METHYLATION - FROM DNA, RNA AND HISTONES TO DISEASES AND TREATMENT Edited by Anica Dricu Methylation - From DNA, RNA and Histones to Diseases and Treatment http://dx.doi.org/10.5772/2932 Edited by Anica Dricu Contributors Anica Dricu, Dmitri Nikitin, Attila Kertesz-Farkas2, Alexander Solonin, Marina Mokrishcheva, Hirokazu Suzuki, Robert Peter Mason, Mark Brown, Xian Wang, Hongchuan Jin, Elena Kubareva, Alexandra Ryazanova, Liudmila Abrosimova, Tatiana Oretskaya, Zvonko Magic, Gordana Supic, Nebojsa Jovic, Mirjana Brankovic-Magic, Jianrong Li, Rita Castro, Byron Baron Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2013 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. 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Publishing Process Manager Iva Simcic Technical Editor InTech DTP team Cover InTech Design team First published February, 2013 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com Methylation - From DNA, RNA and Histones to Diseases and Treatment , Edited by Anica Dricu p. cm. ISBN 978-953-51-0881-8 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface VII Section 1 Gene Expression and Methylation 1 Chapter 1 Breaking the Silence: The Interplay Between Transcription Factors and DNA Methylation 3 Byron Baron Section 2 DNA-Methyltransferases: Structure and Function in Eukaryotic and Prokaryotic System 27 Chapter 2 Diverse Domains of (Cytosine-5)-DNA Methyltransferases: Structural and Functional Characterization 29 A. Yu. Ryazanova, L. A. Abrosimova, T. S. Oretskaya and E. A. Kubareva Chapter 3 Bifunctional Prokaryotic DNA-Methyltransferases 71 Dmitry V. Nikitin, Attila Kertesz-Farkas, Alexander S. Solonin and Marina L. Mokrishcheva Section 3 Protein Arginine Methylation in Mammals 89 Chapter 4 Deciphering Protein Arginine Methylation in Mammals 91 Ruben Esse, Paula Leandro, Isabel Rivera, Isabel Tavares de Almeida, Henk J Blom and Rita Castro Section 4 Cancer Research Through Study of Methylation Cell Processes 117 Chapter 5 Methylation in Tumorigenesis 119 Melissa A. Edwards, Pashayar P. Lookian, Drew R. Neavin and Mark A. Brown Chapter 6 Circulating Methylated DNA as Biomarkers for Cancer Detection 137 Hongchuan Jin, Yanning Ma, Qi Shen and Xian Wang Chapter 7 DNA Methylation, Stem Cells and Cancer 153 Anica Dricu, Stefana Oana Purcaru, Alice Sandra Buteica, Daniela Elise Tache, Oana Daianu, Bogdan Stoleru, Amelia Mihaela Dobrescu, Tiberiu Daianu and Ligia Gabriela Tataranu Chapter 8 DNA Methylation in the Pathogenesis of Head and Neck Cancer 185 Zvonko Magić, Gordana Supić, Mirjana Branković-Magić and Nebojša Jović Section 5 Bacteria, Viruses and Metals Methylation: Risk and Benefit for Human Health 217 Chapter 9 Host-Mimicking Strategies in DNA Methylation for Improved Bacterial Transformation 219 Hirokazu Suzuki Chapter 10 Messenger RNA Cap Methylation in Vesicular Stomatitis Virus, a Prototype of Non‐Segmented Negative‐Sense RNA Virus 237 Jianrong Li and Yu Zhang Chapter 11 The Methylation of Metals and Metalloids in Aquatic Systems 271 Robert P. Mason ContentsVI Preface There is a widespread interest in the today scientific literature for methylation field, which started to be published in the early 60’s and continues to be a future line of research. This book represents a comprehensively reviewed literature on the importance of methylation processes in human health and disease. The book, covers the basic mechanism of DNA and protein methylation, along with the role of mRNA cap methylation in viral replication, gene expression and viral pathogenesis. Human health risks from metals methylation in the natu‐ ral environment has been well describe in the literature. As a consequence, the formation processes, the biotic and abiotic degradation and the accumulation of the methylated metals and metalloids in the aquatic environment is reviwed in the book. DNA methylation is a well-characterized process, allowing cells to control gene expression, while the study of histone methylation is more recent. The enzymes responsible for histone methylation (histone methyltransferases and histone demethylases) are important for tran‐ scriptional regulation in both normal and abnormal states, representing an important target for drug discovery. The interconection between DNA methylation and other regulatory mol‐ ecules such as: enzymes, transcription factors, proteins and growth factors is discussed, pro‐ viding key information about the mechanisms that trigger cell proliferation, differentiation, aging and malignant transformation. This textbook strongly point out the importance of me‐ thylated DNA as a biological marker of cancer an also gives the reader insights into the re‐ cently emerged