Programmed genome
rearrangements

Charmant, Olivia, Julita Gruchota, Olivier Arnaiz, Katarzyna P. Nowak, Nicolas Moisan, Coralie Zangarelli, Mireille Bétermier, et al. 2024. “The PIWI-Interacting Protein Gtsf1 Controls the Selective Degradation of Small RNAs in Paramecium.” Nucleic Acids Research, November, gkae1055. https://doi.org/10.1093/nar/gkae1055.

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.

Gutiérrez-Santiago, Francisco, Verónica Martínez-Fernández, Ana Isabel Garrido-Godino, Cristina Colino-Palomino, Andrés Clemente-Blanco, Christine Conesa, Joël Acker, and Francisco Navarro. 2024. “Maf1 Phosphorylation Is Regulated through the Action of Prefoldin-like Bud27 on PP4 Phosphatase in Saccharomyces Cerevisiae.” Nucleic Acids Research, May, gkae414. https://doi.org/10.1093/nar/gkae414.

Bischerour, Julien, Olivier Arnaiz, Coralie Zangarelli, Vinciane Régnier, Florence Iehl, Virginie Ropars, Jean-Baptiste Charbonnier, and Mireille Bétermier. 2024. “Uncoupling Programmed DNA Cleavage and Repair Scrambles the Paramecium Somatic Genome.” Cell Reports 43 (4): 114001. https://doi.org/10.1016/j.celrep.2024.114001.

Bétermier, Mireille, Lawrence A. Klobutcher, and Eduardo Orias. 2023. “Programmed Chromosome Fragmentation in Ciliated Protozoa: Multiple Means to Chromosome Ends.” Microbiology and Molecular Biology Reviews: MMBR, November, e0018422. https://doi.org/10.1128/mmbr.00184-22.

Bazin-Gélis, Mélanie, Evangelia Eleftheriou, Coralie Zangarelli, Gaëlle Lelandais, Linda Sperling, Olivier Arnaiz, and Mireille Bétermier. 2023. “Inter-Generational Nuclear Crosstalk Links the Control of Gene Expression to Programmed Genome Rearrangement during the Paramecium Sexual Cycle.” Nucleic Acids Research, November, gkad1006. https://doi.org/10.1093/nar/gkad1006.

Gout, Jean-Francois, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, et al. 2023. “Dynamics of Gene Loss Following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex.” Molecular Biology and Evolution, May, msad107. https://doi.org/10.1093/molbev/msad107.

Nguyen, Phong Quoc, Sonia Huecas, Amna Asif-Laidin, Adrián Plaza-Pegueroles, Beatrice Capuzzi, Noé Palmic, Christine Conesa, et al. 2023. “Structural Basis of Ty1 Integrase Tethering to RNA Polymerase III for Targeted Retrotransposon Integration.” Nature Communications 14 (1): 1729. https://doi.org/10.1038/s41467-023-37109-4.

Zangarelli, Coralie, Olivier Arnaiz, Mickael Bourge, Kevin Gorrichon, Yan Jaszczyszyn, Nathalie Mathy, Loic Escoriza, Mireille Betermier, and Vinciane Regnier. 2022. “Developmental Timing of Programmed DNA Elimination in Paramecium Tetraurelia Recapitulates Germline Transposon Evolutionary Dynamics.” Genome Research, November, gr.277027.122. https://doi.org/10.1101/gr.277027.122.

Barkova, Anastasia, Indranil Adhya, Christine Conesa, Amna Asif-Laidin, Amandine Bonnet, Elise Rabut, Carine Chagneau, Pascale Lesage, and Joël Acker. 2022. “A Proteomic Screen of Ty1 Integrase Partners Identifies the Protein Kinase CK2 as a Regulator of Ty1 Retrotransposition.” Mobile DNA 13 (1): 26. https://doi.org/10.1186/s13100-022-00284-0.

Sellis, Diamantis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto, Sascha Krenek, et al. 2021. “Massive Colonization of Protein-Coding Exons by Selfish Genetic Elements in Paramecium Germline Genomes.” PLOS Biology 19 (7): e3001309. https://doi.org/10.1371/journal.pbio.3001309.

Guérineau, Marc, Luiza Bessa, Séverine Moriau, Ewen Lescop, François Bontems, Nathalie Mathy, Eric Guittet, Julien Bischerour, Mireille Bétermier, and Nelly Morellet. 2021. “The Unusual Structure of the PiggyMac Cysteine-Rich Domain Reveals Zinc Finger Diversity in PiggyBac-Related Transposases.” Mobile DNA 12 (1): 12. https://doi.org/10.1186/s13100-021-00240-4.

Sawka-Gądek, Natalia, Alexey Potekhin, Deepankar Pratap Singh, Inessa Grevtseva, Olivier Arnaiz, Simon Penel, Linda Sperling, et al. 2020. “Evolutionary Plasticity of Mating-Type Determination Mechanisms in Paramecium Aurelia Sibling Species.” Genome Biology and Evolution 13 (2): evaa258. https://doi.org/10.1093/gbe/evaa258.

Gogendeau, Delphine, Michel Lemullois, Pierrick Le Borgne, Manon Castelli, Anne Aubusson-Fleury, Olivier Arnaiz, Jean Cohen, et al. 2020. “MKS-NPHP Module Proteins Control Ciliary Shedding at the Transition Zone.” PLoS Biology 18 (3): e3000640. https://doi.org/10.1371/journal.pbio.3000640.

