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.
Author(s): C. David Allis (editor), Marie-Laure Caparros (editor), Thomas Jenuwein (editor), Danny Reinberg (editor)
Edition: 2
Publisher: Cold Spring Harbor Laboratory Press
Year: 2015
Language: English
Pages: 984
Tags: epigenetics
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
