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Identification of the Molecular Partners That Regulate MEIS1A Function This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Identification of the molecular partners that regulate MEIS1A function Ravishankar Chandrasekaran 2013 Ravishankar Chandrasekaran. (2013). Identification of the molecular partners that regulate MEIS1A function. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/59111 https://doi.org/10.32657/10356/59111 Downloaded on 10 Oct 2021 20:51:59 SGT IDENTIFICATION OF THE MOLECULAR PARTNERS THAT REGULATE MEIS1A FUNCTION RAVISHANKAR CHANDRASEKARAN School of Biological Sciences A thesis submitted to the Nanyang Technological University in partial fulfillment of the requirement for the degree of Doctor of philosophy 2013 To My parents Table of Contents ACKNOWLEDGEMENTS ....................................................................................................... v LIST OF FIGURES ................................................................................................................. vii LIST OF TABLES .................................................................................................................... ix LIST OF ABBREVIATIONS .................................................................................................... x ABSTRACT ........................................................................................................................... xiv CHAPTER 1: INTRODUCTION ................................................................................. 1 1.1 Hox genes: An overview ...................................................................................................... 1 1.2 Specificity of HOX proteins: The need for cofactors .......................................................... 3 1.2.1 TALE class of HOX cofactors .............................................................................. 4 1.3 HOX cofactors: The Drosophila paradigm .......................................................................... 7 1.3.1 Extradenticle (EXD) ............................................................................................. 7 1.3.2 Homothorax (HTH) .............................................................................................. 8 1.3.2. A Physiological functions of HTH .......................................................... 9 1.4 TALE cofactor proteins in chordates ................................................................................. 10 1.5 MEIS1 ................................................................................................................................ 11 1.5.1 Isoforms of Meis1 ............................................................................................... 11 1.5.2 Cooperative binding of MEIS1 with PBX-HOX ................................................ 12 1.5.3 Regulation of Meis1 expression .......................................................................... 15 1.5.4 Physiological roles of MEIS1 ............................................................................. 16 1.5.5 MEIS1 in hematopoiesis ..................................................................................... 19 1.5.6 MEIS1 in cancer ................................................................................................. 21 1.5.7 MEIS1 in mixed lineage leukemia (MLL) .......................................................... 22 1.5.8 Mechanism of MEIS1 cancer induction ............................................................. 24 1.5.9 MEIS1 targets ..................................................................................................... 25 i 1.6 MEIS2 ................................................................................................................................ 30 1.7 PBX proteins ...................................................................................................................... 31 1.7.1 Physiological function of PBX ........................................................................... 34 1.8 PKNOX proteins ................................................................................................................ 36 1.8.1 PKNOX1 ............................................................................................................. 36 1.8.2 PKNOX2 ............................................................................................................. 38 1.9 CRTC (CREB regulated transcription coactivator) ........................................................... 39 1.9.1 Physiological roles of CRTC .............................................................................. 41 1.10 MLL1 (Mixed lineage leukemia 1) or HRX .................................................................... 43 1.10.1 Interactions of MLL1 ........................................................................................ 44 1.11 CBX3 or HP1γ ................................................................................................................. 47 1.12 NONO (p54nrb) ................................................................................................................. 48 1.13 NOP56/58 ........................................................................................................................ 50 1.14 Biotin-tagging and purification of protein complexes ..................................................... 51 RATIONALE ................................................................................................................................ 53 CHAPTER 2: Materials and methods ............................................................................. 54 2.1 Plasmid constructs ............................................................................................................. 54 2.2 Antibodies .......................................................................................................................... 55 2.3 Cell culture and transfections............................................................................................. 56 2.4 Preparation of samples for mass spectrometry .................................................................. 57 2.4.1 In-gel digestion ................................................................................................... 58 2.4.2 Mass spectrometry protocol ................................................................................ 58 2.4.3 Protein identification ........................................................................................... 59 2.5 Co-immunoprecipitation (co-IP) protocol ......................................................................... 59 2.6 SDS PAGE and Immunoblotting ....................................................................................... 60 2.7 Luciferase assay protocol ................................................................................................... 60 2.8 Immunofluorescence assay ................................................................................................ 61 ii 2.9 siRNA knockdown ............................................................................................................. 61 CHAPTER 3: Results ............................................................................................................... 63 3.1 PART 1 3.1.1 Creation of expression constructs for BAP-tagged MEIS1A ............................. 63 3.1.2 HEK293T cells as a system for the isolation of MEIS1A ................................. 64 protein partners 3.1.3 Creation of BirA stable lines ............................................................................... 65 3.1.4 In vivo biotinylation of FBM .............................................................................. 67 3.1.5 Test for functionality: Interaction with known partners ..................................... 69 3.1.6 Intracellular localization of FBM........................................................................ 71 3.1.7 Stable expression of FBM in HEK293T/BirA cells ........................................... 75 3.2 PART 2 3.2.1 Identification of MEIS1A interacting proteins ................................................... 76 3.3 PART 3 3.3.1 Investigating the interaction between MEIS1A and NONO............................... 82 3.3.2 Knockdown of endogenous NONO expression does not lead to ........................ 84 a decrease in MEIS1-CRTC1 interaction 3.3.3 NONO does not have any effect on MEIS1A transactivation while .................. 86 while having an inhibitory effect on PKA signaling 3.3.4 Other members of the MEIS family also interact with NONO .......................... 89 3.4 PART 4 3.4.1 MEIS1A interacts with NOP56, NOP58, CBX3 and MLL1 .............................. 90 3.4.2 PKNOX1 and PKNOX2 also interact with NOP56 and NOP58 ........................ 92 but do not interact with CBX3 and MLL1 3.4.3 MLL-AF4 fusion protein also interacts with MEIS1A ....................................... 94 3.4.4 Endogenous MLL1 interacts with MEIS1 in RS4;11 ......................................... 95 lymphoblast cells 3.4.5 MLL1 positively contributes to the MEIS1A-mediated ..................................... 96 transactivation iii 3.4.6 MLL1 interacts with the C-terminal region of MEIS1A .................................... 98 CHAPTER 4: DISCUSSION ...................................................................................... 100 4.1 Identification of novel interaction partners of MEIS1A .................................................
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