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Investigating the Control of Inter-Homologue Recombination and Synapsis During Meiosis in Arabidopsis Thaliana

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Investigating the Control of Inter-Homologue Recombination and Synapsis During Meiosis in Arabidopsis Thaliana Investigating the control of inter-homologue recombination and synapsis during meiosis in Arabidopsis thaliana by MAHEEN FERDOUS A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Biosciences University of Birmingham September 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract During meiosis, axis formation and synapsis of homologous chromosomes are tightly co-ordinated with meiotic recombination. This study investigates the influence of chromosome axis and synaptonemal complex proteins on meiotic crossover formation. The study involved the characterization of a novel protein, AtASY3, required for normal meiosis in Arabidopsis. Analysis of Atasy3 mutants revealed that loss AtASY3 compromises chromosome axis formation, synapsis and normal levels of crossover formation. Further analysis revealed that loss of AtASY3 disrupts the axial organization of AtASY1. In separate studies, colleagues found that AtASY3 and AtASY1 are able to interact. Together, these results suggest that AtASY3 is a functional homologue of the budding yeast axis protein, Red1. Since studies in budding yeast indicate that Red1 and Hop1 (homologue of AtASY1) play a key role in establishing a bias to favour inter-homologue recombination, this study suggests that AtASY3 and AtASY1 may have a similar role in Arabidopsis. The study also involved the analysis of the putative phosphorylation site, residue T295, on AtASY1. This revealed that T295 is essential for AtASY1-mediated crossover formation during meiosis. Additionally, a potential meiotic role for the RECQ DNA helicase, AtRECQ4B was investigated, however, the protein does not appear to be essential for Arabidopsis meiosis. Acknowledgements I would like to thank Prof. Chris Franklin for providing me the opportunity to do such a challenging and rewarding project. I am highly grateful for his exceptional supervision, guidance and support towards my project and academic development. I would like to especially thank Dr. James Higgins for his excellent supervision, guidance and support on all aspects of my project throughout my PhD. I am thankful to Dr. Kim Osman for helping me with protein gel analysis and Dr. Richard Tudor for assistance with molecular biology techniques. I am grateful to Dr. Gareth Jones for his help with Crepis and advice regarding my project. I would also like to thank Dr. Eugenio Sanchez-Moran, Dr. Susan Armstrong and Prof. Noni Franklin-Tong for helpful scientific discussions and guidance throughout my PhD. I am grateful to Ruth Perry and Steve Price for technical assistance and Karen Staples for horticultural support. I am also thankful to all members, past and present, of the Franklin, Armstrong, Franklin-Tong, Sanchez-Moran and Coates labs for their help and support during my PhD. I would like to thank my family, my wife Niki and her family and my friends, especially Rashed Hossain and Mohammad Ahasan, for their love and support over the past few years, which helped me through both the good and difficult times of my PhD. List of Contents ABSTRACT .............................................................................................................................................................. II ACKNOWLEDGEMENTS .............................................................................................................................................. III CHAPTER 1 ....................................................................................................................................................... 1 INTRODUCTION ............................................................................................................................................... 1 1.1. OVERVIEW OF MEIOSIS ...................................................................................................................................... 2 1.1.1. Meiosis I: The first meiotic division ...................................................................................................... 2 1.1.2. Meiosis II: The second meiotic division ................................................................................................ 3 1.2. SISTER CHROMATID COHESION ............................................................................................................................. 6 1.3. PAIRING AND SYNAPSIS OF HOMOLOGOUS CHROMOSOMES ....................................................................................... 8 1.3.1. Homologous chromosome pairing ....................................................................................................... 9 1.3.2. Homologous chromosome synapsis ................................................................................................... 13 1.3.3. Role of meiotic recombination in homologous chromosome pairing and synapsis ........................... 18 1.4. MEIOTIC RECOMBINATION................................................................................................................................ 21 1.4.1. DNA double-strand break formation.................................................................................................. 23 1.4.2. Processing of double-strand breaks ................................................................................................... 25 1.4.3. Strand invasion and exchange ........................................................................................................... 26 1.4.4. Pathways to meiotic crossover formation.......................................................................................... 34 1.4.4.1. MSH4-dependent pathway for crossover formation ...................................................................................35 1.4.4.2. MSH4-independent pathway for CO formation ...........................................................................................43 1.4.5. Double-Holliday junction resolution ................................................................................................... 45 1.4.6. Crossover homeostasis ....................................................................................................................... 48 1.4.7. Crossover control ............................................................................................................................... 50 1.5. INTER-RELATIONSHIP BETWEEN CHROMOSOME AXES AND MEIOTIC RECOMBINATION .................................................... 56 1.5.1. Co-ordination between chromosome axis maturation and recombination ....................................... 56 1.5.2. Spatial association between recombination and chromosome axis/SC ............................................. 58 1.5.3. Role of axis proteins in recombination ............................................................................................... 59 1.6. ARABIDOPSIS THALIANA - A MODEL PLANT FOR MEIOSIS RESEARCH ............................................................................ 60 1.7. AIMS AND OBJECTIVES ..................................................................................................................................... 62 CHAPTER 2 ......................................................................................................................................................64 MATERIALS AND METHODS ............................................................................................................................64 2.1. PLANT MATERIAL AND GROWTH CONDITIONS ........................................................................................................ 65 2.2. NUCLEIC ACID MANIPULATIONS .......................................................................................................................... 65 2.2.1. Isolation of plant DNA ........................................................................................................................ 65 2.2.2. RNA extraction from plant tissue ....................................................................................................... 66 2.2.3. cDNA synthesis ................................................................................................................................... 67 2.2.4. Nucleic acid quantification ................................................................................................................. 67 2.2.5. DNA agarose gel electrophoresis ....................................................................................................... 67 2.2.6. RNA agarose gel electrophoresis ....................................................................................................... 68 2.2.7. Primer design ..................................................................................................................................... 68 2.2.8. Polymerase chain reaction (PCR) ....................................................................................................... 69 2.2.9. PCR for genotyping
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