Cohesion failure and Mitosis: From Molecular Mechanisms to Organismal Consequences Mihailo Mirkovic Dissertation presented to obtain the PhD degree in Molecular Biology Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Research work coordinated by: Instituto Gulbenkian de Ciencia Oeiras, May 2018 1 Table of Contents Declaration………………………………...….................................6 Declaração....................................................................................6 Summary.......................................................................................7 Resumo........................................................................................11 Acknowledgments........................................................................15 List of Publications.......................................................................17 Introduction: 1.0 General Introduction…………………………………........…...19 1.1 Cohesin-Molecular Glue and much more………...............22 1.1.1 The importance of gluing DNA molecules……….…..…..23 1.1.2 The Cohesin Cycle……………………………..…............34 A) The cohesin cycle: Chromatin Loading……..……...........34 B) The cohesin cycle: Cohesion establishment………........36 C) The cohesin cycle: Prophase and Cohesion retention at the centromere……………………………………………….....38 D) The cohesin cycle: The final cut……….…..……….…….41 1.1.3 Multiple-step cohesin removal…………….…….....42 1.1.4 Sister Chromatid Resolution………………..….......43 1.1.5 Inner-centromere defining platfor…………….…....51 1.1.6 Force Balance…………………………………….....53 1.1.7 Anaphase sharpness…………………………….….56 1.1.8 Concluding Remarks………………………….........57 2 1.2 The Guardians of Mitotic Fidelity……………………………70 1.3 Aneuploidy and its Consequences………………………….86 Results: Chapter I: Premature loss of cohesion and Mitosis………………….……100 I.1 Premature Loss of Sister Chromatid Cohesion Does Not Elicit a Robust SAC Response…………………………………………...…104 I.2 Loss of Sister Chromatid Cohesion Activates EC Mechanisms during Early Mitosis……………………………………………...…..107 I.3 Attachments of Single Chromatids to the Mitotic Spindle Are Progressively Stabilized……………………………………….…….113 I.4 Cyclin B Is Gradually Degraded during Cohesin Cleavage….119 I.5 Mathematical Modeling of Multiple Feedback across the Mitotic Network………………………………………………….…….…...…120 I.6 Cells with Premature Loss of Sister Chromatid Cohesion Are Ultrasensitive to Cdk1 Inhibition………………………………....…127 I.7 Discussion……………………………………………….…....…..131 I.8 Materials and Methods…………………………….……..……...132 3 Chapter II: Spindle Assembly Checkpoint aggravates cohesin defects in mitosis……………………………………………….………..….139 II.1 Drosophila wing modifier screen reveals that depletion of Mad2 and Mps1 suppresses the developmental defects associated with loss of cohesion………………………………………..…......…..141 II.2 SAC inactivation rescues chromosome segregation defects associated with loss of cohesion……………………….…........146 II.3 SAC inactivation suppresses chromosome shuffling after loss of cohesion…………………………………………………......…155 II.4 SAC inactivation restores cell survival after loss of cohesion……………………………………………….....…...…..163 II.5 Discussion………………………………………………....…165 II.6 Materials and Methods……………………………….…..…168 Chapter III: Cohesin loss and Aneuploidy in the developing fly………...180 III.1 A genetic system for acute and time-controlled generation of aneuploidy in a developing organism…………..………….......…183 III.2 Reversible removal of cohesin results in a single round of mitotic abnormalities and consequent aneuploidy…………........186 III.3 Larvae challenged with aneuploidy during development hatch into impaired adults…………………………………………….…...196 4 III.4 Aneuploidy results in chromosomal instability and chromosome accumulation in the Neuroblasts……………………….….....….199 III.5 Karyotype restrictions in the proliferating aneuploid Neuroblast population…………………………………………………….…….208 III.6 Aneuploidy elicits a stress response in the brain tissue.….210 III.7 Neural stemness delays aneuploidy stress response……..214 III.8 Developmental aneuploidy does not alter significantly adult brain size and shape………………………………………..…......217 III.9 Protecting only the developing brain from induced aneuploidy rescues the lifespan of the ecloded flies……………………...…219 III.10 Discussion…………………………………..…….…………222 III.11 Materials and Methods………………………………..……229 General Discussion……………………………….……….