Abstract
The Mre11 nuclease is part of the conserved MRX complex involved in DNA double-strand break (DSB) repair. During meiosis in budding yeast, MRX is also required for Spo11-mediated programmed DSB formation to initiate homologous recombination. Recruitment of Mre11 to meiotic DSB sites depends on Rec114-Mei4 and Mer2, proposed to organize the DSB machinery via biomolecular condensation. Here, we show that Mre11 and MRX complexes form DNA-dependent, hexanediol-sensitive condensates in vitro. In vivo, Mre11 assembles into DNA damage-dependent foci during mitosis and DSB-independent foci during meiosis. Both in vitro condensates and in vivo foci require Mre11 C-terminal intrinsically-disordered region (IDR). While dispensable for vegetative DNA repair, Mre11 IDR is essential during meiosis, where it mediates interaction with Mer2 via a short α-helix and contains a SUMO-interacting motif that enhances Mre11 recruitment and DSB formation. Together, these findings provide insights into the biophysical properties of Mre11 and its role in initiating meiotic recombination.
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Data availability
The NMR data generated in this study have been deposited in the Biological Magnetic Resonance Bank with the accession number 53209. Accession codes for protein structures used for AlphaFold models are listed below: AF-P32829-F1, CAA60944, BAA02017, XP_003669210.1 [https://www.ncbi.nlm.nih.gov/protein/XP_003669210.1], XP_003672532.1 [https://www.ncbi.nlm.nih.gov/protein/XP_003672532.1], XP_001647040.1 [https://www.ncbi.nlm.nih.gov/protein/XP_001647040.1], XP_001642997.1 [https://www.ncbi.nlm.nih.gov/protein/XP_001642997.1], XP_003683996.1 [https://www.ncbi.nlm.nih.gov/protein/XP_003683996.1], XP_003686402.1 [https://www.ncbi.nlm.nih.gov/protein/XP_003686402.1] and AF-Q12306-F1. AlphaFold models are available in ModelArchive (modelarchive.org) with the following accession codes: ma-bjxr0 [https://modelarchive.org/doi/10.5452/ma-bjxr0], ma-sljg3 [https://modelarchive.org/doi/10.5452/ma-sljg3], ma-byd98 [https://modelarchive.org/doi/10.5452/ma-byd98], ma-itjlc [https://modelarchive.org/doi/10.5452/ma-itjlc] and ma-b9r3g. Source data are provided in this paper.
References
Cooke, M. S., Evans, M. D., Dizdaroglu, M. & Lunec, J. Oxidative DNA damage: mechanisms, mutation, and disease. FASEB J. 17, 1195–1214 (2003).
De Almeida, L. C., Calil, F. A., Machado-Neto, J. A. & Costa-Lotufo, L. V. DNA damaging agents and DNA repair: From carcinogenesis to cancer therapy. Cancer Genet. 252-253, 6–24 (2021).
Tubbs, A. & Nussenzweig, A. Endogenous DNA damage as a source of genomic instability in cancer. Cell 168, 644–656 (2017).
Oster, S. & Aqeilan, R. I. Programmed DNA damage and physiological DSBs: mapping, biological significance and perturbations in disease states. Cells 9, 1870 (2020).
Börner, G. V., Hochwagen, A. & MacQueen, A. J. Meiosis in budding yeast. Genetics 225, iyad125 (2023).
Zickler, D. & Kleckner, N. Meiosis: dances between homologs. Annu Rev Genet 57, 1–63 (2023).
Lam, I. & Keeney, S. Mechanism and regulation of meiotic recombination initiation. Cold Spring Harb. Perspect. Biol. 7, a016634 (2015).
Yadav, V. K. & Claeys Bouuaert, C. Mechanism and control of meiotic DNA double-strand break formation in S. cerevisiae. Front. Cell Dev. Biol. 9, 642737 (2021).
Claeys Bouuaert, C. et al. DNA-driven condensation assembles the meiotic DNA break machinery. Nature 592, 144–149 (2021).
Claeys Bouuaert, C. et al. Structural and functional characterization of the Spo11 core complex. Nat. Struct. Mol. Biol. 28, 92–102 (2021).
Johnson, D. et al. Concerted cutting by Spo11 illuminates meiotic DNA break mechanics. Nature 594, 572–576 (2021).
Oger, C. & Claeys Bouuaert, C. SPO11 dimers are sufficient to catalyse DNA double-strand breaks in vitro. Nature 639, 792–799 (2025).
