INVESTIGATION OF STRUCTURAL PROPERTIES OF METHYLATED HUMAN PROMOTER REGIONS IN TERMS OF DNA HELICAL RISE A THESIS SUBMITTED TO THE GRADUATE SCHOOL OF INFORMATICS OF MIDDLE EAST TECHNICAL UNIVERSITY BY BURCU YALDIZ IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN BIOINFORMATICS AUGUST 2014 INVESTIGATION OF STRUCTURAL PROPERTIES OF METHYLATED HUMAN PROMOTER REGIONS IN TERMS OF DNA HELICAL RISE submitted by Burcu YALDIZ in partial fulfillment of the requirements for the degree of Master of Science, Bioinformatics Program, Middle East Technical University by, Prof. Dr. Nazife Baykal _____________________ Director, Informatics Institute Assist. Prof. Dr. Yeşim Aydın Son _____________________ Head of Department, Health Informatics, METU Assist. Prof. Dr. Yeşim Aydın Son Supervisor, Health Informatics, METU _____________________ Examining Committee Members: Assoc. Prof. Dr. Tolga Can _____________________ METU, CENG Assist. Prof. Dr. Yeşim Aydın Son _____________________ METU, Health Informatics Assist. Prof. Dr. Aybar Can Acar _____________________ METU, Health Informatics Assist. Prof. Dr. Özlen Konu _____________________ Bilkent University, Molecular Biology and Genetics Assoc. Prof. Dr. Çağdaş D. Son _____________________ METU, Biology Date: 27.08.2014 I hereby declare that all information in this document has been obtained and presented in accordance with academic rules and ethical conduct. I also declare that, as required by these rules and conduct, I have fully cited and referenced all material and results that are not original to this work. Name, Last name : Burcu Yaldız Signature : iii ABSTRACT INVESTIGATION OF STRUCTURAL PROPERTIES OF METHYLATED HUMAN PROMOTER REGIONS IN TERMS OF DNA HELICAL RISE Yaldız, Burcu M.Sc. Bioinformatics Program Advisor: Assist. Prof. Dr. Yeşim Aydın Son August 2014, 60 pages The infamous double helix structure of DNA was assumed to be a rigid, uniformly observed structure throughout the genomic DNA. However, the differences in physical structure of DNA in terms of local helical parameters such as twist, tilt, roll, rise and angles between adjacent base pairs in B-DNA molecule have been shown in many studies. This observed flexibility satisfies the known physical and chemical properties of DNA while providing a better model to explain how DNA fulfills its biological functions. While the relation between human promoters’ methylation status and gene expression profiles in certain cancer types has been established in various studies, the structural properties of methylated promoters were rarely investigated. In this study our goal is to investigate the structural differences between human promoters due to methylation status and gene expression profiles in terms of sequence dependent DNA helical rise. The resulting structural differences have the potential to facilitate further studies to predict the methylation status of human promoters across the whole genome for the investigation of clinically relevant biomarkers in cancer. Keywords: Promoter methylation, nucleosome occupancy, gene silencing, helical rise, DNA structure iv ÖZ METİLASYON GÖSTEREN İNSAN PROMOTÖR BÖLGELERİNİN YAPISININ DNA HELİKSEL YÜKSEKLİĞİ AÇISINDAN İNCELENMESİ Yaldız, Burcu Yüksek Lisans, Biyoenformatik Programı Tez Danışmanı: Yrd. Doç. Dr. Yeşim Aydın Son Ağustos 2014, 60 sayfa DNA’nın çift sarmal yapısının, genom boyunca homojen olduğu kabul edilmekteydi. Ancak, pek çok çalışmada, DNA’nın fiziksel yapısında, burkulmalar, eğilmeler, kaymalar ve açılmalar gibi lokal sarmal parametrelere ve komşu baz çiftleri arasındaki açılara dayalı değişiklikler olduğu gösterilmiştir. Bu durum, DNA’nın biyolojik fonksiyonlarını nasıl yerine getirdiğini açıklayacak daha iyi bir model sunarken, DNA’nın bilinen fiziksel ve kimyasal özelliklerini de sağlar. Pek çok çalışmada, bazı kanser türlerinde insan promotörlerinin metilasyon durumlarıyla gen ekspresyonu profilleri arasındaki ilişki gösterilmiş olmasına karşın metillenmiş promotörlerin yapısal özelliklerini inceleyen çalışmalara sık rastlanmamaktadır. Bu çalışmada bizim amacımız, insan promotörlerinin, metilasyon durumlarına ve gen ekspresyon profillerine göre sekansa bağlı DNA heliksel açıklığı açısından yapısal farklılıklarını incelemektir. Elde edilen yapısal farklılıkların, genom boyunca insan promotörlerinin metilasyon durumlarını öngören klinik açıdan önemli biyo- belirteçler elde edilmesini sağlayacak diğer çalışmalarda kullanılma potansiyeli vardır. Anahtar Kelimeler: Promotör metilasyonu, nükleozom yerleşimi, heliksel yükseklik, gen susturma, DNA yapısı v To my family vi ACKNOWLEDGEMENTS First of all I would like to express my deepest gratitude to my supervisor Assist. Prof. Dr. Yeşim Aydın Son for her guidance, patience and encouragement. She has