Epigenetics

Epigenetic Reprogramming and Genomic Imprinting

Mechanism of Mouse Germ Cell Specification: A Genetic Program Regulating Epigenetic Reprogramming M.A. Surani, K. Ancelin, P. Hajkova, U.C. Lange, B. Payer, P. Western, and M. Saitou 1 Epigenetic Mechanisms in Early Mammalian Development D. Solter, T. Hiiragi, A.V. Evsikov, J. Moyer, W.N. de Vries, A.E. Peaston, and B.B. Knowles 11 Nuclear Cloning, Epigenetic Reprogramming, and Cellular Differentiation R. Jaenisch, K. Hochedlinger, R. Blelloch, Y. Yamada, K. Baldwin, and K. Eggan 19 Chromosome Loops, Insulators, and Histone Methylation: New Insights into Regulation of Imprinting in Clusters W. Reik, A. Murrell, A. Lewis, K. Mitsuya, D. Umlauf, W. Dean, M. Higgins, and R. Feil 29 Genomic Imprinting: Antagonistic Mechanisms in the Germ Line and Early Embryo A.M. Fedoriw, N.I. Engel, and M.S. Bartolomei 39 Drosophila Su(Hw) Regulates an Evolutionarily Conserved Silencer from the Mouse H19 Imprinting Control Region S. Schoenfelder and R. Paro 47 The Air Noncoding RNA: An Imprinted cis-silencing Transcript G. Braidotti, T. Baubec, F. Pauler, C. Seidl, O. Smrzka, S. Stricker, I. Yotova, and D.P. Barlow 55 The (Dual) Origin of Epigenetics D. Haig 67

Chromosome Inactivation

Sex and X-Chromosome-wide Repression in Caenorhabditis elegans B.J. Meyer, P. McDonel, G. Csankovszki, and E. Ralston 71 Targeting Dosage Compensation to the X Chromosome of Drosophila Males H. Oh, X. Bai, Y. Park, J.R. Bone, and M.I. Kuroda 81 Mammalian X-Chromosome Inactivation: An Epigenetics Paradigm E. Heard, J. Chaumeil, O. Masui, and I. Okamoto 89 A Continuity of X-Chromosome Silence from Gamete to Zygote K.D. Huynh and J.T. Lee 103

DNA Methylation

Reading the DNA Methylation Signal A. Bird and D. Macleod 113 Genome Defense and DNA Methylation in Neurospora E.U. Selker 119 Role of De Novo DNA Methyltransferases in Initiation of Genomic Imprinting and X-Chromosome Inactivation M. Kaneda, T. Sado, K. Hata, M. Okano, N. Tsujimoto, E. Li, and H. Sasaki 125 Gene Repression Paradigms in Animal Cells L. Lande-Diner, J. Zhang, T. Hashimshony, A. Goren, I. Keshet, and H. Cedar 131 Control of Development and Transposon Movement by DNA Methylation in Arabidopsis thaliana T. Kakutani, M. Kato, T. Kinoshita, and A. Miura 139 DNA Methylation of the Endogenous PAI Genes in Arabidopsis J. Bender 145 Induced and Natural Epigenetic Variation H. Yi, N.C. Riddle, T.L. Stokes, H.-R. Woo, and E.J. Richards 155

Histone Modification and Nucleosome Structure

Linking Covalent Histone Modifications to Epigenetics: The Rigidity and Plasticity of the Marks Y. Wang, J. Wysocka, J.R. Perlin, L. Leonelli, C.D. Allis, and S.A. Coonrod 161 Steps Toward Understanding the Inheritance of Repressive Methyl-Lysine Marks in Histones D. Reinberg, S. Chuikov, P. Farnham, D. Karachentsev, A. Kirmizis, A. Kuzmichev, R. Margueron, K. Nishioka, T.S. Preissner, K. Sarma, C. Abate-Shen, R. Steward, and A. Vaquero 171 Noncovalent Modification of Chromatin: Different Remodeled Products with Different ATPase Domains H.-Y. Fan, G.J. Narlikar, and R.E. Kingston 183 Acetylation of Yeast Histone H4 Lysine 16: A Switch for Protein Interactions in Heterochromatin and Euchromatin C.B. Millar, S.K. Kurdistani, and M. Grunstein 193 Histone Deposition Proteins: Links between the DNA Replication Machinery and Epigenetic Gene Silencing A.A. Franco and P.D. Kaufman 201 Trilogies of Histone Lysine Methylation as Epigenetic Landmarks of the Eukaryotic Genome M. Lachner, R. Sengupta, G. Schotta, and T. Jenuwein 209 Histone H3 Amino-Terminal Tail Phosphorylation and Acetylation: Synergistic or IndependentTranscriptional Regulatory Marks? C.J. Fry, M.A. Shogren-Knaak, and C.L. Peterson 219 Structural Characterization of Histone H2A Variants S. Chakravarthy, Y. Bao, V.A. Roberts,D. Tremethick, and K. Luger 227

