Nucleolar release of rDNA repeats for repair involves SUMO-mediated untethering by the Cdc48/p97 segregase

Abstract

Ribosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to their repetitive nature and active transcriptional status. Sequestration of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be first released to the nucleoplasm to allow repair by homologous recombination. Nucleolar release of broken rDNA repeats is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP-cohibin complex, releasing membrane-tethered rDNA from the nucleolus in Saccharomyces cerevisiae. Downstream of phosphorylation, SUMOylation of CLIP-cohibin is recognized by Ufd1 via its SUMO-interacting motif, which targets the complex for disassembly through the Cdc48/p97 chaperone. Consistent with a conserved mechanism, UFD1L depletion in human cells impairs rDNA release. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.

The p97/VCP segregase is essential for arsenic-induced degradation of PML and PML-RARA

“…In both fission yeast and budding yeast, it has been demonstrated that Ufd1 not only has the ability to bind ubiquitin but also, via a SIM in its C-terminus, bind SUMO. This appears to facilitate the function of Ufd1 in STUbL mediated genome stability processes (Bergink et al, 2013;Capella et al, 2021;Kohler et al, 2015;Nie et al, 2012;Nie and Boddy, 2016). While we cannot exclude the possibility that SUMO-ubiquitin hybrid chains play a role in arsenic-induced degradation of PML and PML-RARA, the SIM present in the C-terminus of yeast Ufd1 is not present in the human form of UFD1, suggesting that SUMO recognition by Ufd1 is not required in arsenic-induced p97 mediated extraction of PML from nuclear bodies.…”

Multi-level monitoring of EME1-MUS81 in CPT induced nucleolar rDNA repair

“…Then, poly-sumoylated EME1 is extracted by the AAA ATPase VCP/p97-NPL4-UFD1 complex, which we observed in our EME1-IP (Extended Data Fig. 7) and which is established to extract poly-sumoylated and/or ubiquitinated proteins form replication forks and nucleolar repair condensates [49][50][51][52] . This step likely requires poly-sumoylation-dependent ubiquitination, as it best understood for the STUbL RNF4 but may also apply to TRIM25.…”

The inner nuclear membrane protein Lem2 coordinates RNA degradation at the nuclear periphery

“…CoIP assays were performed following a previously described protocol 70 with a few modifications in the lysis buffer. The lysis buffer contained 50 mM HEPES pH 7.4, 100 mM NaCl, 10% glycerol, 1 mM EDTA pH 8, 2.5 mM MgCl 2 , 0.5% NP-40, 1× complete EDTA-free protease inhibitor cocktail (Roche), 2 mM PMSF (Serva), 20 mM N -ethylmaleimide (NEM, Sigma).…”