supported and guided me throughout the programme and my research. Also, she has become a wonderful model for me as an academician and a scientist with her immense knowledge, the importance given to her job, personality, kindness and sincerity. I think I am very lucky to have had such a supervisor in my first step to my academic career. I would like to thank Assoc. Prof. Dr. Vilda Purutçuoğlu for her recommendations on the choice of statistical methods. I would like to thank to Assoc. Prof. Dr. Tolga Can, Assist. Prof. Dr. Aybar Can Acar, Assoc. Prof. Dr. Çağdaş D. Son and Assist. Prof. Dr. Özlen Konu for reviewing my work. I am grateful to Gökçe Oğuz and Zelha Nil for their support, encouragement, and valuable friendship. I also thank to my friends Güngör Budak, Özlem Özkan, Bilge Sürün, Onur Erdoğan, Dr. Cengizhan Açıkel and Alper Döm for their contributions and suggestions. I would like to thank to Informatics Institute members Sibel Gülnar and Hakan Güler for their support. I would like to thank Özlem Özmen for her editorial contributions and for her friendship during the summer periods. My sister Feruze Birer has been always with me and supported me during my whole life. I cannot thank enough to her for her priceless friendship. Also, special thanks to my dear friend Taylan Kutlu for being in my life with his endless support, encouragement and precious friendship. I would like to thank to my brother Özgür Yaldız, my aunts and best friends Ümit Çağlar and Buket Çağlar, my grandmother Mürüvvet Çağlar, my uncle Alp, his wife Esra and cousins Ece and Arda Çağlar for their endless support and love. Last but not least, special thanks to my mother Çiğdem Yaldız and my father Kadir Yaldız for their endless support, love, trust and patience in every step of my life. vii TABLE OF CONTENTS ABSTRACT ...................................................................................................... iv ÖZ ....................................................................................................................... v ACKNOWLEDGEMENTS ............................................................................. vii TABLE OF CONTENTS ................................................................................ viii LIST OF TABLES ............................................................................................ xi LIST OF FIGURES .......................................................................................... xii CHAPTER 1. INTRODUCTION ......................................................................................... 1 1.1 Motivation ............................................................................................... 1 1.2 Goal ......................................................................................................... 2 1.3 Contributions .......................................................................................... 2 2. BACKGROUND AND LITERATURE REVIEW ....................................... 3 2.1 DNA Structure ........................................................................................ 3 2.1.1 Double Helix Structure .................................................................... 3 2.1.2 Different Forms of Double Helix Structure ..................................... 3 2.1.3 Local Helical Parameters ................................................................ 4 2.1.4 Chromatin Structure......................................................................... 8 2.2 Gene Structure ........................................................................................ 9 2.3 Gene Expression Profile and Nucleosome Positioning ........................ 10 2.4 Nucleosome Occupancy and Helical Rise ............................................ 10 viii 2.5 Epigenetics............................................................................................ 11 2.5.1 DNA Methylation ........................................................................... 11 2.5.1.1 Genomic Imprinting ............................................................... 12 2.5.1.2 Methylation of Promoter CpGs .............................................. 12 2.5.2 Histone Modifications ................................................................... 13 2.6 DNA Methylation and Nucleosome Occupancy .................................. 15 3. MATERIALS AND METHODS ................................................................ 17 3.1 Data ....................................................................................................... 17 3.2 Analysis ................................................................................................ 19 3.2.1 Preparation of the data for the analysis ........................................ 19 3.2.2