Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates

• Published in: Molecular cell Vol. 84; no. 3; pp. 429 - 446.e17
• Main Authors: Nosella, Michael L., Kim, Tae Hun, Huang, Shuya Kate, Harkness, Robert W., Goncalves, Monica, Pan, Alisia, Tereshchenko, Maria, Vahidi, Siavash, Rubinstein, John L., Lee, Hyun O., Forman-Kay, Julie D., Kay, Lewis E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.02.2024
• Subjects: biomolecular condensates; cryo-electron microscopy; DNA; DNA repair; histones; NMR spectroscopy; nucleosome interactions; nucleosome structural dynamics; nucleosomes; PARP1; poly(ADP-ribosyl)ation; PARP1; poly(ADP-ribosyl)ation; NMR spectroscopy; nucleosome interactions; nucleosome structural dynamics; DNA repair; biomolecular condensates
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2023.12.019

Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions. [Display omitted] •Nucleosome PARylation enhances H3 tail dynamics without perturbing the histone core•PARylation dramatically enhances ligation of single-strand nicks in nucleosomes•Stacking and self-association of mononucleosomes is inhibited by PARylation•PARylation reorganizes condensates containing nucleosomes and DNA repair factors Nosella et al. establish that poly(ADP-ribosyl)ation of nucleosomes dramatically increases histone H3 tail dynamics and DNA conformational variability while leaving the core structure intact. These changes correlated with enhanced ligation of nucleosome single-strand nicks, disruption of nucleosome oligomers, and colocalization of nucleosomes with DNA repair factors inside biomolecular condensates.