Oger, C. & Claeys Bouuaert, C. In vitro reconstitution of SPO11-mediated DNA cleavage sheds new light on the initiation of meiotic recombination. DNA Cell Biol. 44, 401–406 (2025).
Aït-Bella, H. et al. Dimerization of the S. cerevisiae Spo11 core complex. Preprint at https://doi.org/10.64898/2026.01.16.699991 (2026).
Kleckner, N. Chiasma formation: chromatin/axis interplay and the role(s) of the synaptonemal complex. Chromosoma 115, 175–194 (2006).
Panizza, S. et al. Spo11-Accessory proteins link double-strand break sites to the chromosome axis in early meiotic recombination. Cell 146, 372–383 (2011).
Alani, E., Padmore, R. & Kleckner, N. Analysis of wild-type and rad50 mutants of yeast suggests an intimate relationship between meiotic chromosome synapsis and recombination. Cell 61, 419–436 (1990).
Ivanov, E. L., Korolevt, V. G. & Fabre, F. Xrs2, a DNA Repair gene of saccharomyces cerevisiae, is needed for meiotic recombination. GENETICS 132, 651–664 (1992).
Nairz, K. & Klein, F. mre11S —a yeast mutation that blocks double-strand-break processing and permits nonhomologous synapsis in meiosis. Genes Dev. 11, 2272–2290 (1997).
Keeney, S. Mechanism and control of meiotic recombination initiation. Curr. Top. Dev. Biol. 52, 1–53 (2001).
Moore, J. K. & Haber, J. E. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2164–2173 (1996).
Paull, T. T. & Gellert, M. The 3′ to 5′ Exonuclease activity of Mre11 facilitates repair of DNA double-strand breaks. Mol. Cell 1, 969–979 (1998).
Garcia, V., Phelps, S. E. L., Gray, S. & Neale, M. J. Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1. Nature 479, 241–244 (2011).
Casari, E. et al. Processing of DNA double-strand breaks by the MRX complex in a chromatin context. Front. Mol. Biosci. 6, 43 (2019).
Gobbini, E., Cassani, C., Villa, M., Bonetti, D. & Longhese, M. Functions and regulation of the MRX complex at DNA double-strand breaks. Microbial Cell 3, 329–337 (2016).
Paull, T. T. 20 Years of Mre11 Biology: No End in Sight. Mol. Cell 71, 419–427 (2018).
Tisi, R., Vertemara, J., Zampella, G. & Longhese, M. P. Functional and structural insights into the MRX/MRN complex, a key player in recognition and repair of DNA double-strand breaks. Comput. Struct. Biotechnol. J. 18, 1137–1152 (2020).
Lamarche, B. J., Orazio, N. I. & Weitzman, M. D. The MRN complex in double-strand break repair and telomere maintenance. FEBS Lett. 584, 3682–3695 (2010).
Lu, R. et al. Post-translational modification of MRE11: its implication in DDR and diseases. Genes 12, 1158 (2021).
Oh, J. & Symington, L. S. Role of the Mre11 complex in preserving genome integrity. Genes 9, 589 (2018).
Furuse, M. et al. Distinct roles of two separable in vitro activities of yeast Mre11 in mitotic and meiotic recombination. EMBO J. 17, 6412–6425 (1998).
Usui, T. et al. Complex formation and functional versatility of Mre11 of budding yeast in recombination. Cell 95, 705–716 (1998).
Aithal, R. et al. Physical interaction with Spo11 mediates the localisation of Mre11 to chromatin in meiosis and promotes its nuclease activity. Nucleic Acids Res. 52, 4328–4343 (2024).
Wen, Q. et al. A mutant allele of MRE11 found in mismatch repair-deficient tumor cells suppresses the cellular response to DNA replication fork stress in a dominant negative manner. Mol. Cell. Biol. 19, 1693–1705 (2008).
Tamai, T. et al. Sae2 controls Mre11 endo- and exonuclease activities by different mechanisms. Nat. Commun. 15, 7221 (2024).
Kissling, V. M. et al. Mre11-Rad50 oligomerization promotes DNA double-strand break repair. Nat. Commun. 13, 2374 (2022).
Kroschwald, S., Maharana, S. & Simon, A. Hexanediol: a chemical probe to investigate the material properties of membrane-less compartments. Matters. https://doi.org/10.19185/matters.201702000010 (2017).
Lammens, K. et al. The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. Cell 145, 54–66 (2011).
Rotheneder, M. et al. Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions. Mol. Cell 83, 167–185 (2023).
