21st Century Genetics: Genes at Work

Symposium Participants v Foreword xv

Gene Control

Imaging Transcription: Past, Present, and Future Robert A. Coleman, Zhe Liu, Xavier Darzacq, Robert Tjian, Robert H. Singer, and Timothe´e Lionnet 1 Visualizing the HoxD Gene Cluster at the Nanoscale Level Pierre J. Fabre, Alexander Benke, Suliana Manley, and Denis Duboule 9 Transcriptional Enhancers: Bridging the Genome and Phenome Bing Ren and Feng Yue 17 Regulatory Principles Governing Tissue Specificity of Developmental Enhancers Emma K. Farley, Katrina M. Olson, and Michael S. Levine 27 The Importance of Controlling Transcription Elongation at Coding and Noncoding RNA Loci Benjamin S. Scruggs and Karen Adelman 33

Chromatin Domains and Nuclear Position

Regulatory Domains and Their Mechanisms Nezha S. Benabdallah and Wendy A. Bickmore 45 Large-Scale Chromatin Structure–Function Relationships during the Cell Cycle and Development: Insights from Replication Timing Vishnu Dileep, Juan Carlos Rivera-Mulia, Jiao Sima, and David M. Gilbert 53 Prenucleosomes and Active Chromatin Mai T. Khuong, Jia Fei, Haruhiko Ishii, and James T. Kadonaga 65 HIPMap: A High-Throughput Imaging Method for Mapping Spatial Gene Positions Sigal Shachar, Gianluca Pegoraro, and Tom Misteli 73 Genome Organization and Chromosome Architecture Giorgio Bernardi 83

Genome Stability

A System to Study Aneuploidy In Vivo Sarah J. Pfau and Angelika Amon 93 Resolution of Recombination Intermediates: Mechanisms and Regulation Stephen C. West, Miguel G. Blanco, Ying Wai Chan, Joao Matos, Shriparna Sarbajna, and Haley D.M. Wyatt 103 21st Century Genetics: Mass Spectrometry of Yeast Telomerase Kah Wai Lin and Virginia A. Zakian 111 From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer Genomes Cheng-Zhong Zhang and David Pellman 117 The Evolution of Tumors in Mice and Humans with Germline p53 Mutations Arnold J. Levine, Chang S. Chan, Crissy Dudgeon, Anna Puzio-Kuter, and Pierre Hainaut 139

Germ Cells and Early Development

Mechanism and Reconstitution In Vitro of Germ Cell Development in Mammals Kazuki Kurimoto and Mitinori Saitou 147 Erase–Maintain–Establish: Natural Reprogramming of the Mammalian Epigenome Milena Leseva, Barbara B. Knowles, Daniel M. Messerschmidt, and Davor Solter 155 Regulation of Reprogramming and Cellular Plasticity through Histone Exchange and Histone Variant Incorporation Xavier Gaume and Maria-Elena Torres-Padilla 165 ZFP57 and the Targeted Maintenance of Postfertilization Genomic Imprints Nozomi Takahashi, Dionne Gray, Ruslan Strogantsev, Angela Noon, Celia Delahaye, William C. Skarnes, Peri H. Tate, and Anne C. Ferguson-Smith 177

Embryonic Stem Cells and Development

Biological Networks Governing the Acquisition, Maintenance, and Dissolution of Pluripotency: Insights from Functional Genomics Approaches Kevin Andrew Uy Gonzales and Huck-Hui Ng 189 Monitoring Dynamics of DNA Methylation at Single-Cell Resolution during Development and Disease Yonatan Stelzer and Rudolf Jaenisch 199 Perturbing Chromatin Structure to Understand Mechanisms of Gene Expression Caroline R. Bartman and Gerd A. Blobel 207 Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers Verena M. Link, David Gosselin, and Christopher K. Glass 213

Metabolism and Signaling

Clock-Talk: Interactions between Central and Peripheral Circadian Oscillators in Mammals Ueli Schibler, Ivana Gotic, Camille Saini, Pascal Gos, Thomas Curie, Yann Emmenegger, Flore Sinturel, Pauline Gosselin, Alan Gerber, Fabienne Fleury-Olela, Gianpaolo Rando, Maud Demarque, and Paul Franken 223 Dissecting the Rev-erba Cistrome and the Mechanisms Controlling Circadian Transcription in Liver Bin Fang and Mitchell A. Lazar 233 Modulating the Genomic Programming of Adipocytes Anne Loft, Søren Fisker Schmidt, and Susanne Mandrup 239 Targeting Transcriptional and Epigenetic Reprogramming in Stromal Cells in Fibrosis and Cancer Nasun Hah, Mara H. Sherman, Ruth T. Yu, Michael Downes, and Ronald M. Evans 249 Regulation of RORgt in Inflammatory Lymphoid Cell Differentiation Wendy Huang and Dan R. Littman 257

Evolution

How Transcription Networks Evolve and Produce Biological Novelty Isabel Nocedal and Alexander D. Johnson 265 The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane Itamar Harel and Anne Brunet 275

Transposable Elements, Polydactyl Proteins, and the Genesis of Human-Specific Transcription

Networks Didier Trono 281 Dorcas Cummings Lecture 289 Svante Pa¨a¨bo 291 Conversations at the Symposium 295 Genevie`ve Almouzni 297 Angelika Amon 299 Julius Brennecke 302 Emmanuelle Charpentier 305 Job Dekker 308 Titia de Lange 311 Jennifer Doudna 314 Denis Duboule 316 Ron Evans 318 Anne Ferguson-Smith 321 Edith Heard 324 David Kingsley 327 Arnold Levine 330 Susan Lindquist 332 Dan Littman 334 Richard Morimoto 336 David Page 338 Wolf Reik 340 Bing Ren 342 Ueli Schibler 344 Davor Solter 346 Alexander Tarakhovsky 348 Joanna Wysocka 351 Rick Young 353 Author Index 355 Subject Index 357