Relocation of rDNA repeats for repair is dependent on SUMO-mediated nucleolar release by the Cdc48/p97 segregase

Ribosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to active transcription and their repetitive nature. Compartmentalization of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be released to the nucleoplasm to allow repair by homologous recombination. The process of rDNA relocation 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 targets CLIP-cohibin for disassembly mediated by the Cdc48/p97 chaperone, which recognizes SUMOylated CLIP-cohibin through its cofactor, Ufd1. Consistent with a conserved mechanism, UFD1L depletion impairs rDNA release in human cells. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.

[1]  S. Jentsch,et al.  ESCRT recruitment by the S. cerevisiae inner nuclear membrane protein Heh1 is regulated by Hub1-mediated alternative splicing , 2020, Journal of Cell Science.

[2]  A. Kamgoué,et al.  Quantification of the dynamic behaviour of ribosomal DNA genes and nucleolus during yeast Saccharomyces cerevisiae cell cycle. , 2019, Journal of structural biology.

[3]  D. H. Larsen,et al.  Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair , 2019, Nucleic acids research.

[4]  S. Jentsch,et al.  Slx5/Slx8‐dependent ubiquitin hotspots on chromatin contribute to stress tolerance , 2019, The EMBO journal.

[5]  D. Teis,et al.  ESCRT-III/Vps4 Controls Heterochromatin-Nuclear Envelope Attachments , 2019, bioRxiv.

[6]  S. Jentsch,et al.  Failed mitochondrial import and impaired proteostasis trigger SUMOylation of mitochondrial proteins , 2017, The Journal of Biological Chemistry.

[7]  T. Rapoport,et al.  Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex , 2017, Cell.

[8]  Jisha Chalissery,et al.  Genome maintenance in Saccharomyces cerevisiae: the role of SUMO and SUMO-targeted ubiquitin ligases , 2017, Nucleic acids research.

[9]  Dominik Boos,et al.  Targeting of the Fun30 nucleosome remodeller by the Dpb11 scaffold facilitates cell cycle-regulated DNA end resection , 2017, eLife.

[10]  S. Gasser,et al.  SUMO wrestles breaks to the nuclear ring's edge , 2016, Cell cycle.

[11]  V. Géli,et al.  SUMO-Dependent Relocalization of Eroded Telomeres to Nuclear Pore Complexes Controls Telomere Recombination. , 2016, Cell reports.

[12]  T. Hoppe,et al.  Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin , 2016, Front. Genet..

[13]  Monika Tsai-Pflugfelder,et al.  PolySUMOylation by Siz2 and Mms21 triggers relocation of DNA breaks to nuclear pores through the Slx5/Slx8 STUbL , 2016, Genes & development.

[14]  Christopher M Hickey,et al.  SUMO Pathway Modulation of Regulatory Protein Binding at the Ribosomal DNA Locus in Saccharomyces cerevisiae , 2016, Genetics.

[15]  R. Greenberg,et al.  ATM Dependent Silencing Links Nucleolar Chromatin Reorganization to DNA Damage Recognition. , 2015, Cell reports.

[16]  Chunaram Choudhary,et al.  Ubiquitin-SUMO Circuitry Controls Activated Fanconi Anemia ID Complex Dosage in Response to DNA Damage , 2015, Molecular cell.

[17]  F. Uhlmann,et al.  Nur1 Dephosphorylation Confers Positive Feedback to Mitotic Exit Phosphatase Activation in Budding Yeast , 2015, PLoS genetics.

[18]  P. Nelson,et al.  Neurodegeneration-associated instability of ribosomal DNA. , 2014, Biochimica et biophysica acta.

[19]  S. Jentsch,et al.  Role of Cdc48/p97 as a SUMO-targeted segregase curbing Rad51–Rad52 interaction , 2013, Nature Cell Biology.

[20]  R. Wysocki,et al.  The Swi2–Snf2-like protein Uls1 is involved in replication stress response , 2011, Nucleic acids research.

[21]  Aki Minoda,et al.  Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair , 2011, Cell.

[22]  H. Madhani,et al.  The Cul4-Ddb1Cdt2 Ubiquitin Ligase Inhibits Invasion of a Boundary-Associated Antisilencing Factor into Heterochromatin , 2011, Cell.

[23]  S. Harrison,et al.  The Monopolin Complex Crosslinks Kinetochore Components to Regulate Chromosome-Microtubule Attachments , 2010, Cell.

[24]  S. Gygi,et al.  Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution , 2009, Science.

[25]  S. Jackson,et al.  CDK targets Sae2 to control DNA-end resection and homologous recombination , 2008, Nature.

[26]  J. Pérez-Ortín,et al.  The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression , 2008, The Journal of cell biology.

[27]  F. Melchior,et al.  Concepts in sumoylation: a decade on , 2007, Nature Reviews Molecular Cell Biology.

[28]  Robert J. D. Reid,et al.  The Smc5–Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus , 2007, Nature Cell Biology.

[29]  S. Gygi,et al.  Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. , 2006, Genes & development.

[30]  L. Sistonen,et al.  PDSM, a motif for phosphorylation-dependent SUMO modification. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Marco Foiani,et al.  DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1 , 2004, Nature.

[32]  D. Sinclair,et al.  Inhibition of Silencing and Accelerated Aging by Nicotinamide, a Putative Negative Regulator of Yeast Sir2 and Human SIRT1* , 2002, The Journal of Biological Chemistry.

[33]  Boris Pfander,et al.  RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO , 2002, Nature.

[34]  R. Sternglanz,et al.  Perinuclear localization of chromatin facilitates transcriptional silencing , 1998, Nature.

[35]  E. Craig,et al.  Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. , 1996, Genetics.

[36]  R. Müller,et al.  Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. , 1995, Gene.

[37]  J. Gustafsson,et al.  Ligand-specific transactivation of gene expression by a derivative of the human glucocorticoid receptor expressed in yeast. , 1990, The Journal of biological chemistry.

[38]  R. D. Gietz,et al.  New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. , 1988, Gene.

[39]  A. Varshavsky,et al.  The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses , 1987, Cell.

[40]  Petra Beli,et al.  Quantitative Phosphoproteomics of Selective Autophagy Receptors. , 2019, Methods in molecular biology.

[41]  R. Dohmen,et al.  Methods to study SUMO dynamics in yeast. , 2019, Methods in enzymology.

[42]  Neus Colomina,et al.  Analysis of SUMOylation in the RENT Complex by Fusion to a SUMO-Specific Protease Domain. , 2017, Methods in molecular biology.

[43]  J P McDonald,et al.  Is Dna Damage Inducible and Functions in a Novel Error-free Postreplication Repair Mechanism , 1997 .