Hohl, M., Yu, Y., Kuryavyi, V., Patel, D. & Petrini, J. Structure guided functional analysis of the S. cerevisiae Mre11 complex. Nat. Commun. 16, 7469 (2025).
Borde, V. et al. Association of Mre11p with double-strand break sites during yeast meiosis. Mol. Cell 13, 389–401 (2004).
Bergerat, A. et al. An atypical topoisomerase II from archaea with implications for meiotic recombination. Nature 386, 414–417 (1997).
Rousová, D. et al. Novel mechanistic insights into the role of Mer2 as the keystone of meiotic DNA break formation. ELife 10, e72330 (2021).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Daccache, D. et al. Evolutionary conservation of the structure and function of meiotic Rec114−Mei4 and Mer2 complexes. Genes Dev. 37, 535–553 (2023).
Tessé, S. et al. Asy2/Mer2: an evolutionarily conserved mediator of meiotic recombination, pairing, and global chromosome compaction. Genes Dev. 31, 1880–1893 (2017).
Bhagwat, N. R. et al. SUMO is a pervasive regulator of meiosis. ELife 10, e57720 (2021).
Chen, Y. J. et al. S. cerevisiae Mre11 recruits conjugated SUMO moieties to facilitate the assembly and function of the Mre11-Rad50-Xrs2 complex. Nucleic Acids Res. 44, 2199–2213 (2016).
Zhao, Q. et al. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Res. 42, W325–W330 (2014).
Lascorz, J., Codina-Fabra, J., Reverter, D. & Torres-Rosell, J. SUMO-SIM interactions: From structure to biological functions. Semin. Cell Dev. Biol. 132, 193–202 (2022).
Song, J., Zhang, Z., Hu, W. & Chen, Y. Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif. J. Biol. Chem. 280, 40122–40129 (2005).
Keusekotten, K. et al. Multivalent interactions of the SUMO-interaction motifs in RING finger protein 4 determine the specificity for chains of the SUMO. Biochem. J. 457, 207–214 (2014).
Li, J., Hooker, G. W. & Roeder, G. S. Saccharomyces cerevisiae Mer2, Mei4 and Rec114 form a complex required for meiotic double-strand break formation. Genetics 173, 1969–1981 (2006).
Henderson, K. A., Kee, K., Maleki, S., Santini, P. A. & Keeney, S. Cyclin-Dependent Kinase directly regulates initiation of meiotic recombination. Cell 125, 1321–1332 (2006).
Maleki, S., Neale, M. J., Arora, C., Henderson, K. A. & Keeney, S. Interactions between Mei4, Rec114, and other proteins required for meiotic DNA double-strand break formation in Saccharomyces cerevisiae. Chromosoma 116, 471–486 (2007).
Williams, R. S. et al. Mre11 Dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell 135, 97–109 (2008).
MacQueen, A. J. & Roeder, G. S. Fpr3 and Zip3 Ensure that initiation of meiotic recombination precedes chromosome synapsis in budding yeast. Curr. Biol. 19, 1519–1526 (2009).
Rog, O., Köhler, S. & Dernburg, A. F. The synaptonemal complex has liquid crystalline properties and spatially regulates meiotic recombination factors. ELife 6, e21455 (2017).
Vrielynck, N. et al. Conservation and divergence of meiotic DNA double strand break forming mechanisms in Arabidopsis thaliana. Nucleic Acids Res. 49, 9821–9835 (2021).
Symington, L. S. Mechanism and regulation of DNA end resection in eukaryotes. Crit. Rev. Biochem. Mol. Biol. 51, 195–212 (2016).
Gnügge, R. & Symington, L. S. Keeping it real: MRX–Sae2 clipping of natural substrates. Genes Dev. 31, 2311–2312 (2017).
Chin, G. M. & Villeneuve, A. M. C. elegans mre-11 is required for meiotic recombination and DNA repair but is dispensable for the meiotic G2 DNA damage checkpoint. Genes Dev. 15, 522–534 (2001).
Puizina, J., Siroky, J., Mokros, P., Schweizer, D. & Riha, K. Mre11 deficiency in Arabidopsis is associated with chromosomal instability in somatic cells and Spo11-dependent genome fragmentation during meiosis. Plant Cell 16, 1968–1978 (2004).
Young, J. A., Hyppa, R. W. & Smith, G. R. Conserved and nonconserved proteins for meiotic DNA breakage and repair in yeasts. Genetics 167, 593–605 (2004).
