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

Abstract

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.DOI: http://dx.doi.org/10.7554/eLife.23872.001

Recognition of Nucleosomes by Chromatin Factors: Lessons from Data-Driven Docking-Based Structures of Nucleosome-Protein Complexes

“…Strikingly, RCC1 binds to the acidic patch using the canonical arginine anchor, here contained in a loop, and also binds the nucleosomal DNA through its N-terminal tail. Such synergetic interactions have been observed later in many other nucleosome-binding proteins [50,55,[67][68][69][70]. This study was the first to show such complexity of nucleosomes as interaction platforms.…”

How cells ensure correct repair of DNA double-strand breaks

“…Just as JMJD2A and L3MBTL1 compete with 53BP1 for H4K20Me 2 binding, the E3 ubiquitin ligases RNF169 and RAD18 also compete with 53BP1 for binding to H2AK15ub (53,54). The ability of 53BP1 to bind to H2AK15ub is also limited by phosphorylation or acetylation of key residues within the ubiquitin-dependent recruitment region (13,55,56).…”

Ubiquitin and ubiquitin-like molecules in DNA double strand break repair

“…The deubiquitinase, USP11, counteracts this process by removing polyubiquitin chain from PALB2 and sabotages the BRCA1-PALB2-BRCA2 complex assembly [76]. RNF169 is recruited to DSBs through its ubiquitin-binding MIU2 domain, competes with RNF168, removes 53BP1 and RAP80 bridging ubiquitin and histone surfaces, and promotes HR [77][78][79]. Ubiquitination of RAD51 also impairs RAD51-BRCA2 interaction, and UCHL3 mediated deubiquitination of RAD51 strengthens RAD51-BRCA2 binding and facilitates RAD51 recruitment to DSBs [80].…”