RPA HYPERPHOSPHORYLATION FACILITATES HUMAN RAD52 FUNCTION IN HOMOLOGOUS RECOMBINATION A Dissertation Presented to the Faculty of the Weill Cornell Graduate School of Medical Sciences in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy By Alison Crystal Carley February 2016 ©2016 Alison Crystal Carley RPA HYPERPHOSPHORYLATION FACILITATES HUMAN RAD52 FUNCTION IN HOMOLOGOUS RECOMBINATION Alison Crystal Carley, PhD Cornell University 2016 RAD52 deficiency is synthetically lethal in BRCA1 and BRCA2 deficient tumors. RAD52 is therefore a potential therapeutic target for breast cancer patients with BRCA mutations, but not much is known about its role in humans. RAD52 and the BRCA proteins are involved in the homologous recombination (HR) pathway of DNA double-strand break (DSB) repair. In HR, DSBs are processed to generate single-stranded DNA (ssDNA) overhangs, which are then bound by the RPA complex. RAD51 is then recruited and performs homology search and strand invasion. S. cerevisiae RAD52 and hBRCA2 mediate the exchange of RPA for RAD51 and stimulate RAD51 strand invasion. Recent publications show that hRAD52 provides an alternative mediator pathway in cells that lack the BRCA pathway. RPA hyperphosphorylation and dephosphoprylation after DNA damage are important for HR, but its effect on RAD52 function is not well understood. Here, we show that phosphorylation of RPA is important for the alternative RAD52 pathway. Using BRCA2-depleted human cells, in which the only available mediator pathway is RAD52-dependent, expressing non- phosphorylatable (RPA2-A) and mock phosphorylated (RPA2-D) RPA2, we show that HR is reduced in the RPA2-phosphomutant cells compared to RPA2-WT cells, measured by the DR-GFP recombination assay and RAD51 focus formation. Furthermore, RPA-phosphomutant cells have reduced association of RAD52 and RAD51 by colocalization. Interestingly, there is no effect of RPA phosphorylation on RAD52 recruitment to repair foci in RPA- mutant cells after treatment with camptothecin. However, the RPA- phosphomutants do not colocalize with RAD52 as well as the RPA-WT protein and more RAD52 immunoprecipitates with RPA-WT than RPA-A after camptothecin treatment. Finally, using biochemical assays we show that RPA phosphorylation does not affect RAD51 strand exchange, RAD52-mediation of RAD51 strand exchange, and RAD52-dependent ssDNA annealing, suggesting there are factors in cells not present in these assays that allow RPA phosphorylation to promote RAD52 function, or that cycling of phosphorylation and dephosphorylation is needed. Thus, although RAD52 is able to be recruited regardless of RPA phosphorylation status, RPA phosphorylation improves RAD52’s association with RPA, and subsequently promotes RAD52-HR. RPA phosphorylation is therefore important for both BRCA2-directed and RAD52-directed HR. BIOGRAPHICAL SKETCH Alison Crystal Carley was raised in Babylon Village on Long Island, NY. She attended New York University and graduated in May of 2007, summa cum laude, with a BA in biology and a minor in mathematics. She worked at Mount Sinai Medical Center from 2007-2009 in the lab of Dr. Goutham Narla, where she studied an oncogenic splice variant of the tumor suppressor gene KLF6. In 2009, she began her studies at Weill Cornell Graduate School of Medical Sciences, in the BCMB program. She joined the laboratory of Dr. Simon PowelI at Memorial Sloan Kettering Cancer Center in 2010, where she worked on the homologous recombination DNA repair pathway. iii ACKNOWLEDGMENTS I would like to thank my advisor, Dr. Simon Powell, for his guidance and support, and my thesis committee, Dr. Maria Jasin and Dr. Bill Holloman, for their guidance. I would like to thank the many members of the Powell lab for their scientific and emotional support over the years (especially the post-docs Laura, Sam, Rohini, Adriana, Devi and Jarin). Many thanks also to Dr. Qingwen Zhou and Dr. Ryan Jensen, for their biochemical advice, and the Jensen and Borgstahl labs for generously providing purified proteins. I would also like to thank my family, my parents Pat and Bob, and my siblings Michelle, Melissa, and Brian, who are incredibly supportive, wonderful people, with a special thanks to Michelle for her academic guidance and for getting me my first lab job. Lastly, I would like to thank my fiancé, Nolan Camp, for being a steady, loving, and encouraging partner, and Dr. Will Smith, for feeding me well, endless karaoke duets, and making grad school tolerable. iv TABLE OF CONTENTS BIOGRAPHICAL SKETCH ........................................................................ iii ACKNOWLEDGEMENTS ......................................................................... iv TABLE OF CONTENTS ............................................................................. v LIST OF FIGURES .................................................................................. viii LIST OF ABBREVIATIONS ....................................................................... ix CHAPTER ONE: INTRODUCTION ............................................................ 1 DNA DOUBLE-STRAND BREAK REPAIR ................................................. 1 Replication stress ....................................................................................... 3 DNA damage response signaling ............................................................... 5 Homologous Recombination ...................................................................... 8 Homologous Recombination: BRCA1 ...................................................... 11 Homologous Recombination: Resection .................................................. 12 Homologous Recombination: After resection--strand invasion or SSA .... 16 Homologous Recombination: Completing HR .......................................... 17 REPLICATION PROTEIN A (RPA) .......................................................... 20 RPA structure ........................................................................................... 21 RPA DNA binding ..................................................................................... 25 RPA and the DNA damage response ....................................................... 26 RPA-RAD52 interaction ............................................................................ 27 Other human SSBs .................................................................................. 28 RPA phosphorylation ................................................................................ 30 RPA phosphorylation: effect of hyperphosphorylation on RPA-DNA binding ................................................................................................................. 34 v RPA phosphorylation: RPA recruitment and phosphorylation .................. 35 RPA phosphorylation: RPA phosphorylation, DNA repair and replication stress ................................................................................................................. 38 RPA phosphorylation: Regulation by phosphatases ................................. 46 RAD52 AND MEDIATORS OF RECOMBINATION .................................. 48 RAD51 ...................................................................................................... 52 BRCA2 ..................................................................................................... 55 RAD52 phenotypes .................................................................................. 59 RAD52 structure and biochemistry ........................................................... 65 RAD52-BRCA synthetic lethality .............................................................. 74 Other mediators ........................................................................................ 79 CHAPTER TWO: RPA HYPERPHOSPHORYLATION PROMOTES RAD52 MEDIATOR FUNCTION IN HUMAN CELLS THROUGH IMPROVED RPA- RAD52 ASSOCIATION ............................................................................ 84 INTRODUCTION ...................................................................................... 84 RESULTS ................................................................................................. 86 RAD52-mediated HR is promoted by RPA hyperphosphorylation ............ 86 RAD52-RPA interaction is promoted by RPA hyperphosphorylation ...... 101 MATERIALS AND METHODS ................................................................ 104 CHAPTER THREE: INVESTIGATING THE EFFECT OF RPA2 HYPERPHOSPHORYLATION ON ITS IN VITRO FUNCTIONS ............ 111 INTRODUCTION .................................................................................... 111 RESULTS ............................................................................................... 113 RPA ssDNA-binding is not significantly affected by phosphorylation ..... 113 RAD51 strand exchange is not affected by RPA phosphorylation in vitro ........................................................................................................ 113 vi RAD52-mediated strand exchange is not promoted by RPA phosphorylation in vitro ........................................................................................................ 122 RAD52-mediated annealing is not promoted by RPA phosphorylation in vitro ............................................................................................................... 126 MATERIALS AND METHODS ................................................................ 126 CHAPTER FOUR: DISCUSSION ..........................................................