investigate reversal mechanisms of these heterochromatin marks after DSB repair, including the removal of macroH2A1.2, H3K9me2/3, and their importance for transcription recovery.…”

Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin

“…For recruitment to DNA damage sites, PHD1 but not PHD3 was required to support KDM5A translocation to breaks ( Gong et al, 2017 ). Recently, the localization of KDM5A to sites of DNA damage was also found to be dependent on the presence of the histone variant macro H2A1.2 (mH2A1.2) and PARP1 activity ( Kumbhar et al, 2021 ). Depletion of either mH2A1.2 or PARP1 disrupted the localization of KDM5A to DSBs and perturbed the ability of KDM5A to promote DNA repair and transcriptional repression.…”

“…Interestingly, the association between KDM5A and PAR chains was found to be mediated by a previously unidentified coiled-coil domain (cc domain) within the C-terminus of KDM5A spanning residues 1,501–1,562. The presence of this domain was also found to be required to support KDM5A localization and function at break sites ( Kumbhar et al, 2021 ). Further analysis uncovered that KDM5A exhibits preferential binding to extended PAR chains (ex.…”