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Structural Analysis of the Cohesin Complex Yan Li Structural analysis of the cohesin complex Yan Li To cite this version: Yan Li. Structural analysis of the cohesin complex. Structural Biology [q-bio.BM]. Université Grenoble Alpes, 2019. English. NNT : 2019GREAV012. tel-03187406 HAL Id: tel-03187406 https://tel.archives-ouvertes.fr/tel-03187406 Submitted on 1 Apr 2021 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. THESIS / THÈSE To obtain the title of / Pour obtenir le grade de DOCTEUR DE L’UNIVERSITÉ GRENOBLE ALPES Discipline / Spécialité : Structure Biology and Nanotechnology Arrêté ministériel : 7 août 2006 Presented by / Présentée par Yan LI Thesis supervisor / Thèse dirigée par Dr. Daniel Panne Thesis prepared at / Thèse préparée au sein du European Molecular Biology Laboratory (EMBL), Grenoble/ In / Dans l'École Doctorale de Chimie et Science du Vivant Structural analysis of the Cohesin Complex / Analyse structurale du complexe de la cohésine Public defense on / Thèse soutenue publiquement le 01/04/2019 Jury members / devant le jury composé de : Dr. Benjamin ROWLAND Reviewer / Rapporteur Dr. Camilla BJORKEGREN Reviewer / Rapporteur Dr. Ramesh PILLAI President / Président Dr. Joanna TIMMINS Examiner / Examinateur 1 Table of Contents 2 Table of Contents ....................................................................................................................... 2 List of Abbreviations ................................................................................................................. 9 List of Figures / Tables ............................................................................................................ 14 Genome cohesion and condensation during the cell cycle ............................................... 15 Role of CTCF in the regulation of paternal and maternal imprinting .............................. 15 Model for CTCF-mediated cohesin binding and for the generation of TADs by convergently oriented CTCF sites .................................................................................... 16 Abstract .................................................................................................................................... 18 Résumé ..................................................................................................................................... 21 Introduction .............................................................................................................................. 24 1.1 The cell cycle ................................................................................................................. 26 1.2 Chromosomes are organised by SMC-kleisin enzymes ................................................. 27 Figure 1.1 Genome cohesion and condensation during the cell cycle. ............................ 28 1.3 Organisation of the core cohesin complex ..................................................................... 29 Figure 1.2 Structure of the cohesin core subunits and domain boundaries. ..................... 32 Figure 1.3 Structure of the human SA2-Scc1 complex and domain boundaries. ............. 34 1.4 Overview of the cohesin cycle ....................................................................................... 34 Figure 1.4 Cartoon illustration of the ring-shape cohesin and its accessory factors. ....... 36 Table 1.1 Cohesin and its related factors in different species .......................................... 37 1.5 Cohesin ATPase dimerization ........................................................................................ 37 Figure 1.5 Cartoon of cohesin functional cycle and regulators. ....................................... 40 1.6 The cohesin loading complex ......................................................................................... 40 1.7 Cleavage-independent cohesin unloading ...................................................................... 41 Figure 1.6 Structure of the yeast Pds5-Scc1 complex and domain boundaries................ 42 Figure 1.7 Structure of the human Wapl-C domain and domain boundaries. .................. 43 1.8 SMC3 acetylation (establishment of cohesion) .............................................................. 43 Figure 1.8 Structure of human Esco1 and domain boundaries. ........................................ 44 3 1.9 Cohesin stabilization ...................................................................................................... 45 1.10 Cohesin release at chromosome arms .......................................................................... 45 1.11 Cohesion protection at the centromere ......................................................................... 45 Figure 1.9 Structure of the Sgo1-PP2A complex and domain boundaries. ...................... 47 1.12 Cohesin cleavage at the centromere ............................................................................. 48 Figure 1.10 Structure of the yeast Separase-Securin complex and domain boundaries. .. 49 1.13 Cohesin beyond cohesion ............................................................................................. 49 1.14 CTCF ............................................................................................................................ 50 Figure 1.11 Model of CTCF zinc fingers 2-9 in complex with DNA. ............................. 51 Figure 1.12 Role of CTCF in the regulation of paternal and maternal imprinting. .......... 52 Table 1.2 CTCF interaction partners ................................................................................ 53 1.15 Cohesin and CTCF ....................................................................................................... 54 1.16 Loop extrusion model and different levels of the mammalian genome folding .......... 55 Figure 1.13 Levels of Genome folding............................................................................. 57 Scientific aims .......................................................................................................................... 59 Materials and Methods ............................................................................................................. 61 Matériels et méthodes .............................................................................................................. 62 2.1 Construct Cloning .......................................................................................................... 64 2.2 Protein expression .......................................................................................................... 64 2.2.1 Protein expression ................................................................................................... 64 2.2.2 Selenomethionine-labelled protein expression ........................................................ 65 2.3 Protein purification ......................................................................................................... 65 2.3.1 Purification with His or His-GST tag ...................................................................... 65 2.3.2 Purification with GST tag ........................................................................................ 66 2.3.3 Ion-exchange purification ........................................................................................ 66 2.3.4 Size exclusion .......................................................................................................... 66 2.4 Crystallisation................................................................................................................. 67 4 Table 2.1 Scc3T-Scc1K crystallisation screen conditions. .............................................. 67 2.4.1 Crystals of ctSmc1hd-CScc1 complex .................................................................... 67 2.4.2 Crystals of the Scc3-Scc1-DNA complex ............................................................... 68 2.4.3 Crystal seeding ........................................................................................................ 68 2.4.4 Crystals of the SA2T-Scc1H complex .................................................................... 68 2.5 Structure determination .................................................................................................. 69 2.5.1 Structure of the ctSmc1-CScc1 complex ................................................................. 69 2.5.2 Structure of the Scc3-Scc1-DNA complex .............................................................. 69 2.5.3 Structure of the SA2-Scc1-CTCF complex ............................................................. 70 2.6 Bioinformatic methods ................................................................................................... 71 2.6.1 Sequence alignment ................................................................................................. 71 2.7 Protein biochemistry ...................................................................................................... 71 2.7.1 In vitro pull down ...................................................................................................
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