…….242 5 Declaration I declare that this dissertation and the data presented are the result of my own work, developed between 2014 and 2018 in the laboratory of Dr. Raquel Oliveira at the Instituto Gulbenkian de Ciência in Oeiras, Portugal. Specific author contributions are indicated in each chapter, in the Acknowledgements section. Financial support was granted by Fundação para a Ciência e a Tecnologia, doctoral fellowship PD/BD/52438/2013 and ERC Starting Grant (StG), LS3, ERC-2014-STG-638917, Marie Curie Career Integration Grant (MCCIG321883/CCC) and an EMBO Installation Grant (IG2778). Declaração Declaro que esta dissertação de doutoramento e os dados nela apresentados são o resultado do meu trabalho, desenvolvido entre 2014 e 2018 no laboratório do Dr.Raquel Oliveria no Instituto Gulbenkian de Ciência em Oeiras, Portugal. As contribuições de cada autor são indicadas em cada capítulo na secção dos Agradecimentos/Acknowledgements.O apoio financeiro foi concedido pela Fundação para a Ciência e Tecnologia, através da bolsa de doutorame nto PD/BD/52438/2013e porfundos do Conselho Europeu de Investigação ERC Starting Grant (StG), LS3, ERC-2014-STG-638917, Marie Curie Career Integration Grant (MCCIG321883/CCC), EMBO Installation Grant (IG2778). 6 Summary Mitosis is a dynamic culmination of the cell cycle, resulting in generation of two daughter cells from one mother. In order for this to happen, the cell must package its DNA into chromosomes and divide it equally amongst progeny. To ensure this process happens accurately, the cell glues identical chromosomes together so it can segregate them in symmetrical fashion during anaphase. The glue holding chromosomes together is a molecule called cohesin, which encompasses replicated DNA fibers via topological entrapment. The aim of this thesis was to study the immediate mitotic response to premature cohesion loss, as well as the long term consequences of such perturbed mitosis for the cell and the whole organism. In order to study cohesion loss in mitosis, we utilized an established acute system for cohesin depletion, via the use of TEV protease, which cleaves TEV sites inserted into cohesin within hours after heat shock induction, or minutes after injection. To study cohesion loss in the entire organism, we modified the existing TEV tool in D.melanogaster to include a cohesin rescue step, generating a transient cohesin loss, which would impair mitosis in a window time, while minimizing chronic damage to the organism. The Chapter I of the thesis focuses on the interplay between cohesin loss and mechanisms protecting mitotic fidelity. It has previously been demonstrated that premature cohesion loss triggers the activation of the Spindle Assembly Checkpoint (SAC), a system for mitotic delay generated by unattached chromosomes, whose main role is to provide more time for Aurora B, the main error correction protagonist, do destabilize erroneously attached chromosomes and allow for biorientation. However, cells escape 7 SAC surveillance upon cohesion loss relatively fast, resulting in aneuploidy. Our work provided additional insight on why cohesin loss is not robustly detected by the SAC. We have demonstrated that upon premature cohesion loss, chromosomes undergo cycles of attachment and detachment to the mitotic spindle, which are Aurora B dependent. However these cycles of detachment and consecutive SAC generation decline during the arrest and result in aberrant mitotic exit. The likely reason behind this is the fact that Aurora B, as well as SAC are dependent on the activity of Cdk1- Cyclin B complex. On the other hand, the stability of Cyclin B is SAC dependent, as SAC abolishment leads to Cyclin B degradation. To add an additional layer of complexity, Aurora B activity, which leads to SAC generation, is also Cyclin B dependent. This places the entire system in a positive feedback state, where the activity decline in any of the three main modules (SAC, Aurora B and Cyclin B) results in a mitotic exit, despite the dire consequences for the cell. In the Chapter II of the thesis, we examined situations that alleviate mitotic defects caused by premature loss of cohesin. An interesting modulator screen of our collaborators, in the Drosophila wing disc, revealed that cohesion defects can be suppressed if the SAC is downregulated. This is a very counterintuitive result, as the SAC is one of the main guardians of mitotic fidelity. However, we demonstrate that the prolonged mitosis due to SAC activation in the absence of cohesin is actually detrimental to the symmetry of genome segregation, when compared to mitosis without cohesion where SAC is not active. The culprit behind this aggravated 8 asymmetry when mitosis is prolonged is the error correction and Aurora B activation, which results in continuous cycles of chromosome shuffling, attachment and detachment. Live imaging and the quantification of centromere segregation at the anaphase in the embryo, as well as the wing disc, demonstrated that mitotic fidelity can be enhanced in the absence of cohesin in two major ways. The first is the SAC inhibition, which shortens mitosis and allows for mitotic