Bétermier, Mireille, Valérie Borde, and Jean-Pierre de Villartay. 2020. “Coupling DNA Damage and Repair: An Essential Safeguard during Programmed DNA Double-Strand Breaks?” Trends in Cell Biology 30 (2): 87–96. https://doi.org/10.1016/j.tcb.2019.11.005.

Sperling, Linda. 2020. “Janine Beisson, Pioneer of Cytoplasmic Heredity (June 9, 1931, Saïda – August 30, 2020, Megève).” Protist 171 (6): 125769. https://doi.org/10.1016/j.protis.2020.125769.

Vanssay, Augustin de, Amandine Touzeau, Olivier Arnaiz, Andrea Frapporti, Jamie Phipps, and Sandra Duharcourt. 2020. “The Paramecium Histone Chaperone Spt16-1 Is Required for Pgm Endonuclease Function in Programmed Genome Rearrangements.” PLoS Genetics 16 (7): e1008949. https://doi.org/10.1371/journal.pgen.1008949.

Abello, Arthur, Vinciane Régnier, Olivier Arnaiz, Romain Le Bars, Mireille Bétermier, and Julien Bischerour. 2020. “Functional Diversification of Paramecium Ku80 Paralogs Safeguards Genome Integrity during Precise Programmed DNA Elimination.” PLoS Genetics 16 (4): e1008723. https://doi.org/10.1371/journal.pgen.1008723.

Arnaiz, Olivier, Eric Meyer, and Linda Sperling. 2020. “ParameciumDB 2019: Integrating Genomic Data across the Genus for Functional and Evolutionary Biology.” Nucleic Acids Research 48 (D1): D599–605. https://doi.org/10.1093/nar/gkz948.

Nekrasova, Irina, Vera Nikitashina, Simran Bhullar, Olivier Arnaiz, Deepankar P. Singh, Eric Meyer, and Alexey Potekhin. 2019. “Loss of a Fragile Chromosome Region Leads to the Screwy Phenotype in Paramecium Tetraurelia.” Genes 10 (7): 513. https://doi.org/10.3390/genes10070513.

Frapporti, Andrea, Caridad Miró Pina, Olivier Arnaiz, Daniel Holoch, Takayuki Kawaguchi, Adeline Humbert, Evangelia Eleftheriou, et al. 2019. “The Polycomb Protein Ezl1 Mediates H3K9 and H3K27 Methylation to Repress Transposable Elements in Paramecium.” Nature Communications 10 (1): 2710. https://doi.org/10.1038/s41467-019-10648-5.

Godau, Julia, Lorenza P. Ferretti, Anika Trenner, Emeline Dubois, Christine von Aesch, Antoine Marmignon, Lauriane Simon, et al. 2019. “Identification of a Miniature Sae2/Ctp1/CtIP Ortholog from Paramecium Tetraurelia Required for Sexual Reproduction and DNA Double-Strand Break Repair.” DNA Repair 77:96–108. https://doi.org/10.1016/j.dnarep.2019.03.011.

Shi, Lei, France Koll, Olivier Arnaiz, and Jean Cohen. 2018. “The Ciliary Protein IFT57 in the Macronucleus of Paramecium.” The Journal of Eukaryotic Microbiology 65 (1): 12–27. https://doi.org/10.1111/jeu.12423.

Bhullar, Simran, Cyril Denby Wilkes, Olivier Arnaiz, Mariusz Nowacki, Linda Sperling, and Eric Meyer. 2018. “A Mating-Type Mutagenesis Screen Identifies a Zinc-Finger Protein Required for Specific DNA Excision Events in Paramecium.” Nucleic Acids Research 46 (18): 9550–62. https://doi.org/10.1093/nar/gky772.

Bischerour, Julien, Simran Bhullar, Cyril Denby Wilkes, Vinciane Régnier, Nathalie Mathy, Emeline Dubois, Aditi Singh, et al. 2018. “Six Domesticated PiggyBac Transposases Together Carry out Programmed DNA Elimination in Paramecium.” ELife 7:e37927. https://doi.org/10.7554/eLife.37927.

Morellet, Nelly, Xianghong Li, Silke A. Wieninger, Jennifer L. Taylor, Julien Bischerour, Séverine Moriau, Ewen Lescop, et al. 2018. “Sequence-Specific DNA Binding Activity of the Cross-Brace Zinc Finger Motif of the PiggyBac Transposase.” Nucleic Acids Research 46 (5): 2660–77. https://doi.org/10.1093/nar/gky044.

Arnaiz, Olivier, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy, and Linda Sperling. 2017. “Improved Methods and Resources for Paramecium Genomics: Transcription Units, Gene Annotation and Gene Expression.” BMC Genomics 18 (1): 483. https://doi.org/10.1186/s12864-017-3887-z.

Dubois, Emeline, Nathalie Mathy, Vinciane Régnier, Julien Bischerour, Céline Baudry, Raphaëlle Trouslard, and Mireille Bétermier. 2017. “Multimerization Properties of PiggyMac, a Domesticated PiggyBac Transposase Involved in Programmed Genome Rearrangements.” Nucleic Acids Research 45 (6): 3204–16. https://doi.org/10.1093/nar/gkw1359.

Maliszewska-Olejniczak, Kamila, Julita Gruchota, Robert Gromadka, Cyril Denby Wilkes, Olivier Arnaiz, Nathalie Mathy, Sandra Duharcourt, Mireille Bétermier, and Jacek K. Nowak. 2015. “TFIIS-Dependent Non-Coding Transcription Regulates Developmental Genome Rearrangements.” PLoS Genetics 11 (7): e1005383. https://doi.org/10.1371/journal.pgen.1005383.