Epigenetics, Second Edition - Cold Spring Harbor Lab Press

1 EPIGENETICSS econd EditionThis is a free sample of content from epigenetics , 2e. Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights TITLES FROM COLD Spring Harbor LABORATORY PRESSM ammalian Development: Networks, Switches, and Morphogenetic ProcessesMolecular Biology of the Gene, Seventh EditionProtein Synthesis and Translational ControlRNA Worlds: From Life s Origins to Diversity in Gene RegulationSignal Transduction: Principles, Pathways, and ProcessesFROMCOLD Spring Harbor PERSPECTIVES IN BIOLOGYGliaInnate Immunity and InflammationThe Genetics and Biology of Sexual ConflictThe Origin and Evolution of EukaryotesEndocytosisMitochondriaSignali ng by Receptor Tyrosine KinasesDNA Repair, Mutagenesis, and Other Responses to DNA DamageCell Survival and Cell DeathImmune ToleranceDNA ReplicationEndoplasmic ReticulumWnt SignalingProtein Synthesis and Translational ControlThe SynapseExtracellular Matrix BiologyProtein HomeostasisCalcium SignalingThe GolgiGerm CellsThe Mammary Gland as an Experimental ModelThe Biology of Lipids: Trafficking, Regulation, and FunctionThis is a free sample of content from epigenetics , 2e.

2 Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights EditionEDITORSC. David AllisMarie-Laure CaparrosThe Rockefeller University, New YorkLondonThomas JenuweinDanny ReinbergMax Planck Institute of Immunobiologyand epigenetics , FreiburgHoward Hughes Medical InstituteNew York University School of Medicine-SmilowResearch CenterASSOCIATEEDITORM onika LachnerMax Planck Institute of Immunobiology and epigenetics , FreiburgCOLD Spring Harbor LABORATORY PRESSCold Spring Harbor , New York is a free sample of content from epigenetics , 2e. Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights , Second EditionChapters online at rights reserved#2015 by Cold Spring Harbor Laboratory Press , Cold Spring Harbor , New YorkPrinted in IndiaPublisherJohn InglisDirector of Editorial DevelopmentJan ArgentineProject ManagerInez SialianoPermissions CoordinatorCarol BrownProduction EditorKathleen BubbeoProduction ManagerDenise WeissCover DesignerMichael AlbanoFront cover artwork: Depicted is a schematic representation of the chromatin template.

3 Epigenetic regula-tion affects and modulates this template through noncoding RNAs (ncRNAs) that associate with it, throughcovalent modification of histone tails (mod), methylation of DNA (Me), remodeling factors (blue oval),and nucleosomes that contain standard as well as variant histone proteins (the yellow nucleosome). In thebackground is a representation of several model organisms in which epigenetic control has been lefttobottom right: Pair of mouse chromosomes that may differ in their genomic imprint; aSaccha-romyces cerevisiaecolony, showing epigenetically inherited variegation of gene expression; anatomy ofCaenorhabditis elegans; illustration ofTetrahymena thermophila, showing the large active macronucleusand the smaller silent micronucleus;Drosophila melanogaster; maize section with kernel color variega-tion; of Congress Cataloging-in-Publication DataEpigenetics (Allis) epigenetics /edited by C.

4 David Allis, Marie-Laure Caparros, ThomasJenuwein, Danny Reinberg ; associate editor, Monica Lachner. bibliographical references and 978-1-936113-59-0 (hardcover)I. Allis, C. David, editor. II. Caparros, Marie-Laure, editor. III. Jenuwein, Thomas, editor. IV. Reinberg, Danny,editor. V. Title.[DNLM: 1. Epigenesis, Genetic. 2. Gene Expression Regulation. QU 475] 65--dc23201402947410987654321 All World Wide Web addresses are accurate to the best of our knowledge at the time of to photocopy items for internal or personal use, or the internal or personal use of specific clients,is granted by Cold Spring Harbor Laboratory Press , provided that the appropriate fee is paid directly to the Copy-right Clearance Center (CCC). Write or call CCC at 222 Rosewood Drive, Danvers, MA 01923 (978-750-8400)for information about fees and regulations.

5 Prior to photocopying items for educational classroom use, contactCCC at the above address. Additional information on CCC can be obtained at CCC Online a complete catalog of all Cold Spring Harbor Laboratory Press publications, visit our website is a free sample of content from epigenetics , 2e. Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights before epigenetics changed from little more than a diverse collection of bizarre phenomena to awell-respected field covered by its own textbook, a talented group of foresighted molecular biologistslaid a rich foundation upon which the modern era of chromatin biology and epigenetics is group includes Vince Allfrey, Wolfram Ho rz, Robert Simpson, Hal Weintraub, Jonathan Widom,Alan Wolffe, and Abe Worcel.

