A Novel Role for RNA Methylation (m6A) in the DNA Damage Response

Every day our cells undergo substantial amounts of DNA damage from exogenous and endogenous sources. UV light, in particular, can cause an estimated 100,000 lesions per cell every day. Left unrepaired, these DNA lesions could lead to induction of senescence, cell death or mutations, which could be responsible for the development of cancer, neurodegeneration and several other diseases. However, our organisms have developed a mechanism to recognize the DNA damage caused by UV light and other damaging agents, in the DNA-damage response (DDR) pathway. This pathway is mediated by members of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family and members of the poly (ADP-ribose) polymerase (PARP) family, and allows the cells to recognize the DNA damage and facilitate recruitment and activation of DNA repair proteins.

RNA methylation specifically at position 6 of adenosine, 6-methyladenosine (m6A), is the most abundant internal modification in messenger RNA (mRNA), and is also present in transfer RNA (tRNA), ribosomal RNA (rRNA) and other non-coding RNAs. m6A has several roles in RNA metabolism, including regulating splicing, translation, and stability of mRNA.

Recently, Yang Xiang and colleagues have reported a novel role for RNA methylation (m6A) in the ultraviolet-induced DNA damage response. Here we’ll summarize how this RNA epigenetic mark serves as a signal in the DDR.

Post translational modifications often coordinate the DNA damage response early on, by allowing chromatin access and mediating recruitment of repair factors to DNA damage sites. Therefore, to investigate the modifications involved in the DNA damage response, this group screened for modifications localized to DNA damage sites in several cancer cell lines, including U2OS osteosarcoma, A375 melanoma, and HeLa cervical cancer cells.

They found that an antibody to m6A stained intensely at sites of UV-induced DNA damage. The induction of m6A was specific to UV irradiation, as other types of DNA damage did not induce accumulation of m6A. Treatment of cells with RNAse A abolished accumulation of m6A at damaged sites, indicating that RNA was the subject of methylation, and not DNA, and the signal derived mostly from Poly(A)+ transcripts.

Methyltransferase like-3 (METTL3) and METTL14 are two enzymatic components of the methyltransferase complex responsible for adenosine methylation (m6A). The researchers confirmed that the catalytic activity of METTL3 and METTL14 were necessary for m6A accumulation, which was rapidly detected just 2 minutes after UV irradiation. The m6A mark was transient and dissipated quickly suggesting demethylation shortly thereafter, which was shown to be catalyzed by the RNA demethylase FTO (fat mass and obesity-associated protein). In the UV-irradiated cells, PARP was necessary for m6A accumulation, indicating that PARP may mediate recruitment of METTL3 to damaged sites, with subsequent RNA methylation. The METTL3 knock-out cells had delayed removal of the DNA lesions and reduced survival, indicating that METTL3 and RNA methylation were important for repair of the lesions and cellular resistance.

Next they assessed which DNA polymerases could be acting downstream. They found that polymerase κ, an enzyme involved in several DNA repair pathways, co-localized with m6A at damaged sites and mediated the removal of cyclobutane pyrimidine dimers (CPDs), the principal lesions observed upon UV irradiation. METTL3 and METTL14 were necessary for pol κ localization to damaged sites, altogether suggesting that m6A may be important for recruitment of pol k to DNA damage sites and for pol κ-induced DNA repair.

The authors propose a DNA repair model in which upon UV irradiation, PARP mediates the accumulation of m6A at DNA damaged sites, possibly by recruiting METTL3, and m6A mediates the recruitment of pol κ, promoting DNA repair and cellular survival. Factors responsible for pol κ recruitment still need to be further elucidated, as direct binding of pol κ to m6A was not detected in this study. However, these findings suggest a novel role for RNA methylation as a signal mediating the recruitment of pol κ to UV-induced damage sites, thus facilitating DNA repair and cellular resistance to UV-induced DNA damage.

References:

1. Xiang Y, et al. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature. 2017 Mar 23;543(7646):573-576.
2. Ciccia A and Elledge SJ. The DNA Damage Response: Making it safe to play with knives. Mol Cell. 2010 Oct 22;40(2):179-204.