Epigenetic control of ribosome biogenesis homeostasis Jerôme Deraze To cite this version: Jerôme Deraze. Epigenetic control of ribosome biogenesis homeostasis. Cellular Biology. Université Pierre et Marie Curie - Paris VI, 2017. English. NNT : 2017PA066342. tel-01878354 HAL Id: tel-01878354 https://tel.archives-ouvertes.fr/tel-01878354 Submitted on 21 Sep 2018 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 Pierre et Marie Curie Ecole doctorale : Complexité du Vivant IBPS – UMR7622 Laboratoire de Biologie du Développement UPMC CNRS Epigenetic control of developmental homeostasis and plasticity Epigenetic Control of Ribosome Biogenesis Homeostasis Par Jérôme Deraze Thèse de doctorat de Biologie Moléculaire et Cellulaire Dirigée par Frédérique Peronnet et Sébastien Bloyer Présentée et soutenue publiquement le 19 Septembre 2017 Devant un jury composé de : Pr Anne-Marie MARTINEZ Professeur Rapporteur Dr Jacques MONTAGNE Directeur de Recherche Rapporteur Dr Olivier JEAN-JEAN Directeur de Recherche Examinateur Dr Michel COHEN-TANNOUDJI Directeur de Recherche Examinateur Dr Françoise JAMEN Maître de Conférences Examinateur Dr Nicolas NEGRE Maître de Conférences Examinateur Dr Frédérique PERONNET Directrice de Recherche Directrice de thèse Pr Sébastien BLOYER Professeur Co-directeur de thèse Table of contents Table of contents ..................................................................................................................................... 2 Table of figures ........................................................................................................................................ 5 Table of abreviations ............................................................................................................................... 7 Introduction ........................................................................................................................................... 11 I. The ribosome .................................................................................................................................. 12 A. Ribosome and translation ......................................................................................................... 12 1. Composition of the ribosome ...................................................................................... 13 2. Translation initiation ................................................................................................................. 15 3. Translation elongation ........................................................................................................... 17 4. Translation termination ......................................................................................................... 19 B. Ribosome biogenesis ................................................................................................................ 19 1. Ribosomal RNA transcription ................................................................................................ 19 2. Ribosomal RNA processing .................................................................................................... 23 3. rRNA modifications and snoRNPs .......................................................................................... 25 4. Ribosomal proteins biogenesis .............................................................................................. 27 5. Ribosomal protein assembly ................................................................................................. 29 6. Pre-ribosomal factors and quality control ............................................................................. 31 7. tRNA biogenesis ..................................................................................................................... 33 II. Ribosome biogenesis as a conductor of cell metabolism.............................................................. 35 A. Metabolic cues dictate the activity of ribosome synthesis ....................................................... 35 1. Cell growth and proliferation signals..................................................................................... 36 2. The cell cycle .......................................................................................................................... 39 3. Energy levels .......................................................................................................................... 42 4. Metabolic stress .................................................................................................................... 45 B. Ribosome biogenesis regulates homeostasis ............................................................................ 49 1. Ribosome biogenesis is monitored at several stages of cell life ........................................... 49 2. Ribosome biogenesis drives cellular organization ................................................................ 53 3. Phenotypic consequences of ribosome biogenesis defects .................................................. 56 III. Ribosomes regulate gene expression: the second lives of the housekeepers ............................. 61 A. Ribosome-mediated regulation of translation .......................................................................... 61 1. Ribosomes interact with mRNA cis-regulatory elements...................................................... 61 2. Trans-acting factors control translation ................................................................................ 67 3. Ribosome heterogeneity ....................................................................................................... 71 B. Extra-ribosomal functions of r-proteins .................................................................................... 77 2 1. When are r-proteins free? ..................................................................................................... 77 2. r-proteins participate in cell metabolism .............................................................................. 82 3. r-proteins are bound to chromatin ....................................................................................... 85 IV. Regulation of ribosome homeostasis by uL11 and Corto ............................................................ 89 A. The ribosomal protein uL11 ...................................................................................................... 89 1. General features of Drosophila uL11 .................................................................................... 90 2. Known functions of uL11 on and off the ribosome ............................................................... 92 3. Methylation of uL11 .............................................................................................................. 95 B. The transcription factor corto ................................................................................................... 97 1. General features of Corto ...................................................................................................... 97 2. corto participates in epigenetic maintenance of segmental identity during development. ................................................................................................................................................. 100 3. corto may be involved in developmental homeostasis ....................................................... 101 V. Presentation of the thesis project ............................................................................................... 103 Results ................................................................................................................................................. 106 I. Ribosomal protein uL11 tri-methylated on lysine 3 binds broad genomic regions and displays an exclusion pattern with Corto on chromatin. ................................................................................... 106 A. Results ................................................................................................................................. 107 B. Discussion ................................................................................................................................ 119 C. Materials and methods ........................................................................................................... 122 II. Editing essential genes: a marker independent CRISPR mutagenesis strategy. ......................... 127 A. Overview ................................................................................................................................. 127 B. Article ...................................................................................................................................... 127 C. Complementary data ............................................................................................................... 165 III. Mutation of a single amino-acid on ribosomal protein uL11 generates a Minute-like phenotype in Drosophila.