6 This book is dedicated to their collective memory. Their passion and com-mitment to the study of chromatin biology inspired all of us who followed their work, and we now benefitfrom their many is a free sample of content from epigenetics , 2e. Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights is a free sample of content from epigenetics , 2e. Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights , ixAcknowledgments, xiii1A Brief History of epigenetics , 1 Gary Felsenfeld2 The Next Generation: Young Scientists Forging ExcitingNew Discoveries in Epigenetic Research, 11 The Discovery of Histone Demethylases, 13 Yujiang Geno Shi and Yu-ichi TsukadaCellular Reprogramming, 16 Kazutoshi TakahashiIncRNAs: Linking RNA to Chromatin, 18 John L.

7 RinnEnhancer RNAs: A Class of Long Noncoding RNAsSynthesized at Enhancers, 21 Tae-Kyung Kim, Martin Hemberg, and Jesse M. GrayExpanding the Epigenetic Landscape: NovelModifications of Cytosine in Genomic DNA, 24 Skirmantas Kriaucionis and Mamta TahilianiPlant Mobile Small RNAs, 27 Patrice Dunoyer, Charles Melnyk, Attila Molnar, andR. Keith SlotkinCpG Island Chromatin Is Shaped by Recruitment ofZF-CxxC Proteins, 30 Neil P. Blackledge, John P. Thomson, and Peter J. SkeneBromodomain and Extraterminal Domain Inhibitors(BETi) for Cancer Therapy: Chemical Modulation ofChromatin Structure, 33 Jun QiPharmacological Inhibition of Bromodomain-Containing Proteins in Inflammation, 36 Uwe SchaeferHistone H3 Mutations in Pediatric Brain Tumors, 40 Xiaoyang Liu, Troy A. McEachron, JeremySchwartzentruber, and Gang WuChromosome Folding: Driver or Passenger ofEpigenetic State?

8 , 44 Tom Sexton and Eitan Yaffe3 Overview and Concepts, 47C. David Allis, Marie-Laure Caparros, Thomas Jenuwein,Monika Lachner, and Danny Reinberg4 Writers and Readers of Histone Acetylation: Structure,Mechanism, and Inhibition, 117 Ronen Marmorstein and Ming-Ming Zhou5 Erasers of Histone Acetylation: The Histone DeacetylaseEnzymes, 143 Edward Seto and Minoru Yoshida6 Structural and Functional Coordination of DNA andHistone Methylation, 169 Xiaodong Cheng7A Structural Perspective on Readout of EpigeneticHistone and DNA Methylation Marks, 193 Dinshaw J. Patel8 epigenetics inSaccharomyces cerevisiae, 241 Michael Grunstein and Susan M. Gasser9 Epigenetic Regulation of Chromatin States inSchizosaccharomyces pombe, 269 Robin C. Allshire and Karl Ekwall10 Neurospora crassa,a Model System for EpigeneticsResearch, 295 Rodolfo Aramayo and Eric U.

9 Selker11 epigenetics of Ciliates, 313 Douglas L. Chalker, Eric Meyer, and Kazufumi Mochizuki12 Position-Effect Variegation, HeterochromatinFormation,and Gene Silencing inDrosophila, 337 Sarah Elgin and Gunter Reuter13 Epigenetic Regulation in Plants, 363 Craig S. Pikaard and Ortrun Mittelsten ScheidviiThis is a free sample of content from epigenetics , 2e. Click here for more information on how to buy the book. 2015 by Cold Spring Harbor Laboratory Press . All rights Use of Mouse Models to Study epigenetics , 395 Marnie Blewitt and Emma Whitelaw15 DNA Methylation in Mammals, 423En Li and Yi Zhang16 RNAi and Heterochromatin Assembly, 445 Robert Martienssen and Danesh Moazed17 Transcriptional Silencing byPolycomb-Group Proteins,463 Ueli Grossniklaus and Renato Paro18 Transcriptional Regulation by Trithorax-GroupProteins, 489 Robert E.

10 Kingston and John W. Tamkun19 Long-Range Chromatin Interactions, 507 Job Dekker and Tom Misteli20 Histone Variants and epigenetics , 529 Steven Henikoff and M. Mitchell Smith21 Nucleosome Remodeling and epigenetics , 555 Peter B. Becker and Jerry L. Workman22 Maintenance of Epigenetic Information, 575 Genevie`ve Almouzni and Howard Cedar23 Regulation of the X Chromosomes inCaenorhabditiselegans, 599 Susan Strome, William G. Kelly, Sevinc Ercan,and Jason D. Lieb24 Dosage Compensation inDrosophila, 621 John C. Lucchesi and Mitzi I. Kuroda25 Dosage Compensation in Mammals, 641 Neil Brockdorff and Bryan M. Turner26 Genomic Imprinting in Mammals, 667 Denise P. Barlow and Marisa S. Bartolomei27 Germline and Pluripotent Stem Cells, 687 Wolf Reik and M. Azim Surani28 Induced Pluripotency and EpigeneticReprogramming, 711 Konrad Hochedlinger and Rudolf Jaenisch29 Epigenetic Control of Immunity, 737 Meinrad Busslinger and Alexander Tarakhovsky30 Metabolic Signaling to Chromatin, 763 Shelley L.