University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School January 2015 Functional Analysis of the Ovarian Cancer Susceptibility Locus at 9p22.2 Reveals a Transcription Regulatory Network Mediated by BNC2 in Ovarian Cells Melissa Buckley University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Biology Commons, Genetics Commons, and the Molecular Biology Commons Scholar Commons Citation Buckley, Melissa, "Functional Analysis of the Ovarian Cancer Susceptibility Locus at 9p22.2 Reveals a Transcription Regulatory Network Mediated by BNC2 in Ovarian Cells" (2015). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/5649 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Functional Analysis of the Ovarian Cancer Susceptibility Locus at 9p22.2 Reveals a Transcription Regulatory Network Mediated by BNC2 in Ovarian Cells by Melissa A. Buckley A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Cell Biology, Microbiology, and Molecular Biology College of Arts and Sciences University of South Florida Major Professor: Alvaro N.A. Monteiro, Ph.D. Committee: Jiandong Chen, Ph.D. Javier Cuevas, Ph.D. Cathy Phelan, Ph.D. Date of Approval: July 8, 2015 Keywords: Single Nucleotide Polymorphism, Allele, Genome Wide Association Studies, Zinc Finger Domain Copyright © 2015, Melissa A. Buckley DEDICATION I would like to dedicate my thesis to my friends and family who have supported me throughout the whole process. First and foremost a very special thanks to my husband, Kip. It takes a lot of perseverance and patience to be the spouse of a PhD candidate and I am so thankful I have married the most patient person I know. You have kept me grounded throughout the process and made me laugh and ensured me that we would get through it. I also want to thank my daughter for emulating me and therefore motivating me to reach for the best and be my best self. I also want to thank my mom and dad, Harry and Kelly, for their enormous support throughout my PhD by providing a home away from home for my husband working in another city and helping take care of my daughter while I learned to become Mommy, PhD. I also want to thank my parents and grandparents and brothers for all their love and encouragement throughout my life in which without it, I would not have made it this far. I also want to thank my mother and father in law for their love, support, and encouragement. You truly have treated me like another daughter in giving me advice and reminding me how proud you are of me. I also want to thank my good friend, Christine, whom in 3rd grade started to motivate me on this path. We were after school science lab partners in elementary school to room-mates and best friends in college studying pre-med. Thank you for being there for me and having fun with me in our free time. Last but not least, I would like to thank my best friend Jessica. They say people develop bonds when under stressful or difficult circumstances. I think grad school must fall under this category since we truly developed a strong friendship from the very beginning of our time at Moffitt. Thanks for being a shoulder to cry on when experiments failed again and again. I am glad I had someone to run marathons with to de-stress and I am so glad we got to share experiences of getting married, having children, and getting those three letters added to the end of our name. ACKNOWLEDGMENTS First I would like to thank my mentor, Dr. Monteiro for guiding me through this process, sharing all his knowledge and stories, and providing a tremendous amount of support through tough situations. I would also like to thank my committee members, Jiandong Chen, Javier Cuevas, and Catherine Phelan for their guidance. I would also like to thank the Monteiro lab members, present and past, Rebekah Baskin, Olga Golubeva, Ankita Jhuraney, Alex Valle, Renato Carvalho, and Aneliya Velkova with a special thanks to Gustavo Mendoza-Fandino, Anxhela Gjyshi, Xueli Li, and Paulo Cilas M. Lyra for helping perform difficult experiments that contributed to this work. I am glad we all had such a great sense of comradery in the lab which made graduate school much more pleasant. I would also like to thank a former post-doc in the lab, Nicholas Woods, and a former post-doc in a collaborating lab Howie Shen for being my second mentors. They taught me how to do experiments, provided insight and ideas, and also advised how to maintain a work-life balance in academia. Additionally, thank you Nick for helping the project move off the ground. I am pretty sure it would still be there if it was not for you. Additional experimental support has been provided by Kate Lawrenson, Dennis Hazelett, Simon G. Coetzee, and Houtan Noushmehr. They provided the RNA-seq, FAIRE-seq, and ChIP-seq for histone markers data to support and base my scientific hypotheses on. Ally Yang and Hamed Shateri Najafabadi from Timothy Hughes lab also performed the cutting edge experiments with the PBM and bioinformatics analysis of the zinc finger binding sites. I would also like to thank members of the Ovarian Cancer Association Consortium, specifically, Thomas Sellers, Catherine Phelan, Simon Gayther, Paul Pharoah, and Ellen Goode for their guidance and for allowing me to contribute to the cause of the consortium. It has been quite the learning experience which I do not think many graduate students get to encounter. It has been really special to see the small contribution I am making, influences a greater cause. I would also like to thank the NIH for financial support with the Ruth L. Kirschstein National Research Service Award. Also, thank you ARCS (Achievement Rewards for College Scientists) Foundation for their financial support and striving to promote science in the United States. TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................... i LIST OF TABLES ........................................................................................................... iv LIST OF FIGURES .......................................................................................................... v ABSTRACT ................................................................................................................... viii CHAPTER ONE: BACKGROUND ................................................................................... 1 Ovarian Cancer .................................................................................................... 1 Ovarian Cancer Subtypes .......................................................................... 1 Risk Factors and Pathogenesis ................................................................. 3 Genetic Predisposition to Ovarian Cancer ................................................. 5 Genome Wide Association Studies ...................................................................... 7 Linkage Analysis versus GWAS ................................................................ 8 Principles of GWAS ................................................................................. 10 Caveats of GWAS ................................................................................. 12 Ovarian Cancer GWAS ............................................................................ 13 Functional Analysis of Susceptibility Loci................................................. 16 Transcriptional Regulation ................................................................................. 18 Basics of Transcriptional Regulation ........................................................ 18 Transcription Factor Binding .................................................................... 21 Chromatin Structure ................................................................................. 22 3D Structure of the Genome .................................................................... 24 CHAPTER TWO: IDENTIFYING FUNCTIONAL SNPS ................................................. 27 Introduction ......................................................................................................... 27 Results ............................................................................................................... 28 Candidate Functional SNPs ..................................................................... 28 Functional Analysis of SNPs .................................................................... 31 Mapping SNPs to regulatory elements .......................................... 31 Development of Enhancer Scanning method ................................ 33 Experimental Design .......................................................... 33 Choice of template, tile verification, and host cell ............... 35 Controls .............................................................................. 36 Statistical analysis .............................................................. 37 Anticipated results .............................................................. 37 Limitations .......................................................................... 38 Mapping SNPs to regions of enhancer activity .............................