Beyond the Trinity of ATM, ATR, and DNA-PK: Multiple Kinases Shape the DNA Damage Response in Concert With RNA Metabolism

Abstract

Our genome is constantly exposed to endogenous and exogenous sources of DNA damage resulting in various alterations of the genetic code. DNA double-strand breaks (DSBs) are considered one of the most cytotoxic lesions. Several types of repair pathways act to repair DNA damage and maintain genome stability. In the canonical DNA damage response (DDR) DSBs are recognized by the sensing kinases Ataxia-telangiectasia mutated (ATM), Ataxia-telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK), which initiate a cascade of kinase-dependent amplification steps known as DSB signaling. Recent evidence suggests that efficient recognition and repair of DSBs relies on the transcription and processing of non-coding (nc)RNA molecules by RNA polymerase II (RNAPII) and the RNA interference (RNAi) factors Drosha and Dicer. Multiple kinases influence the phosphorylation status of both the RNAPII carboxy-terminal domain (CTD) and Dicer in order to regulate RNA-dependent DSBs repair. The importance of kinase signaling and RNA processing in the DDR is highlighted by the regulation of p53-binding protein (53BP1), a key regulator of DSB repair pathway choice between homologous recombination (HR) and non-homologous end joining (NHEJ). Additionally, emerging evidence suggests that RNA metabolic enzymes also play a role in the repair of other types of DNA damage, including the DDR to ultraviolet radiation (UVR). RNAi factors are also substrates for mitogen-activated protein kinase (MAPK) signaling and mediate the turnover of ncRNA during nucleotide excision repair (NER) in response to UVR. Here, we review kinase-dependent phosphorylation events on RNAPII, Drosha and Dicer, and 53BP1 that modulate the key steps of the DDR to DSBs and UVR, suggesting an intimate link between the DDR and RNA metabolism.

Keywords: 53BP1; DNA damage response; RNA metabolism; RNA polymerase II; dicer; kinase; phosphorylation.

Figure 1

Locally permissive transcription in response to DSBs despite global transcription shutdown. Upon DSB induction, RNAPII transcription of protein-coding genes is globally impaired via ATM signaling. Non-permissive heterochromatin forms to facilitate the silencing of actively transcribed loci. However, transcriptionally permissive open chromatin has been suggested to form locally in response to DSBs, allowing nascent RNA synthesis to occur at the site of the DSB (created by Biorender).

Figure 2

Damage-induced kinases regulate the RNA metabolism in response to DSBs. In response to DSBs, DNA-PK, and ATM phosphorylate and activate c-Abl kinase, which can phosphorylate HR factors such as Rad51. c-Abl can also phosphorylate the CTD of RNAPII at Tyr1, which is required for the recruitment and activity of RNAPII at DSBs. Damage responsive transcripts and dsRNA can then be produced at the DSB, recruiting a subset of DDR factors. Alongside RNAPII, Drosha and Dicer are also required for the formation of DSB-derived dsRNA. Cytoplasmic Dicer is phosphorylated by Erk1/2 at Ser1728 and Ser1853. Dicer phosphorylation at Ser1016 is necessary and sufficient for nuclear Dicer localization. p38 phosphorylates Drosha, promoting its dissociation from DGCR8, nuclear export of phosphorylated Drosha, and subsequent proteasomal degradation. DGCR8 can be phosphorylated by c-Abl at Tyr267, which stimulates processing of a specific miRNA precursor to promote the DDR at the post-transcriptional level (created by Biorender).

Figure 3

53BP1 recruitment DSBs and its regulation by phosphorylation. Recruitment of 53BP1 to DSBs involves recognition of the DSB by the MRN complex, ATM activation, and phosphorylation of histone H2A.X on residue Ser139 (γH2A.X). 53BP1 is phosphorylated on its 28 S/TQ sites by ATM. The ubiquitin ligases RNF8 and RNF168 are recruited downstream of ATM phosphorylation of yH2AX and are required for 53BP1 recruitment to chromatin. DYRK1A modulates the recruitment of 53BP1 to DSBs through interaction with RNF169. RNF169 competes with RNF168 for binding of 53BP1 and has a function in repair pathway choice by limiting 53BP1 at DSBs. Thus, DYRK1A enhances NHEJ by regulating the recruitment of RNF169 and 53BP1 to DSB sites. BRCA1 together with the DNA endonuclease CtIP trigger dephosphorylation of 53BP1, which repositions 53BP1 to the periphery and allows recruitment of HR factors such as BRCA1, Exo,1 and RPA to the center of the DDR focus, promoting HR (created by Biorender).