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University of California, Merced UNIVERSITY OF CALIFORNIA, MERCED SUMOylation is a regulator of regional cell fate and genomic integrity in planarians by Manish Thiruvalluvan A dissertation submitted in satisfaction of the requirements for the degree Doctor of Philosophy in Quantitative and Systems Biology Committee in Charge: Professor Kirk Jensen, Chair Professor Jennifer Manilay, Member Professor Anna Beaudin, Member Professor Néstor J. Oviedo, Advisor 2018 i Copyright Manish Thiruvalluvan, 2018 All rights reserved ii The dissertation of Manish Thiruvalluvan is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Jennifer Manilay Anna Beaudin Kirk Jensen, Chair University of California, Merced 2018 iii TABLE OF CONTENTS vi. List of figures vii. List of abbreviations viii. Acknowledgements ix. Curriculum vitae xii. Abstract 1. Introduction 1.1. Regional signals influence cell fate decisions in health and disease 1.2. SUMOylation – a type of posttranslational modification 1.3. The planarian model Schmidtea mediterranea 1.4. Research summary 2. Materials and Methods 2.1. Materials 2.1.1. Organisms 2.1.2. Selection of primers and cloning 2.1.3. Antibodies, enzymes and other reagents 2.1.4. Solutions and buffers 2.2. Methods 2.2.1. Planarian husbandry 2.2.2. Identification of orthologs and phylogenetic analysis 2.2.3. PCR amplification and gel electrophoresis 2.2.4. Planarian Amputation 2.2.5. Irradiation 2.2.6. RNAi by bacteria feeding 2.2.7. Fixation protocols 2.2.8. RNA extraction 2.2.9. Planarian cell dissociation 2.2.10. Immunocytochemistry 2.2.11. RNA probe synthesis 2.2.12. In situ hybridization 2.2.13. Quantitative PCR (qPCR) 2.2.14. Protein extraction and Western blot 2.2.15. COMET assay 2.2.16. Flow cytometry 2.2.17. Karyotyping 2.2.18. Planarian datamining 2.2.19. Imaging and data processing 2.2.20. Statistical analysis iv 2.2.21. RNA Sequencing and Differential Expression Analysis 3. Results 3.1. SUMO pathway genes are conserved in the planarian Schmidtea mediterranea 3.2. UBC9 is required for regional tissue maintenance 3.3. UBC9 is actively expressed by the stem cell compartment 3.4. UBC9 is required for proper stem cell function and cell cycle transition 3.5. UBC9 is necessary for maintenance of neoblasts and postmitotic cells 3.6. Downregulation of SUMO pathway components recapitulates UBC9 RNAi phenotype 3.7. UBC9 knockdown leads to regional increase in cell death 3.8. Regional defects after UBC9 RNAi are mediated through repression of Hedgehog signaling pathway 3.9. Loss of UBC9 leads to defects in regeneration and attenuation of the cephalic ganglia 3.10. UBC9 is required for maintenance of genomic integrity 3.11. UBC9 facilitates nuclear transport of RAD51 to repair double stranded breaks 3.12. RNA Sequencing reveals MADD as a novel regulator of neoblast function 3.13. Knockdown of MADD rescues UBC9 phenotype by reducing cell death in the posterior 4. Discussion 4.1. SUMOylation is required for proper cell function and tissue homeostasis in planarians 4.2. A novel role for UBC9 and SUMOylation in regeneration 4.3. UBC9 and RAD51 knockdown models to study genomic instability and cancer 4.4. Rescue of UBC9 phenotype by MADD highlights long-range neural control of cell fate 4.5. Final remarks and future direction 5. References v LIST OF FIGURES 1. Figure 1: SUMOylation and the planarian model Schmidtea mediterranea 2. Figure 2: The SUMOylation pathway is conserved in the planarian model Schmidtea mediterranea 3. Figure 3: UBC9 is required for regional tissue maintenance 4. Figure 4: UBC9 is actively expressed by the stem cell compartment 5. Figure 5: UBC9 is required for neoblast proliferation 6. Figure 6: UBC9 is responsible for proper cell cycle transition 7. Figure 7: UBC9 is necessary for maintenance of proliferative and post- mitotic cells 8. Figure 8: Downregulation of SUMO pathway components recapitulates UBC9 RNAi phenotype 9. Figure 9: UBC9 knockdown leads to regional increase in cell death 10. Figure 10: Planarian posterior polarity is maintained by the Hedgehog signaling pathway 11. Figure 11: Regional defects after UBC9 RNAi after partially mediated through a repression of Hedgehog signaling 12. Figure 12: UBC9 is required for proper regeneration 13. Figure 13: Double knockdown of Patched and UBC9 eliminates blastema formation 14. Figure 14: UBC9 is required to maintain genomic integrity along the anteroposterior axis 15. Figure 15: UBC9 facilitates nuclear transport of RAD51 to repair double stranded breaks 16. Figure 16: UBC9 and RAD51 work synergistically to maintain tissue homeostasis 17. Figure 17: Transcriptomic analysis of UBC9 knockdown model identifies MADD as a potential regulator of neoblast function 18. Figure 18: MADD regulates fissioning behavior and neoblast maintenance 19. Figure 19: MADD knockdown rescues UBC9 RNAi abnormalities by ablating cell death in the posterior region 20. Figure 20: RAD51 and UBC9 knockdown yields high levels