Reversible RNA ADP-ribosylation on uracil bases

ADP-ribosylation is a conserved modification that uses NAD+ as a co-substrate to regulate essential cellular processes, such as genome stability and transcription, with Poly(ADP-ribose) Polymerases (PARPs) serving as the major catalyzing enzymes in humans. Historically defined as a protein post-translational modification, ADP-ribosylation on nucleic acids has been increasingly recognized in recent years, particularly in bacterial systems, but remains poorly understood in higher organisms. Here, we identify human PARP10 as a candidate enzyme that ADP-ribosylates nucleic acid bases, showing apparent activity on uracil bases in RNA, and a relatively weaker activity toward thymine bases in DNA. Furthermore, we show that human TARG1, a neurodegenerative disorder-linked protein previously reported to hydrolyse thymine base ADP-ribosylation, also efficiently reverses uracil base ADP-ribosylation (U-ADPr). To improve the efficient characterization of the enzymes for U-ADPr reversal, we developed chemical probes. Using these probes, we demonstrated that human TARG1 and TARG1-like macrodomain proteins are the efficient hydrolases for U-ADPr reversal in humans, Drosophila melanogaster, and bacterial homologues. The widespread distribution of U-ADPr hydrolases among different organisms suggests the potential evolutionary conservation of U-ADPr as a biological signal.