NFATC2IP is a mediator of SUMO-dependent genome integrity

Abstract

The post-translational modification of proteins by SUMO is crucial for cellular viability and mammalian development in part due to the contribution of SUMOylation to genome duplication and repair. To investigate the mechanisms underpinning the essential function of SUMO, we undertook a genome-scale CRISPR/Cas9 screen probing the response to SUMOylation inhibition. This effort identified 130 genes whose disruption reduces or enhances the toxicity of TAK-981, a clinical-stage inhibitor of the SUMO E1-activating enzyme. Among the strongest hits, we validated and characterized NFATC2IP, an evolutionarily conserved protein related to the fungal Esc2 and Rad60 proteins that harbors tandem SUMO-like domains. Cells lacking NFATC2IP are viable but are hypersensitive to SUMO E1 inhibition, likely due to the accumulation of mitotic chromosome bridges and micronuclei. NFATC2IP primarily acts in interphase and associates with nascent DNA, suggesting a role in the postreplicative resolution of replication or recombination intermediates. Mechanistically, NFATC2IP interacts with the SMC5/6 complex and UBC9, the SUMO E2, via its first and second SUMO-like domains, respectively. AlphaFold-Multimer modeling suggests that NFATC2IP positions and activates the UBC9–NSMCE2 complex, the SUMO E3 ligase associated with SMC5/SMC6. We conclude that NFATC2IP is a key mediator of SUMO-dependent genomic integrity that collaborates with the SMC5/6 complex.

Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions

“…Importantly, it performed well on proteins in different compartments and pathways, as expected given that training was pathway-and compartment-agnostic (Figure S5C and Table S1). Moreover, whereas conventional metrics generally distributed pairs evenly across their respective score ranges, SPOC more clearly separated the TP from the TNs (Figure 4B, Figure S5A-C; Note that the classifier's top hit in the SLF1 mini-screen was RAD18, a SLF1 interactor [47][48][49] . Finally, we assessed how SPOC ranked DONSON's five interactors (MCM3, SLD5, TOPB1, DPOE2, and DONSON; Figure S2A) in our previous proteome-wide screen for DONSON interactors 50 .…”

SUMO and the DNA damage response

“…The SUMO binding function of SLX4 is needed for the recognition of DNA damage sensors MRN, RPA and TRF2 (telomeric repeat binding factor 2) [ 137 ]. SLX4 SUMOylation is also promoted by NIP45 (nuclear factor of activated T cells 2 interacting protein), an SLD-containing protein that stimulates Ubc9 activity towards a subset of proteins [ 140 , 141 ]. SUMOylated SLX4 also facilitates the resolution of catenated DNA structures before M-phase [ 140 ].…”