Molecular Assemblies
and Genome Integrity

Ceppi, Ilaria, Maria Rosaria Dello Stritto, Martin Mütze, Stefan Braunshier, Valentina Mengoli, Giordano Reginato, Hồ Mỹ Phúc Võ, et al. 2024. “Mechanism of BRCA1-BARD1 Function in DNA End Resection and DNA Protection.” Nature, September. https://doi.org/10.1038/s41586-024-07909-9.

Nocente, Marina C., Anida Mesihovic Karamitsos, Emilie Drouineau, Manon Soleil, Waad Albawardi, Cécile Dulary, Florence Ribierre, et al. 2024. “CBAF Generates Subnucleosomes That Expand OCT4 Binding and Function beyond DNA Motifs at Enhancers.” Nature Structural & Molecular Biology, July. https://doi.org/10.1038/s41594-024-01344-0.

Nicolas, Yoann, Hélène Bret, Elda Cannavo, Ananya Acharya, Petr Cejka, Valérie Borde, and Raphaël Guerois. 2024. “Molecular Insights into the Activation of Mre11-Rad50 Endonuclease Activity by Sae2/CtIP.” Molecular Cell, June, S1097-2765(24)00442-8. https://doi.org/10.1016/j.molcel.2024.05.019.

Acharya, Ananya, Hélène Bret, Jen-Wei Huang, Martin Mütze, Martin Göse, Vera Maria Kissling, Ralf Seidel, Alberto Ciccia, Raphaël Guérois, and Petr Cejka. 2024. “Mechanism of DNA Unwinding by MCM8-9 in Complex with HROB.” Nature Communications 15 (1): 3584. https://doi.org/10.1038/s41467-024-47936-8.

Ouasti, Fouad, Maxime Audin, Karine Fréon, Jean-Pierre Quivy, Mehdi Tachekort, Elizabeth Cesard, Aurélien Thureau, et al. 2024. “Disordered Regions and Folded Modules in CAF-1 Promote Histone Deposition in Schizosaccharomyces Pombe.” ELife 12 (February):RP91461. https://doi.org/10.7554/eLife.91461.

Leuzzi, Giuseppe, Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa M. Firestone, Allison R. Hickman, Wendy Mao, et al. 2024. “SMARCAL1 Is a Dual Regulator of Innate Immune Signaling and PD-L1 Expression That Promotes Tumor Immune Evasion.” Cell, January, S0092-8674(24)00010-2. https://doi.org/10.1016/j.cell.2024.01.008.

Bret, Hélène, Jinmei Gao, Diego Javier Zea, Jessica Andreani, and Raphaël Guerois. 2024. “From Interaction Networks to Interfaces, Scanning Intrinsically Disordered Regions Using AlphaFold2.” Nature Communications 15 (1): 597. https://doi.org/10.1038/s41467-023-44288-7.

Versini, Raphaelle, Sujith Sritharan, Burcu Aykac Fas, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, et al. 2023. “A Perspective on the Prospective Use of AI in Protein Structure Prediction.” Journal of Chemical Information and Modeling, December. https://doi.org/10.1021/acs.jcim.3c01361.

Muzyukina, Polina, Anton Shkaruta, Noemi M. Guzman, Jessica Andreani, Adair L. Borges, Joseph Bondy-Denomy, Anna Maikova, Ekaterina Semenova, Konstantin Severinov, and Olga Soutourina. 2023. “Identification of an Anti-CRISPR Protein That Inhibits the CRISPR-Cas Type I-B System in Clostridioides Difficile.” MSphere, November, e0040123. https://doi.org/10.1128/msphere.00401-23.

Liu, Siyu, Judith Miné-Hattab, Marie Villemeur, Raphaël Guerois, Henrik Dahl Pinholt, Leonid A. Mirny, and Angela Taddei. 2023. “Author Correction: In Vivo Tracking of Functionally Tagged Rad51 Unveils a Robust Strategy of Homology Search.” Nature Structural & Molecular Biology, November. https://doi.org/10.1038/s41594-023-01180-8.

