The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition Alexandre Segelle To cite this version: Alexandre Segelle. The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition. Agricultural sciences. Université Montpellier, 2020. English. NNT : 2020MONTT017. tel-03137009 HAL Id: tel-03137009 https://tel.archives-ouvertes.fr/tel-03137009 Submitted on 10 Feb 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. 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THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Biologie Moléculaire et Cellulaire École doctorale Sciences Chimiques et Biologiques pour la Santé (ED CBS2 168) Unité de recherche UMR9002 CNRS-UM – Institut de Génétique Humaine (IGH) The role of histone modifications in the regulation of alternative splicing during the epithelial-to-mesenchymal transition Présentée par Alexandre Segelle Le 28 Septembre 2020 Sous la direction de Reini Fernandez de Luco Devant le jury composé de Anne-Marie MARTINEZ, Professeure, Université de Montpellier Présidente du jury Christian MUCHARDT, DR et Chef d’équipe, Institut Pasteur de Paris Rapporteur Juan VALCARCEL, Research Professor et Chef d’équipe, Institut CRG de Barcelone Rapporteur Franck MORTREUX, CR, Institut LBMC de Lyon Examinateur Reini FERNANDEZ DE LUCO, CR et Chef d’équipe, Institut IGH de Montpellier Directrice de thèse The Role of histone modifications in the regulation of alternative splicing during the EMT With the support of – Avec le soutien de: I G H INSTITUTE OF HUMAN GENETICS 1 The Role of histone modifications in the regulation of alternative splicing during the EMT Table of Contents ACKNOWLEDGMENTS - REMERCIEMENTS .............................................................................................. 5 LIST OF FIGURES ...................................................................................................................................... 8 LIST OF TABLES ...................................................................................................................................... 10 ABREVIATIONS ....................................................................................................................................... 11 SUMMARY – SYNTHESE EN FRANCAIS................................................................................................... 13 INTRODUCTION ................................................................................................................................. 15 Chapter 1: RNA splicing, alternative splicing (AS) and underlying mechanisms ........................... 16 1.1 History of splicing .......................................................................................................... 16 1.1.1 Discovery of RNA splicing ...................................................................................... 16 1.1.2 Discovery of alternative splicing ............................................................................ 17 1.2 RNA splicing ................................................................................................................... 18 1.2.1 RNA splicing reaction ............................................................................................. 20 1.2.2 Intron definition .................................................................................................... 22 a Donor site and acceptor site ..................................................................................... 22 b Branch point .............................................................................................................. 23 1.2.3 Spliceosomal complex ........................................................................................... 23 a Spliceosome composition .......................................................................................... 23 b Spliceosome assembling and catalytic activity .......................................................... 25 1.3 Alternative splicing ........................................................................................................ 28 1.3.1 Different alternative splicing events ..................................................................... 28 a Cassette exons ........................................................................................................... 28 b Mutually exclusive exons ........................................................................................... 28 c Alternative 5’ and 3’ splice sites ................................................................................ 29 d Intron retention ......................................................................................................... 30 e Alternative promoters and polyadenylation sites ..................................................... 30 1.3.2 Regulatory elements ............................................................................................. 30 a Cis regulatory elements ............................................................................................. 31 b Trans regulatory elements ........................................................................................ 32 1.4 Deregulation of alternative splicing in cancer ............................................................... 34 1.4.1 Alteration of alternative splicing programs in cancer ........................................... 34 a Alternatively spliced genes in cancer ........................................................................ 34 b Splicing factors in cancer ........................................................................................... 36 1.4.2 Oncogenic and tumor suppressor functions of AS variants .................................. 37 2 The Role of histone modifications in the regulation of alternative splicing during the EMT 1.4.3 Therapeutic strategies based on splicing variants ................................................ 38 Chapter 2: The relationship between chromatin and splicing ...................................................... 40 2.1 Chromatin ...................................................................................................................... 40 2.1.1 Discovery of chromatin ......................................................................................... 40 2.1.2 Chromatin structure .............................................................................................. 40 a Nucleosome ............................................................................................................... 41 b Chromatin higher-order structure ............................................................................. 42 c Euchromatin and heterochromatin ........................................................................... 43 2.1.2 Chromatin: a dynamic structure ............................................................................ 45 a Chromatin remodeling .............................................................................................. 45 b Histone chaperones ................................................................................................... 46 c Histone variants ......................................................................................................... 47 d Histone post-translational modifications .................................................................. 48 e DNA methylation ....................................................................................................... 50 2.2 Genome and epigenome editing: the CRISPR/(d)Cas9 system ..................................... 51 2.2.1 Discovery and description of CRISPR/Cas .............................................................. 51 2.2.2 Genome editing with CRISPR/Cas9........................................................................ 53 2.2.3 CRISPR/dCas9: a powerful tool for chromatin regulation ..................................... 55 a Transcriptional regulation ......................................................................................... 55 b Epigenome editing ..................................................................................................... 55 2.3 Alternative splicing and chromatin signature ............................................................... 56 2.4 Relationship between chromatin, transcription and alternative splicing ..................... 58 2.4.1 Coupling between alternative splicing and transcription ..................................... 59 2.4.2 Chromatin affects alternative splicing ................................................................... 60 a Kinetic model ............................................................................................................. 60 b Recruitment model .................................................................................................... 61 Chapter 3: The epithelial-to-mesenchymal transition (EMT) and its regulation .......................... 63 3.1