of DNA damage, but different neoblast responses 21. Figure 21: Schematic summary representing Smed UBC9 acts as an upstream regulator of different functions in the adult body vi LIST OF ABBREVIATIONS 1. Smed – Schmidtea mediterranea 2. DSB – double stranded breaks 3. SUMO pathway – includes the entire signaling pathway, including the SUMO enzymes 4. SUMO - small-ubiquitin like modifier 5. DDR – DNA damage repair 6. DSBs – double stranded breaks 7. ASCs – Adult stem cells 8. SENP – sentrin specific protease 9. SAE1/2 – SUMO activating enzyme subunit 1/2 10. Hh – Hedgehog 11. Ptc – Patched 12. Smo -Smoothened 13. Sfrp1 – secreted frizzled like protein 1 14. Fz4 – frizzled like protein 1 15. AP axis - anteroposterior axis 16. DNA damage and repair – DDR 17. ROS – reactive oxygen species 18. D. melanogaster – drosophila melanogaster 19. C. elegans - Caenorhabditis elegans 20. BRCA1 – breast cancer associated 1 21. XRCC4 - X-ray repair cross-complementing protein 4 22. Ku70 - Lupus Ku autoantigen protein p70 23. ATM - ATM serine/threonine kinase 24. ATR - ataxia telangiectasia and Rad3 related 25. RANGAP1 - Ran GTPase Activating Protein 1 26. RanBP2 - RAN Binding Protein 2 27. PIAS - protein inhibitor of activated STAT 28. H2Ax - H2A histone family, member X 29. PTEN - Phosphatase and tensin homolog 30. COMET - single cell gel electrophoresis 31. MADD - MAP kinase activating death domain 32. Rb – retinoblastoma protein 33. p53 – tumor protein p53 vii ACKNOWLEDGEMENTS First, I want to thank Dr. Nestor Oviedo for believing in me ever since he took me in as an undergraduate and encouraged me to get my PhD when all other paths were closed. He has helped me not only becoming a better scientist, but a better teacher and a better person. I greatly enjoyed my time working with him and sincerely appreciate everything he has done for me. In the same vein, I would like to thank all members of my lab, especially Paul, who has helped me immensely in carrying out experiments. It was my pleasure to work day in and day out with my colleagues who made the tedious process of bench work more enjoyable. Special thanks to Dr. David Ardell and Melanie LeGro for their work with transcriptomic analysis as this data drove the late stages of my research. I would also like to thank members of my committee, Dr. Jennifer Manilay, Dr. Anna Beaudin and Dr. Kirk Jensen, who stuck with me and helped me finish my doctoral journey. In addition, I would like to thank Dr. Limor Broday and her lab for their expertise in SUMOylation and for helping bring forth and develop this idea into a successful project. I am extremely grateful to my parents for bringing me to this country and providing me with a once in a lifetime opportunity to pursue higher education. Finally, I want to thank my wife Sandra, who has been at my side for most of my adult life and has encouraged me to pursue and achieve my dreams. When I started my PhD, I was twenty-one and just graduated college. Now, I’m a husband and father to my son Alex. Without her help, I would not have been able to come this far. viii CURRICULUM VITAE Manish Thiruvalluvan Ph.D. Quantitative and Systems Biology School of Natural Sciences 5200 N Lake Rd, Merced, CA 95340 (408) 910-9028 | [email protected] I. EDUCATION 2013 – present Ph.D., Quantitative and Systems Biology, University of California Merced • Worked with the planarian model system to study stem cell proliferation and regeneration • Conceived, developed and conducted independent research directed at identifying the molecular mechanism behind differential rates of cancer formation • Identified epigenetic modifications through UBC9 and the SUMOylation is responsible for regulating regional maintenance of cell survival and DNA damage in the adult body • Presented my research at various conferences and meetings around the United States • Dissertation: Role of SUMOylation in stem cell regulation and DNA damage repair in planarians • Advisor: Nestor J. Oviedo 2009 – 2013 Bachelor of Science, Human Biology, University of California Merced (Cum Laude) • Dean's List: Awarded four times • Academic Chair of Hermanos Unidos Organization, 2011-2013 • Leadership position in Tae Kwon Do Club, 2010-2012 2007 – 2011 Stockton Delta College • Attended part time as a high school student and undergraduate • Classes Taken: Psychology, Writing, Statistics, Mythology, Music Theory and Speech II. PUBLICATIONS 1. Thiruvalluvan, M., Barghouth, P. G., Tsur, A., Broday, L., & Oviedo, N. J. (2018). SUMOylation controls stem cell proliferation and regional cell death through Hedgehog signaling in planarians. Cellular and Molecular Life Sciences: CMLS, 75(7), 1285–1301. https://doi.org/10.1007/s00018-017-2697-4 2. Barghouth, P. G., Thiruvalluvan, M., LeGro, M., & Oviedo, N. J. (2018). DNA damage and tissue repair: What we can learn from planaria. Seminars in Cell & Developmental Biology. https://doi.org/10.1016/j.semcdb.2018.04.013 ix 3.
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