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

Michael L Nosella; Tae Hun Kim; Shuya Kate Huang; Robert W Harkness; Monica Goncalves; Alisia Pan; Maria Tereshchenko; Siavash Vahidi; John L Rubinstein; Hyun O Lee; Julie D Forman-Kay; Lewis E Kay

doi:10.1016/j.molcel.2023.12.019

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

Mol Cell. 2024 Feb 1;84(3):429-446.e17. doi: 10.1016/j.molcel.2023.12.019. Epub 2024 Jan 11.

Authors

Affiliations

¹ Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
² Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
³ Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
⁴ Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
⁵ Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
⁶ Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada.
⁷ Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: [email protected].
⁸ Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: [email protected].

PMID: 38215753
DOI: 10.1016/j.molcel.2023.12.019

Abstract

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.

Keywords: DNA repair; NMR spectroscopy; PARP1; biomolecular condensates; nucleosome interactions; nucleosome structural dynamics; poly(ADP-ribosyl)ation.

MeSH terms

Biomolecular Condensates
Cryoelectron Microscopy
DNA / genetics
DNA / metabolism
DNA Damage
DNA Repair
Histones / genetics
Histones / metabolism
Nucleosomes* / genetics
Poly (ADP-Ribose) Polymerase-1 / metabolism
Poly ADP Ribosylation* / genetics
Poly(ADP-ribose) Polymerases / metabolism

Substances

Nucleosomes
Poly(ADP-ribose) Polymerases
Histones
DNA
Poly (ADP-Ribose) Polymerase-1