Chromatin Structure and Dynamics

Epigenetics, Histone H3 Variants, and the Inheritance of Chromatin States S. Henikoff, E. McKittrick, and K. Ahmad 235 Chromatin Boundaries and Chromatin Domains G. Felsenfeld, B. Burgess-Beusse, C. Farrell,M. Gaszner, R. Ghirlando, S. Huang, C. Jin, M. Litt, F. Magdinier, V. Mutskov, Y. Nakatani, H. Tagami, A. West, and T. Yusufzai 245 Do Higher-Order Chromatin Structure and Nuclear Reorganization Play a Role in Regulating Hox Gene Expression during Development? W.A. Bickmore, N.L. Mahy, and S. Chambeyron 251 SIR1 and the Origin of Epigenetic States in Saccharomyces cerevisiae L. Pillus and J. Rine 259 Analyzing Heterochromatin Formation Using Chromosome Four of Drosophila melanogaster K.A. Haynes, B.A. Leibovitch, S.H. Rangwala, C. Craig, and S.C.R. Elgin 267 Two Distinct Nucleosome Assembly Pathways: Dependent or Independent of DNA Synthesis Promoted by Histone H3.1 and H3.3 Complexes Y. Nakatani, D. Ray-Gallet, J.-P. Quivy,H. Tagami, and G. Almouzni 273 The Chromatin Accessibility Complex: Chromatin Dynamics through Nucleosome Sliding P.B. Becker 281 Histone H2B Ubiquitylation and Deubiquitylation in Genomic Regulation N.C.T. Emre and S.L. Berger 289

Polycomb and Related Silencing Mechanisms

Polycomb Silencing Mechanisms in Drosophila Y.B. Schwartz, T.G. Khan, G.I. Dellino, and V. Pirrotta 301 Mechanism of Polycomb Group Gene Silencing Y. Zhang, R. Cao, L. Wang, and R.S. Jones 309 Emerging Roles of Polycomb Silencing in X-Inactivation and Stem Cell Maintenance I. Muyrers-Chen, I. Hernández-Muñoz, A.H. Lund, M.E. Valk-Lingbeek, P. van der Stoop, E. Boutsma, B. Tolhuis, S.W.M. Bruggeman, P. Taghavi, E. Verhoeven, D. Hulsman, S. Noback, E. Tanger, H. Theunissen, and M. van Lohuizen 319

Nuclear Organization and Dynamics

The Function of Telomere Clustering in Yeast: The Circe Effect S.M. Gasser, F. Hediger, A. Taddei, F.R. Neumann, and M.R. Gartenberg 327 Genetic Instability in Aging Yeast: A Metastable Hyperrecombinational State M.A. McMurray and D.E. Gottschling 339 Restructuring the Genome in Response to Adaptive Challenge: McClintock’s Bold Conjecture Revisited R.A. Jorgensen 349 Poetry of b1 Paramutation: cis- and trans-Chromatin Communication V.L. Chandler 355

Heterochromatin and Transposon Silencing

RNA Silencing Pathways in Plants A.J. Herr and D.C. Baulcombe 363 Transposons, Tandem Repeats, and the Silencing of Imprinted Genes R. Martienssen, Z. Lippman, B. May, and M. Vaughn 371 Transposon Silencing and Imprint Establishment in Mammalian Germ Cells T.H. Bestor and D. Bourc’his 381 RNA Interference, Heterochromatin, and Centromere Function R.C. Allshire 389 RNA Interference, Transposon Silencing, and Cosuppression in the Caenorhabditis elegans Germ Line: Similarities and Differences V.J.P. Robert, N.L. Vastenhouw, and R.H.A. Plasterk 397

RNA Interference and Related Mechanisms

Plant RNA Interference in Vitro C. Matranga and P.D. Zamore 403 A Conserved microRNA Signal Specifies Leaf Polarity M.C.P. Timmermans, M.T. Juarez, and T.L. Phelps-Durr 409 RNA Interference and Epigenetic Control of Heterochromatin Assembly in Fission Yeast H. Cam and S.I.S. Grewal 419 Regulation of Caenorhabditis elegans RNA Interference by the daf-2 Insulin Stress and Longevity Signaling Pathway D. Wang and G. Ruvkun 429 Interrelationship of RNA Interference and Transcriptional Gene Silencing in Drosophila M. Pal-Bhadra, U. Bhadra, and J.A. Birchler 433 Functional Identification of Cancer-relevant Genes through Large-Scale RNA Interference Screens in Mammalian Cells T.R. Brummelkamp, K. Berns, E.M. Hijmans, J. Mullenders, A. Fabius, M. Heimerikx, A. Velds, R.M. Kerkhoven, M. Madiredjo, R. Bernards, and R.L. Beijersbergen 439

Epigenetic Regulation of Phenotypes

The New Field of Epigenomics: Implications for Cancer and Other Common Disease Research H.T. Bjornsson, H. Cui, D. Gius, M.D. Fallin, and A.P. Feinberg 447 Epigenetic Regulation in the Control of Flowering J. Mylne, T. Greb, C. Lister, and C. Dean 457 Transposons and Tandem Repeats Are Not Involved in the Control of Genomic Imprinting at the MEDEA Locus in Arabidopsis C. Spillane, C. Baroux, J.-M. Escobar-Restrepo, D.R. Page, S. Laoueille, and U. Grossniklaus 465 Toward Molecular Understanding of Polar Overdominance at the Ovine Callipyge Locus M. Georges, C. Charlier, M. Smit, E. Davis, T. Shay, X. Tordoir, H. Takeda, F. Caiment, and N. Cockett 477 Dscam-mediated Self- versus Non-Self-Recognition by Individual Neurons G. Neves and A. Chess 485 Prions of Yeast Are Genes Made of Protein: Amyloids and Enzymes R.B. Wickner, H.K. Edskes, E.D. Ross, M.M. Pierce, F. Shewmaker, U. Baxa, and A. Brachmann 489 A Possible Epigenetic Mechanism for the Persistence of Memory K. Si, S. Lindquist, and E. Kandel 497 An Epigenetic Hypothesis for Human Brain Laterality, Handedness, and Psychosis Development A.J.S. Klar 499 Summary: Epigenetics—from Phenomenon to Field D. Gottschling 521 Author Index 521 Subject Index 523