Liu Y., Lin Z., Yan J., Zhang X. & Tong M. H. A Rad50-null mutation in mouse germ cells causes reduced DSB formation, abnormal DSB end resection and complete loss of germ cells. Development. 151, https://doi.org/10.1242/dev.202312 (2024).
Kim, S. et al. Mouse MRE11-RAD50-NBS1 is needed to start and extend meiotic DNA end resection. Nat. Commun. 16, https://doi.org/10.1038/s41467-025-57928-x (2025).
Hayashi, M., Chin, G. M. & Villeneuve, A. M. C. elegans germ cells switch between distinct modes of double-strand break repair during meiotic prophase progression. PLOS Genet. 3, https://doi.org/10.1371/journal.pgen.0030191, (2007).
Girard, C., Roelens, B., Zawadzki, K. A. & Villeneuve, A. M. Interdependent and separable functions of Caenorhabditis elegans MRN-C complex members couple formation and repair of meiotic DSBs. Proc. Natl. Acad. Sci. USA 115, https://doi.org/10.1073/pnas.1719029115 (2018).
Bishop, K. & Kleckner, N. DMCI: A meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell 69, 439–456 (1992).
Tran, P. T., Erdeniz, N., Dudley, S. & Liskay, R. M. Characterization of nuclease-dependent functions of Exo1p in Saccharomyces cerevisiae. DNA Repair 1, 895–912 (2002).
Joshi, N., Brown, M. S., Bishop, D. K. & Börner, G. V. Gradual implementation of the meiotic recombination program via checkpoint pathways controlled by global DSB levels. Mol. Cell 57, 797–811 (2015).
Mimitou, E. P., Yamada, S. & Keeney, S. A global view of meiotic double-strand break end resection. Science 335, 40–45 (2017).
Yunus, A. A. & Lima, C. D. Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation. Methods Mol. Biol.https://doi.org/10.1007/978-1-59745-566-4_11 (2009).
Cannavo, E., Cejka, P.& Kowalczykowski, S. C. Relationship of DNA degradation by Saccharomyces cerevisiae Exonuclease 1 and its stimulation by RPA and Mre11-Rad50-Xrs2 to DNA end resection. Proc. Natl. Acad. Sci. USA 110, https://doi.org/10.1073/pnas.1305166110. (2013).
Murakami, H., Borde, V., Nicolas, A. & Keeney, S. Gel electrophoresis assays for analyzing DNA double-strand breaks in Saccharomyces cerevisiae at various spatial resolutions. Methods Mol. Biol. 557, 117–142 (2009).
Delaglio, F. et al. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277–293 (1995).
Vranken, W. F. et al. The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins 59, 687–696 (2005).
Sheng, W. & Liao, X. Solution structure of a yeast ubiquitin-like protein Smt3: The role of structurally less defined sequences in protein–protein recognitions. Protein Sci. 11, 1482–1491 (2002).
Dosztanyi, Z., Csizmok, V., Tompa, P. & Simon, I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21, 3433–3434 (2005).
Acknowledgements
We thank David Alvarez Melo for generating Mer2-iV5 tagged strains, John Weir for plasmids and strains, and C.C.B. laboratory members for discussion. We thank the Biological Imaging facility (IMABIOL) at UCLouvain and Marie-Christine Eloy for providing training in the use of the epifluorescence microscope. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement 802525 to C.C.B.), and the Fonds National de la Recherche Scientifique (PDR grant T.0031.22 to C.C.B.). P.P. is funded by FNRS Aspirant fellowships (project 1.A908.22). C.C.B. is an FNRS Research Associate. W.E.Y.M. and S.B. acknowledge the Research Council of VUB for support through the Strategic Research Program SRP95 and the infrastructure grant OZR3939. NIH NIGMS grant R01GM074223 supported NH, who is also an Investigator of the Howard Hughes Medical Institute.
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P.P. designed, executed, and analyzed all experiments except as noted; M.S. performed Southern blot experiments; W.E.Y.M. synthesized peptides under the supervision of S.B., performed ITC experiments and analyzed NMR data; A.N.V. acquired and analyzed NMR data; R.B. performed yeast 2-hybrid experiments under the supervision of N.H.; C.C.B. supervised the research and secured funding. P.P. and C.C.B wrote the paper with input from all authors.
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Priyadarshini, P., Survi, M., El Yazidi Mouloud, W. et al. Recruitment of Mre11 to recombination sites during meiosis. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71310-5
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DOI: https://doi.org/10.1038/s41467-026-71310-5


