N(6)-Adenosine Methylation in RNA and a Reduced m(3)G/TMG Level in Non-Coding RNAs Appear at Microirradiation-Induced DNA Lesions

The DNA damage response is mediated by both DNA repair proteins and epigenetic markers. Here, we observe that N(6)-methyladenosine (m(6)A), a mark of the epitranscriptome, was common in RNAs accumulated at UV-damaged chromatin; however, inhibitors of RNA polymerases I and II did not affect the m(6)A RNA level at the irradiated genomic regions. After genome injury, m(6)A RNAs either diffused to the damaged chromatin or appeared at the lesions enzymatically. DNA damage did not change the levels of METTL3 and METTL14 methyltransferases. In a subset of irradiated cells, only the METTL16 enzyme, responsible for m(6)A in non-coding RNAs as well as for splicing regulation, was recruited to microirradiated sites. Importantly, the levels of the studied splicing factors were not changed by UVA light. Overall, if the appearance of m(6)A RNAs at DNA lesions is regulated enzymatically, this process must be mediated via the coregulatory function of METTL-like enzymes. This event is additionally accompanied by radiation-induced depletion of 2,2,7-methylguanosine (m(3)G/TMG) in RNA. Moreover, UV-irradiation also decreases the global cellular level of N(1)-methyladenosine (m(1)A) in RNAs. Based on these results, we prefer a model in which m(6)A RNAs rapidly respond to radiation-induced stress and diffuse to the damaged sites. The level of both (m(1)A) RNAs and m(3)G/TMG in RNAs is reduced as a consequence of DNA damage, recognized by the nucleotide excision repair mechanism.