Epigenetics

Description

In many biological processes the regulation of gene expression involves epigenetic mechanisms. In this new edition of Epigenetics, 36 chapters written by experts in the field introduce and explain epigenetic effects from many perspectives. These include the varied molecular mechanisms underpinning epigenetic regulation, discussion of cellular processes that rely on this kind of regulation, and surveys of model organisms in which epigenetic effects have been most studied. The original chapters have all been rewritten and brand new chapters cover topics such as the structure, function, and dynamics of histone-modifying enzymes and histone-interacting proteins. Other chapters address chromatin remodeling, DNA methylation, siRNAs, and gene silencing; X-chromosome inactivation, dosage compensation, and imprinting; and epigenetics in microbes, plants, insects, and mammals. How epigenetic mechanisms act in cell division and cell type specification, and how errors in these pathways contribute to cancer and other human diseases are also considered, along with the importance of epigenetics for induced pluripotency and reprogramming. In addition, new chapters describe the involvement of epigenetic processes in epigenetic inheritance, neuronal development, metabolism and signaling, responses to the environment, and long-range chromatin interactions. A series of short essays highlight important recent discoveries. All the chapters provide conceptual illustrations that help readers understand epigenetic control. The book is thus a benchmark text for advanced undergraduate and graduate courses on gene regulation, as well as an essential resource for scientists interested in this rapidly moving field. Contents Preface Acknowledgments 1 A Brief History of Epigenetics Gary Felsenfeld 2 The Next Generation: Young Scientists Forging Exciting New Discoveries in Epigenetic Research The Discovery of Histone Demethylases Yujiang Geno Shi and Yu-ichi Tsukada Cellular Reprogramming Kazutoshi Takahashi IncRNAs: Linking RNA to Chromatin John L. Rinn Enhancer RNAs: A Class of Long Noncoding RNAs Synthesized at Enhancers Tae-Kyung Kim, Martin Hemberg, and Jesse M. Gray Expanding the Epigenetic Landscape: Novel Modifications of Cytosine in Genomic DNA Skirmantas Kriaucionis and Mamta Tahiliani Plant Mobile Small RNAs Patrice Dunoyer, Charles Melnyk, Attila Molnar, and R. Keith Slotkin CpG Island Chromatin Is Shaped by Recruitment of ZF-CxxC Proteins Neil P. Blackledge, John P. Thomson, and Peter J. Skene Bromodomain and Extraterminal Domain Inhibitors (BETi) for Cancer Therapy: Chemical Modulation of Chromatin Structure Jun Qi Pharmacological Inhibition of Bromodomain-Containing Proteins in Inflammation Uwe Schaefer Histone H3 Mutations in Pediatric Brain Tumors Xiaoyang Liu, Troy A. McEachron, Jeremy Schwartzentruber, and Gang Wu Chromosome Folding: Driver or Passenger of Epigenetic State? Tom Sexton and Eitan Yaffe 3 Overview and Concepts C. David Allis, Marie-Laure Caparros, Thomas Jenuwein, Monika Lachner, and Danny Reinberg 4 Writers and Readers of Histone Acetylation: Structure, Mechanism, and Inhibition Ronen Marmorstein and Ming-Ming Zhou 5 Erasers of Histone Acetylation: The Histone Deacetylase Enzymes Edward Seto and Minoru Yoshida 6 Structural and Functional Coordination of DNA and Histone Methylation Xiaodong Cheng 7 A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks Dinshaw J. Patel 8 Epigenetics in Saccharomyces cerevisiae Michael Grunstein and Susan M. Gasser 9 Epigenetic Regulation of Chromatin States in Schizosaccharomyces pombe Robin C. Allshire and Karl Ekwall 10 Neurospora crassa, a Model System for Epigenetics Research Rodolfo Aramayo and Eric U. Selker 11 Epigenetics of Ciliates Douglas L. Chalker, Eric Meyer, and Kazufumi Mochizuki 12 Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila Sarah C.R. Elgin and Gunter Reuter 13 Epigenetic Regulation in Plants Craig S. Pikaard and Ortrun Mittelsten Scheid 14 The Use of Mouse Models to Study Epigenetics Marnie Blewitt and Emma Whitelaw 15 DNA Methylation in Mammals En Li and Yi Zhang 16 RNAi and Heterochromatin Assembly Robert Martienssen and Danesh Moazed 17 Transcriptional Silencing by Polycomb-Group Proteins Ueli Grossniklaus and Renato Paro 18 Transcriptional Regulation by Trithorax-Group Proteins Robert E. Kingston and John W. Tamkun 19 Long-Range Chromatin Interactions Job Dekker and Tom Misteli 20 Histone Variants and Epigenetics Steven Henikoff and M. Mitchell Smith 21 Nucleosome Remodeling and Epigenetics Peter B. Becker and Jerry L. Workman 22 Maintenance of Epigenetic Information Geneviève Almouzni and Howard Cedar 23 Regulation of the X Chromosomes in Caenorhabditis elegans Susan Strome, William G. Kelly, Sevinc Ercan, and Jason D. Lieb 24 Dosage Compensation in Drosophila John C. Lucchesi and Mitzi I. Kuroda 25 Dosage Compensation in Mammals Neil Brockdorff and Bryan M. Turner 26 Genomic Imprinting in Mammals Denise P. Barlow and Marisa S. Bartolomei 27 Germline and Pluripotent Stem Cells Wolf Reik and M. Azim Surani 28 Induced Pluripotency and Epigenetic Reprogramming Konrad Hochedlinger and Rudolf Jaenisch 29 Epigenetic Control of Immunity Meinrad Busslinger and Alexander Tarakhovsky 30 Metabolic Signaling to Chromatin Shelley L. Berger and Paolo Sassone-Corsi 31 Epigenetic Regulation in Plant Responses to the Environment David C. Baulcombe and Caroline Dean 32 Histone and DNA Modifications as Regulators of Neuronal Development and Function Stavros Lomvardas and Tom Maniatis 33 Epigenetics and Human Disease Huda Y. Zoghbi and Arthur L. Beaudet 34 Epigenetic Determinants of Cancer Stephen B. Baylin and Peter A. Jones 35 Histone Modifications and Cancer James E. Audia and Robert M. Campbell 36 The Necessity of Chromatin: A View in Perspective Vincenzo Pirrotta Appendix 1: WWW Resource Pages Appendix 2: Comprehensive Catolog of Currently Documented Histone Modifications Yinming Zhao and Benjamin A. Garcia Index