The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage

• Published in: eLife Vol. 6
• Main Authors: Kitevski-LeBlanc, Julianne, Fradet-Turcotte, Amélie, Kukic, Predrag, Wilson, Marcus D, Portella, Guillem, Yuwen, Tairan, Panier, Stephanie, Duan, Shili, Canny, Marella D, van Ingen, Hugo, Arrowsmith, Cheryl H, Rubinstein, John L, Vendruscolo, Michele, Durocher, Daniel, Kay, Lewis E
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 13-04-2017; eLife Sciences Publications, Ltd
• Subjects: Arginine; Biochemistry; Biophysics and Structural Biology; BRCA1 protein; Cancer; Chromatin; Cryoelectron Microscopy; Deoxyribonucleic acid; DNA; DNA Breaks, Double-Stranded; DNA damage; DNA repair; Histones - metabolism; Humans; Magnetic Resonance Spectroscopy; Medical research; Molecular Dynamics Simulation; NMR; Nuclear magnetic resonance; Nucleosomes; Peptides; Protein Binding; Proteins; Spectroscopy; Ubiquitin; ubiquitin-based signalling; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - metabolism; ubiquitylated-histone reader; DNA damage; ubiquitin-based signalling; structural biology; D. melanogaster; biophysics; human; ubiquitylated-histone reader
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.23872

Site-specific histone ubiquitylation plays a central role in orchestrating the response to DNA double-strand breaks (DSBs). DSBs elicit a cascade of events controlled by the ubiquitin ligase RNF168, which promotes the accumulation of repair factors such as 53BP1 and BRCA1 on the chromatin flanking the break site. RNF168 also promotes its own accumulation, and that of its paralog RNF169, but how they recognize ubiquitylated chromatin is unknown. Using methyl-TROSY solution NMR spectroscopy and molecular dynamics simulations, we present an atomic resolution model of human RNF169 binding to a ubiquitylated nucleosome, and validate it by electron cryomicroscopy. We establish that RNF169 binds to ubiquitylated H2A-Lys13/Lys15 in a manner that involves its canonical ubiquitin-binding helix and a pair of arginine-rich motifs that interact with the nucleosome acidic patch. This three-pronged interaction mechanism is distinct from that by which 53BP1 binds to ubiquitylated H2A-Lys15 highlighting the diversity in site-specific recognition of ubiquitylated nucleosomes.