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Cell Cycle-Dependent Regulation and Function of ARGONAUTE 1 in Plants Adrien Trolet

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Cell Cycle-Dependent Regulation and Function of ARGONAUTE 1 in Plants Adrien Trolet Cell cycle-dependent regulation and function of ARGONAUTE 1 in plants Adrien Trolet To cite this version: Adrien Trolet. Cell cycle-dependent regulation and function of ARGONAUTE 1 in plants. Vegetal Biology. Université de Strasbourg, 2018. English. NNT : 2018STRAJ110. tel-02945310 HAL Id: tel-02945310 https://tel.archives-ouvertes.fr/tel-02945310 Submitted on 22 Sep 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE 414 Institut de Biologie Moléculaire des Plantes THÈSE présentée par : Adrien TROLET soutenue le : 14 septembre 2018 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Science de la vie et de la santé, aspects moléculaire et cellulaire de la biologie Cell cycle-dependent regulation and function of ARGONAUTE 1 in plants THÈSE dirigée par : M. Pascal Genschik Docteur, Université de Strasbourg RAPPORTEURS : M. Crisanto Guttierez Professeur, Université de Madrid Mme. Cécile Raynaud Docteur, Université Paris-Saclay AUTRES MEMBRES DU JURY : Mme. Laurence Marechal-Drouard Docteur, Université de Strasbourg M. Arp Schnittger Professeur, Université de Hambourg Acknowledgments First, I want to thank Pascal Genschik for hosting me in the lab and supervising my work during these four years of thesis, as well as Marie -Claire Criqui, who helped me a lot at the bench, especially with BY-2 cells and synchronization experiments. I want to thank also Blake C. Meyers and Patricia Baldrich for our great and fruitful collaboration on the bioinformatic analysis. I also thank Cécile Raynaud, Laurence Maréchal-Drouard, Cristanto Gutierrez and Arp Schnittger for accepting to evaluate my thesis. I want also to thank all IBMP colleagues and especially people from the IBMP platforms: -Sandrine and Malek for the sequencing and their help on the qRT-PCR. -Nicolas and Laurence for their help and advices on gel filtration experiments. -Jérôme from the microscopy platform for his help on the confocal and ImageJ software. -All the gardeners, Richard, Michel, Fabrice and Sebastien, who took care of my plants. Many thanks to all the member of the 612 lab , and to those who leaved, for sharing advices, the nice scientific discussions, and also the less serious ones! Finally, I want to thank my friends, Chloe, Cédric, Marieke, Marion, Marco, Pierre, Thibaut, Maxime, Franck, Lucie and Hélène, for all the nice moments we had in and out of the lab, and my family for their unshakeable support. List of figures and tables .................................................................................................................. 1 List of abbreviations ......................................................................................................................... 3 Introduction ...................................................................................................................................... 5 A. The cell cycle in eukaryotes ................................................................................................... 5 1. General principles of cell cycle .......................................................................................... 5 2. Cell cycle regulation .......................................................................................................... 6 a. CDKs drive progression through the cell cycle ............................................................ 7 b. Diversity and functions of eukaryotic CDK/Cyclins complexes ................................... 7 The eukaryotic CDKs ........................................................................................................ 7 Cyclins .............................................................................................................................. 8 c. Regulation of CDK activity ......................................................................................... 9 CDK activation by cyclins ................................................................................................. 9 Post-translational modifications of CDKs ........................................................................ 10 CDK/Cyclins inhibitors (CKIs) ........................................................................................ 10 d. Selective degradation of cell cycle components.......................................................... 11 SCF complexes ................................................................................................................ 12 Anaphase-promoting complex/Cyclosome ....................................................................... 13 Monomeric RING E3 ligases ........................................................................................... 14 The mammalian CRL4CDT2 complex ................................................................................ 15 e. Transcriptional regulation of cell cycle genes............................................................. 15 Control of G1/S transition ................................................................................................ 15 Control of G2/M transition............................................................................................... 17 The DREAM and MMB complexes ................................................................................. 18 f. Cell cycle regulation by non-coding RNAs .................................................................... 18 Long non-coding RNAs (LncRNAs) ................................................................................ 19 Small RNAs (sRNAs) ...................................................................................................... 20 B. Mechanisms and functions of RNA interference in eukaryotes ............................................. 20 1. General principles ............................................................................................................ 20 2. Biogenesis and functions of micro-RNAs......................................................................... 21 3. Biogenesis and functions of small interfering RNAs (siRNAs) ......................................... 23 a. Trans-acting RNAs (tasiRNAs) ................................................................................. 24 b. Heterochromatic siRNAs (hetsiRNAs)....................................................................... 25 4. tRNA-derived fragments .................................................................................................. 25 5. ARGONAUTE proteins ................................................................................................... 27 a. Structural features of ARGONAUTE proteins ........................................................... 27 b. Assembly of mature RISC complexes ........................................................................ 28 c. Plants and Human ARGONAUTEs ........................................................................... 29 d. Regulation of Argonaute proteins .............................................................................. 31 6. The fate of RISC-targeted transcripts: slicing or translational inhibition ........................... 32 7. Human miRNAs functions in cell cycle and cancer .......................................................... 34 8. Small RNA functions in plant development...................................................................... 36 a. Post-transcriptional control of auxin signaling ........................................................... 37 b. Control of cell proliferation by miR319 and miR396 ................................................. 38 Results............................................................................................................................................. 41 A. AGO1 depletion affects Arabidopsis cell division and root meristem activity ....................... 41 1. Arabidopsis ago1 mutants are impaired in root developments .......................................... 41 2. AGO1 is required for the maintenance of the root meristem ............................................. 42 3. Loss of AGO1 affects cell proliferation in the root apical meristem .................................. 43 B. AGO1 regulation in synchronized BY-2 cells ....................................................................... 45 1. Generation of transgenic GFP-AGO1 BY-2 cell suspension and detection optimization ... 45 2. Lines selection for synchronization experiments .............................................................. 46 3. AGO1 steady state level remains constant during cell cycle progression ........................... 47 4. AGO1 localizes to different cellular bodies in synchronized BY-2 cells ........................... 49 C. Differential gene expression in synchronized BY-2 cells ...................................................... 52 1. Transcriptomic analysis of synchronized BY-2 ................................................................ 52 2. Expression and targets of miRNAs in synchronized BY-2 cells .......................................
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