Vrielynck, Nathalie, Marion Peuch, Stéphanie Durand, Qichao Lian, Aurélie Chambon, Aurélie Hurel, Julie Guérin, et al. 2023. “SCEP1 and SCEP2 Are Two New Components of the Synaptonemal Complex Central Element.” Nature Plants, November. https://doi.org/10.1038/s41477-023-01558-y.

Kefala Stavridi, Antonia, Amandine Gontier, Vincent Morin, Philippe Frit, Virginie Ropars, Nadia Barboule, Carine Racca, et al. 2023. “Structural and Functional Basis of Inositol Hexaphosphate Stimulation of NHEJ through Stabilization of Ku-XLF Interaction.” Nucleic Acids Research, October, gkad863. https://doi.org/10.1093/nar/gkad863.

Liu, Siyu, Judith Miné-Hattab, Marie Villemeur, Raphaël Guerois, Henrik Dahl Pinholt, Leonid A. Mirny, and Angela Taddei. 2023. “Publisher Correction: In Vivo Tracking of Functionally Tagged Rad51 Unveils a Robust Strategy of Homology Search.” Nature Structural & Molecular Biology, September. https://doi.org/10.1038/s41594-023-01114-4.

Gareil, Nelly, Alison Gervais, Nicolas Macaisne, Guillaume Chevreux, Julie C. Canman, Jessica Andreani, and Julien Dumont. 2023. “An Unconventional TOG Domain Is Required for CLASP Localization.” Current Biology: CB 33 (16): 3522-3528.e7. https://doi.org/10.1016/j.cub.2023.07.009.

Liu, Siyu, Judith Miné-Hattab, Marie Villemeur, Raphaël Guerois, Henrik Dahl Pinholt, Leonid A. Mirny, and Angela Taddei. 2023. “In Vivo Tracking of Functionally Tagged Rad51 Unveils a Robust Strategy of Homology Search.” Nature Structural & Molecular Biology, August. https://doi.org/10.1038/s41594-023-01065-w.

Szatkownik, Antoine, Diego Javier Zea, Hugues Richard, and Elodie Laine. 2023. “Building Alternative Splicing and Evolution-Aware Sequence-Structure Maps for Protein Repeats.” Journal of Structural Biology, July, 107997. https://doi.org/10.1016/j.jsb.2023.107997.

Schweke, Hugo, Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten Schwede, Frédéric Cazals, Alix Lhéritier, et al. 2023. “Discriminating Physiological from Non-Physiological Interfaces in Structures of Protein Complexes: A Community-Wide Study.” Proteomics, June, e2200323. https://doi.org/10.1002/pmic.202200323.

Wang, Yanan, Giovanni Chiappetta, Raphaël Guérois, Yijun Liu, Stéphane Romero, Daniel J. Boesch, Matthias Krause, et al. 2023. “PPP2R1A Regulates Migration Persistence through the NHSL1-Containing WAVE Shell Complex.” Nature Communications 14 (1): 3541. https://doi.org/10.1038/s41467-023-39276-w.

Ceppi, Ilaria, Elda Cannavo, Hélène Bret, Rosa Camarillo, Francesca Vivalda, Roshan Singh Thakur, Amador Romero-Franco, et al. 2023. “PLK1 Regulates CtIP and DNA2 Interplay in Long-Range DNA End Resection.” Genes & Development, February. https://doi.org/10.1101/gad.349981.122.

Singh, Dipesh Kumar, Rigel Salinas Gamboa, Avinash Kumar Singh, Birgit Walkemeier, Jelle Van Leene, Geert De Jaeger, Imran Siddiqi, Raphael Guerois, Wayne Crismani, and Raphael Mercier. 2023. “The FANCC-FANCE-FANCF Complex Is Evolutionarily Conserved and Regulates Meiotic Recombination.” Nucleic Acids Research, January, gkac1244. https://doi.org/10.1093/nar/gkac1244.

