Bridging a DNA Break to Leave a Poly(ADP-Ribose) Mark on Chromatin

Summary: DNA strand breaks recruit PARP1 and its paralogue PARP2 to modify histones and many other substrates with mono- and poly(ADP-ribose) (PAR)1–5. In DNA damage response, the PAR post-translational modification occurs predominantly on serine amino acids6–8, which requires HPF1, an accessory factor that switches the amino-acid specificity of PARP1/2 from aspartate/glutamate to serine residues9,10. Poly(ADP) ribosylation (PARylation) is important for subsequent chromatin decompaction and serves as an anchor to recruit a variety of downstream signaling and repair factors to the sites of DNA breaks2,11. To understand the molecular mechanism of DNA break recognition by PARP enzymes in the context of chromatin, we determined cryo-EM structure of PARP2/HPF1 bound to a nucleosome. The structure shows that PARP2/HPF1 bridges two nucleosomes, with the broken DNA aligned in a ligation-competent position, revealing the initial step in double-strand DNA break repair. The bridging induces structural changes in PARP2 that signal DNA break recognition to the catalytic domain, which licenses HPF1 binding and PARP2 activation. Our data suggest that active PARP2 cycles through different conformational states to exchange NAD+ and substrate, which may enable PARP enzymes to be processive while bound to chromatin. The mechanisms of PARP activation and catalytic cycle we describe can explain resistance mechanisms to PARP inhibitors, and will aid development of better inhibitors for cancer treatments12–16.