Specific Gene Expression and Epigenetics The Interplay Between the Genome and Its Environment

This title includes a number of Open Access chapters. This new volume on gene expression and epigenetics discusses environmental effects related to specific gene expression. The book also shows methods for bioinformatic analysis of the epigenome. The book is broken into two sections: the first looks at eukaryotic DNA methylation and the second addresses how to integrate genomic medicine into clinical practice. The book includes chapters on these topics: • Gene expression in colon cancer tissue • Epigenetics in human acute kidney injury • Embryologically relevant candidate genes in MRKH patients • DNA methylation in common skeletal disorders • Causal relationships in genomics • Predicting severe asthma exacerbations in children • Epigenetic understanding of gene-environment interactions in psychiatric disorders

Introduction Part I: Eukaryotic DNA Methylation Renal Kallikrein Excretion and Epigenetics in Human Acute Kidney Injury: Expression, Mechanisms and Consequences; Sun Woo Kang, Pei-an Betty Shih, Roy O. Mathew, Manjula Mahata, Nilima Biswas, Fangwen Rao, Liying Yan, Josee Bouchard, Rakesh Malhotra, Ashita Tolwani, Srikrishna Khandrika, Ravindra L. Mehta, and Daniel T. O’Connor COX-2 Gene Expression in Colon Cancer Tissue Related to Regulating Factors and Promoter Methylation Status; Annika Gustafsson Asting, Helena Carén, Marianne Andersson, Christina Lönnroth, Kristina Lagerstedt, and Kent Lundholm Down-Regulation of Promoter Methylation Level of CD4 Gene After MDV Infection in MD-Susceptible Chicken Line; Juan Luo, Ying Yu, Huanmin Zhang, Fei Tian, Shuang Chang, Hans H. Cheng, and Jiuzhou Song A Combination of Transcriptome and Methylation Analyses Reveals Embryologically Relevant Candidate Genes in MRKH Patients; Katharina Rall, Gianmaria Barresi, Michael Walter, Sven Poths, Karina Haebig, Karin Schaeferhoff, Birgitt Schoenfisch, Olaf Riess, Diethelm Wallwiener, Michael Bonin, and Sara Brucker The Role of DNA Methylation in Common Skeletal Disorders; Jesús Delgado-Calle and José A. Riancho Enrichment-Based DNA Methylation Analysis Using Next-Generation Sequencing: Sample Exclusion, Estimating Changes in Global Methylation, and the Contribution of Replicate Lanes; Michael P. Trimarchi, Mark Murphy, David Frankhouser, Benjamin A. T. Rodriguez, John Curfman, Guido Marcucci, Pearlly Yan, and Ralf Bundschuh Part II: Integrating Genomic Medicine into the Clinical Practice Assessing Causal Relationships in Genomics: From Bradford-Hill Criteria to Complex Gene-Environment Interactions and Directed Acyclic Graphs; Sara Geneletti, Valentina Gallo, Miquel Porta, Muin J. Khoury, and Paolo Vineis Genome Wide Association Study to Predict Severe Asthma Exacerbations in Children Using Random Forests Classifiers; Mousheng Xu, Kelan G. Tantisira, Ann Wu, Augusto A. Litonjua, Jen-hwa Chu, Blanca E. Himes, Amy Damask, and Scott T. Weiss Potential Utility of Natural Products as Regulators of Breast Cancer-Associated Aromatase Promoters; Shabana I. Khan, Jianping Zhao, Ikhlas A. Khan, Larry A. Walker, and Asok K. Dasmahapatra Therapeutic Potential of Cladribine in Combination with STAT3 Inhibitor Against Multiple Myeloma; Jian Ma, Shuiliang Wang, Ming Zhao, Xin-Sheng Deng, Choon-Kee Lee, Xiao-Dan Yu, and Bolin Liu Epigenetic Understanding of Gene-Environment Interactions in Psychiatric Disorders: A New Concept of Clinical Genetics; Takeo Kubota, Kunio Miyake, and Takae Hirasawa An Imprinted Rheumatoid Arthritis Methylome Signature Reflects Pathogenic Phenotype; John W. Whitaker, Robert Shoemaker, David L. Boyle, Josh Hillman, David Anderson, Wei Wang, and Gary S. Firestein Index

Kasirajan Ayyanathan, PhD, received his PhD from the Department of Biochemistry, Indian Institute of Science. Subsequently, at Temple University School of Medicine, Philadelphia, Pennsylvania, USA, he conducted post-doctoral research on the signal transduction by purinergic receptors, a class of G-Protein Coupled Receptors (GPCR), in erythroleukemia cancer cells. Next, he was trained as a staff scientist at the Wistar Institute, Philadelphia, for almost ten years and studied transcription regulation, chromatin, and epigenetic regulatory mechanisms in cancer. Currently, he is at the Center for Molecular Biology and Biotechnology as a research associate professor at Florida Atlantic University (FAU) in Boca Raton. He is the recipient of the Chern Memorial Award, presented by the Wistar Institute, and Howard Temin Career Research Award, presented by the National Cancer Institute. Dr. Ayyanathan is well trained in molecular biology, cell biology, and biochemistry with a main focus on studying transcription factors and gene regulation. He has contributed to several projects such as the generation of conditional transcriptional repressors that are directed against the endogenous oncogenes to inhibit malignant growth, the establishment of stable cell lines that express chromatin integrated transcriptional repressors and reporter genes to study the epigenetic mechanisms of KRAB repression, and identification of novel SNAG repression domain interacting proteins to understand their roles in transcriptional repression and oncogenesis. Dr. Ayyanathan has published several research articles in peer-reviewed journals in these subject areas.