Cargemel, Claire, Sonia Baconnais, Magali Aumont-Nicaise, Magali Noiray, Lia Maurin, Jessica Andreani, Hélène Walbott, et al. 2023. “Structural Insights of the DciA Helicase Loader in Its Relationship with DNA.” International Journal of Molecular Sciences 24 (2): 1427. https://doi.org/10.3390/ijms24021427.

Andreani, Jessica, Brian Jiménez-García, and Masahito Ohue. 2023. “Editorial: Web Tools for Modeling and Analysis of Biomolecular Interactions Volume II.” Frontiers in Molecular Biosciences 10:1190855. https://doi.org/10.3389/fmolb.2023.1190855.

Zönnchen, Josua, Johannes Gantner, Dmitry Lapin, Karen Barthel, Lennart Eschen-Lippold, Jessica L. Erickson, Sergio Landeo Villanueva, et al. 2022. “EDS1 Complexes Are Not Required for PRR Responses and Execute TNL-ETI from the Nucleus in Nicotiana Benthamiana.” New Phytologist n/a (n/a). https://doi.org/10.1111/nph.18511.

Prakash, Rohit, Yashpal Rawal, Meghan R. Sullivan, McKenzie K. Grundy, Hélène Bret, Michael J. Mihalevic, Hayley L. Rein, et al. 2022. “Homologous Recombination–Deficient Mutation Cluster in Tumor Suppressor RAD51C Identified by Comprehensive Analysis of Cancer Variants.” Proceedings of the National Academy of Sciences 119 (38): e2202727119. https://doi.org/10.1073/pnas.2202727119.

Miele, Solange, James Iain Provan, Justine Vergne, Christophe Possoz, Françoise Ochsenbein, and François-Xavier Barre. 2022. “The Xer Activation Factor of TLCΦ Expands the Possibilities for Xer Recombination.” Nucleic Acids Research 50 (11): 6368–83. https://doi.org/10.1093/nar/gkac429.

Kissling, Vera M., Giordano Reginato, Eliana Bianco, Kristina Kasaciunaite, Janny Tilma, Gea Cereghetti, Natalie Schindler, et al. 2022. “Mre11-Rad50 Oligomerization Promotes DNA Double-Strand Break Repair.” Nature Communications 13 (1): 2374. https://doi.org/10.1038/s41467-022-29841-0.

Andreani, Jessica, Masahito Ohue, and Brian Jiménez-García. 2022. “Editorial: Web Tools for Modeling and Analysis of Biomolecular Interactions.” Frontiers in Molecular Biosciences 9 (April). https://www.frontiersin.org/article/10.3389/fmolb.2022.875859.

Pyatnitskaya, Alexandra, Jessica Andreani, Raphaël Guérois, Arnaud De Muyt, and Valérie Borde. 2021. “The Zip4 Protein Directly Couples Meiotic Crossover Formation to Synaptonemal Complex Assembly.” Genes & Development, December. https://doi.org/10.1101/gad.348973.121.

Bordelet, Hélène, Rafaël Costa, Clémentine Brocas, Jordane Dépagne, Xavier Veaute, Didier Busso, Amandine Batté, Raphaël Guérois, Stéphane Marcand, and Karine Dubrana. 2021. “Sir3 Heterochromatin Protein Promotes Non-Homologous End Joining by Direct Inhibition of Sae2.” The EMBO Journal, November, e108813. https://doi.org/10.15252/embj.2021108813.

Porro, Antonio, Mohiuddin Mohiuddin, Christina Zurfluh, Vincent Spegg, Jingqi Dai, Florence Iehl, Virginie Ropars, et al. 2021. “FAN1-MLH1 Interaction Affects Repair of DNA Interstrand Cross-Links and Slipped-CAG/CTG Repeats.” Science Advances 7 (31): eabf7906. https://doi.org/10.1126/sciadv.abf7906.

