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Proteomic Identification of the Transcription Factors Ikaros And 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
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