European School of Molecular Medicine (SEMM) University of Milan and University of Naples “Federico II” PhD degree in Systems Medicine (curriculum in Molecular Oncology) Settore disciplinare: BIO/11 Proteomic identification of the transcription factors Ikaros and Aiolos as new Myc interactors on chromatin Chiara Veronica Locarno Matricola: R10755 Center for Genomic Science IIT@SEMM, Milan Supervisor: Bruno Amati, PhD IEO, Milan Added Supervisor: Arianna Sabò, PhD IEO, Milan Academic year 2017-2018 Table of contents List of abbreviations ........................................................................................................... 4 List of figures ....................................................................................................................... 8 List of tables ....................................................................................................................... 11 Abstract .............................................................................................................................. 12 1. INTRODUCTION ......................................................................................................... 13 1.1 Myc ........................................................................................................................................ 13 1.1.1 Myc discovery and structure ........................................................................................... 13 1.1.2. Role of Myc in physiological and pathological conditions ............................................ 15 1.1.3. Myc interactions on chromatin ....................................................................................... 17 1.1.3.1. Myc binding to DNA ............................................................................................................ 17 1.1.3.2. Mechanisms of transcriptional control by Myc .................................................................... 19 1.1.4. Myc and cancer therapy ................................................................................................. 21 1.2. B-cell development ............................................................................................................ 22 1.2.1. Early development .......................................................................................................... 22 1.2.2. Maturation ...................................................................................................................... 24 1.2.3. Antibody production and memory ................................................................................. 25 1.2.4. Role of Myc in B lymphopoiesis .................................................................................... 27 1.3. Ikaros and Aiolos ................................................................................................................ 28 1.3.1. Ikaros discovery and structure ........................................................................................ 28 1.3.2. Function of Ikaros and Aiolos in hematopoiesis ............................................................ 30 1.3.3. Expression pattern of Ikaros family members ................................................................ 32 1.3.4. Ikaros and Aiolos role in B lymphocyte development ................................................... 33 1.3.4.1. Priming of the lymphoid lineage ........................................................................................... 33 1.3.4.2. Ikaros role in early B cell progenitors ................................................................................... 34 1.3.4.3. Role of Aiolos in mature B cells ........................................................................................... 35 1.3.5. Mechanisms of action ..................................................................................................... 35 1.3.6. Pathologies and therapies ............................................................................................... 38 1 Aim of the project ............................................................................................................... 40 2. MATERIALS AND METHODS ................................................................................. 41 2.1. Cell lines ................................................................................................................... 41 2.2. Cell transfection ....................................................................................................... 42 2.3. Cell transduction ...................................................................................................... 43 2.4. Proliferation assays .................................................................................................. 43 2.5. Chromatin proteomics (ChroP) ........................................................................................ 44 2.5.1. Chromatin Immunoprecipitation (ChIP) ........................................................................ 44 2.5.2. In-gel digestion for MS .................................................................................................. 45 2.5.3. Liquid chromatography and tandem Mass Spectrometry (LC-MS/MS) ........................ 46 2.5.4. Protein identification by MaxQuant software and data analysis .................................... 47 2.6. ChIP-qPCR ............................................................................................................... 48 2.7. Western Blot (WB) .................................................................................................. 48 2.8. Co-Immunoprecipitation (coIP) ............................................................................... 49 2.9. ChIP-sequencing (ChIP-seq) .................................................................................... 49 2.10. ChIP-seq analysis ................................................................................................... 50 2.11. RNA extraction and analysis: quantitative PCR (qPCR) and RNA-seq. ............... 51 2.12. RNA-seq data analysis ........................................................................................... 51 2.13. Motif analysis ......................................................................................................... 52 2.14. Functional annotation ............................................................................................. 52 2.15. List of primers ................................................................................................................... 53 3. RESULTS ....................................................................................................................... 54 3.1. Identification of Myc interactors through mass spectrometry analysis ...................... 54 3.1.1. Myc modulation in p493-6 cells ..................................................................................... 54 3.1.2. Setting of the label-free ChroP technique. ..................................................................... 56 3.1.3. Identification of new Myc interactors ............................................................................ 59 3.1.4. Validation of Myc interactors ......................................................................................... 62 2 3.2. Ikaros, Aiolos and Myc interaction in p493-6 cells ....................................................... 64 3.2.1. Ikaros and Aiolos coimmunoprecipitate with Myc ........................................................ 64 3.2.2. Genome-wide distribution of Ikaros, Aiolos and Myc ................................................... 69 3.2.3. Identification of direct Myc-regulated genes. ................................................................ 79 3.3. Combined activation of Ikaros and Myc in BH1 cells .................................................. 81 3.3.1. IkarosER and Tet-Myc inducible system ....................................................................... 81 3.3.2. Ikaros and Myc have an opposite effect on cell proliferation ........................................ 89 3.3.3. Transcriptional effect of Ikaros and Myc induction ....................................................... 92 4. DISCUSSION .............................................................................................................. 101 4.1. Identification of new Myc interactors using a MS-based approach. ......................... 101 4.2. Interplay between Ikaros/Aiolos and Myc .................................................................... 104 5. APPENDIX .................................................................................................................. 110 5.1. Experimental design ......................................................................................................... 110 5.2. Materials and methods ..................................................................................................... 112 5.2.1. Cell culture ................................................................................................................... 112 5.2.2. SILAC ChroP ............................................................................................................... 112 5.2.3. MS analysis .................................................................................................................. 112 5.2.4. siRNA tranfection ......................................................................................................... 112