Quignot, Chloé, Guillaume Postic, Hélène Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacón, Jessica Andreani, Pierre Tufféry, and Raphaël Guerois. 2021. “InterEvDock3: A Combined Template-Based and Free Docking Server with Increased Performance through Explicit Modeling of Complex Homologs and Integration of Covariation-Based Contact Maps.” Nucleic Acids Research 49 (W1): W277–84. https://doi.org/10.1093/nar/gkab358.

Postic, Guillaume, Jessica Andreani, Julien Marcoux, Victor Reys, Raphaël Guerois, Julien Rey, Emmanuelle Mouton-Barbosa, et al. 2021. “Proteo3Dnet: A Web Server for the Integration of Structural Information with Interactomics Data.” Nucleic Acids Research 49 (W1): W567–72. https://doi.org/10.1093/nar/gkab332.

Marsin, Stéphanie, Yazid Adam, Claire Cargemel, Jessica Andreani, Sonia Baconnais, Pierre Legrand, Ines Li de la Sierra-Gallay, et al. 2021. “Study of the DnaB:DciA Interplay Reveals Insights into the Primary Mode of Loading of the Bacterial Replicative Helicase.” Nucleic Acids Research 49 (11): 6569–86. https://doi.org/10.1093/nar/gkab463.

Dai, Jingqi, Aurore Sanchez, Céline Adam, Lepakshi Ranjha, Giordano Reginato, Pierre Chervy, Carine Tellier-Lebegue, et al. 2021. “Molecular Basis of the Dual Role of the Mlh1-Mlh3 Endonuclease in MMR and in Meiotic Crossover Formation.” Proceedings of the National Academy of Sciences of the United States of America 118 (23): e2022704118. https://doi.org/10.1073/pnas.2022704118.

Ma, Emilie, Laurent Maloisel, Léa Le Falher, Raphaël Guérois, and Eric Coïc. 2021. “Rad52 Oligomeric N-Terminal Domain Stabilizes Rad51 Nucleoprotein Filaments and Contributes to Their Protection against Srs2.” Cells 10 (6). https://doi.org/10.3390/cells10061467.

Ribeiro, Jonathan, Pauline Dupaigne, Cynthia Petrillo, Cécile Ducrot, Clotilde Duquenne, Xavier Veaute, Carole Saintomé, et al. 2021. “The Meiosis-Specific MEIOB-SPATA22 Complex Cooperates with RPA to Form a Compacted Mixed MEIOB/SPATA22/RPA/SsDNA Complex.” DNA Repair 102 (June):103097. https://doi.org/10.1016/j.dnarep.2021.103097.

Vernekar, Dipti Vinayak, Giordano Reginato, Céline Adam, Lepakshi Ranjha, Florent Dingli, Marie-Claude Marsolier, Damarys Loew, et al. 2021. “The Pif1 Helicase Is Actively Inhibited during Meiotic Recombination Which Restrains Gene Conversion Tract Length.” Nucleic Acids Research 49 (8): 4522–33. https://doi.org/10.1093/nar/gkab232.

Quignot, Chloé, Pierre Granger, Pablo Chacón, Raphael Guerois, and Jessica Andreani. 2021. “Atomic-Level Evolutionary Information Improves Protein-Protein Interface Scoring.” Bioinformatics (Oxford, England), April, btab254. https://doi.org/10.1093/bioinformatics/btab254.

Mbianda, Johanne, May Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. 2021. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances 7 (12): eabd9153. https://doi.org/10.1126/sciadv.abd9153.

Öz, Robin, Jing L. Wang, Raphael Guerois, Gaurav Goyal, Sriram Kk, Virginie Ropars, Rajhans Sharma, et al. 2021. “Dynamics of Ku and Bacterial Non-Homologous End-Joining Characterized Using Single DNA Molecule Analysis.” Nucleic Acids Research, February. https://doi.org/10.1093/nar/gkab083.