treatment modalities targeting methylation mechanism, in various diseases including cancer. The textbook addresses the following topics: Gene expression and methylation, DNA-meth‐ yltransferases: structure and function in eukaryotic and prokaryotic system; Protein arginine methylation in mammals; Cancer research through study of methylation cell processes; Bac‐ teria, viruses and metals methylation: risk and benefit for human health. The book aims at the advanced undergraduate and graduate biomedical students and re‐ searchers working in the epigenetic area, providing readers with both classical and relevant recent discoveries that have been made in the research field of methylation and also point‐ ing out pathways where questions remain. Prof. Anica Dricu University of Medicine and Pharmacy Faculty of Medicine Craiova, Romania Section 1 Gene Expression and Methylation [...]... appa‐ rently by interfering with the formation of the transcriptional initiation complex [187] 9 10 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment GABP is a methylation- sensitive transcription factor [110] and its modulation is best seen in the transactivation of the Cyp2d-9 promoter for the male-specific steroid 16a-hydroxylase... and malignant peripheral nerve sheath tumours, Genome Res 2011: 21, 51 5-5 24 [85] Ogoshi K, Hashimoto S, Nakatani Y, Qu W, Oshima K, Tokunaga K, Sugano S, Hat‐ tori M, Morishita S, Matsushima K Genome-wide profiling of DNA methylation in human cancer cells, Genomics 2011: 98, 28 0-2 87 17 18 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment. .. genes such as ER, IGF2, N33 and MyoD in colon cancer, NKX 2-5 in prostate cancer and several Polycomb-group protein target genes, which suggests they probably have common epigenetic mechanisms driving them [6 8-7 0] 5 6 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment 3 Methylation in carcinogenesis DNA methylation can either affects... zygote Curr Biol 2000: 10, 475–478 [59] Howlett SK, Reik W Methylation levels of maternal and paternal genomes during preimplantation development Development 1991: 113, 11 9-1 27 15 16 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment [60] Carlson LL, Page AW, Bestor TH Properties and localization of DNA methyltrans‐ ferase in preimplantation... directed to the nucleus where they affect transcription by binding to activation sites in the promoters of indu‐ 7 8 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment cible genes and interacting with transcription initiation factors They can be activated either di‐ rectly by tyrosine or serine kinases at the cell surface or by complex... island hypermethylation and tumour suppressor genes: a booming present, a brighter future Oncogene 2002: 21, 5427–5440 [5] Berdasco M, Esteller M Aberrant epigenetic landscape in cancer: how cellular identi‐ ty goes awry, Dev Cell 2010: 19, 69 8-7 11 11 12 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment [6] Yoder JA, Walsh CP, Bestor... Overlapping and CpG methylation- sensitive protein–DNA interactions at the histone H4 transcriptional cell cycle domain: distinctions between two human H4 gene promoters Mol Cell Biol 1992: 12, 3273–3287 19 20 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment [113] List HJ, Patzel V, Zeidler U, Schopen A, Ruhl G, Stollwerk J, Klock G Methylation. .. unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited 4 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment DNA methylation generally occurs when a cytosine is adjacent 5’ to a guanine, called a CpG di‐ nucleotide Such dinucleotides are spread all over the genome and over 70% of CpGs are... DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment [194] Juttermann R, Li E, Jaenisch R Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation Proc Natl Acad Sci USA 1994: 91, 11797–11801 [195] Wallace RE, Lindh D, Durr FE Arabinofuranosyl- 5- azacytosine:... Wada T, Handa H Transcription factor E4TF1 contains two subunits with different functions EMBO J 1990: 9, 841– 847 [167] Thompson CC, Brown TA, McKnight SL Convergence of Ets and notch-related structural motifs in a heteromeric DNA binding complex Science 1991: 253, 762– 768 23 24 Methylation - From DNA, RNA and Histones to Diseases and Treatment From DNA, RNA and Histones to Diseases and Treatment . METHYLATION - FROM DNA, RNA AND HISTONES TO DISEASES AND TREATMENT Edited by Anica Dricu Methylation - From DNA, RNA and Histones to Diseases and Treatment http://dx.doi.org/10.5772/2932 Edited. proliferation and differentiation Methylation - From DNA, RNA and Histones to Diseases and Treatment8 Methylation - From DNA, RNA and Histones to Diseases and Treatment [14 2-1 45],