Rahman, Md Maminur, Mohiuddin Mohiuddin, Islam Shamima Keka, Kousei Yamada, Masataka Tsuda, Hiroyuki Sasanuma, Jessica Andreani, et al. 2020. “Genetic Evidence for the Involvement of Mismatch Repair Proteins, PMS2 and MLH3, in a Late Step of Homologous Recombination.” The Journal of Biological Chemistry 295 (51): 17460–75. https://doi.org/10.1074/jbc.RA120.013521.

Sanchez, Aurore, Céline Adam, Felix Rauh, Yann Duroc, Lepakshi Ranjha, Bérangère Lombard, Xiaojing Mu, et al. 2020. “Exo1 Recruits Cdc5 Polo Kinase to MutLγ to Ensure Efficient Meiotic Crossover Formation.” Proceedings of the National Academy of Sciences of the United States of America 117 (48): 30577–88. https://doi.org/10.1073/pnas.2013012117.

Postic, Guillaume, Julien Marcoux, Victor Reys, Jessica Andreani, Yves Vandenbrouck, Marie-Pierre Bousquet, Emmanuelle Mouton-Barbosa, et al. 2020. “Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration.” Journal of Proteome Research 19 (7): 2807–20. https://doi.org/10.1021/acs.jproteome.0c00066.

Omrane, Mohyeddine, Amanda Souza Camara, Cyntia Taveneau, Nassima Benzoubir, Thibault Tubiana, Jinchao Yu, Raphaël Guérois, et al. 2020. “Septin 9 Has Two Polybasic Domains Critical to Septin Filament Assembly and Golgi Integrity.” IScience 13 (May):138–53. https://doi.org/10.1016/j.isci.2019.02.015.

Takedachi, A., E. Despras, S. Scaglione, R. Guérois, J. H. Guervilly, M. Blin, S. Audebert, et al. 2020. “SLX4 Interacts with RTEL1 to Prevent Transcription-Mediated DNA Replication Perturbations.” Nature Structural & Molecular Biology 27 (5): 438–49. https://doi.org/10.1038/s41594-020-0419-3.

Phongsavanh, Xaysongkhame, Noha Al-Qatabi, Mohammed Samer Shaban, Fawzi Khoder-Agha, Merwan El Asri, Martine Comisso, Raphaël Guérois, and Marc Mirande. 2020. “How HIV-1 Integrase Associates with Human Mitochondrial Lysyl-TRNA Synthetase.” Viruses 12 (10): 1202. https://doi.org/10.3390/v12101202.

Nadaradjane, Aravindan Arun, Chloé Quignot, Seydou Traoré, Jessica Andreani, and Raphaël Guerois. 2020. “Docking Proteins and Peptides under Evolutionary Constraints in Critical Assessment of PRediction of Interactions Rounds 38 to 45.” Proteins: Structure, Function, and Bioinformatics 88 (8): 986–98. https://doi.org/https://doi.org/10.1002/prot.25857.

Andreani, Jessica, Chloe Quignot, and Raphael Guerois. 2020. “Structural Prediction of Protein Interactions and Docking Using Conservation and Coevolution.” Wiley Interdisciplinary Reviews-Computational Molecular Science 10 (6): e1470. https://doi.org/10.1002/wcms.1470.

Bakail, May, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. 2019. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology 26 (11): 1573-1585.e10. https://doi.org/10.1016/j.chembiol.2019.09.002.

Vilela, Fernando, Christophe Velours, Mélanie Chenon, Magali Aumont-Nicaise, Valérie Campanacci, Aurélien Thureau, Olena Pylypenko, Jessica Andreani, Paola Llinas, and Julie Ménétrey. 2019. “Structural Characterization of the RH1-LZI Tandem of JIP3/4 Highlights RH1 Domains as a Cytoskeletal Motor-Binding Motif.” Scientific Reports 9 (1): 16036. https://doi.org/10.1038/s41598-019-52537-3.