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21st Century Genetics: Genes at Work

(Cold Spring Harbor Symposia on Quantitative Biology LXXX)

Subject Area(s):  Gene TherapyGeneticsMicrobiology

Edited by Terri Grodzicker, Cold Spring Harbor Laboratory; David Stewart, Cold Spring Harbor Laboratory; Bruce Stillman, Cold Spring Harbor Laboratory

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Sample Conversation with Jennifer Doudna
Sample Conversation with Job Dekker

© 2016 • 361 pages, illustrated (107 color, 98 B&W), index
Hardcover •
ISBN  978-1-621821-47-2

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The 80th Cold Spring Harbor Symposium was held to mark the 150th anniversary of Gregor Mendel’s landmark 1865 presentation of his paper “Experiments on Plant Hybridization”, which laid the groundwork for modern genetics. The Symposium Proceedings addresses 21st Century Genetics: Genes at Work, and provides a current synthesis of genetic mechanisms and genome/chromosome biology. This volume spans a broad range of topics that reflect our current understanding of genetic mechanisms in humans and other organisms. Themes include chromosome biology and nuclear structure, topologically associating domains, gene-enhancer interactions, chromatin and epigenetics, gene regulation and control, developmental regulation, RNA controlling elements, maintenance of genome stability, nuclear receptors, circadian clocks and aging, and genome editing. The Conversations included in this volume are based on interviews conducted during the Symposium and offer a broader anecdotal perspective on this fascinating subject by many of the world’s leading investigators.


Symposium Participants
Gene Control

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

Regulatory Domains and Their Mechanisms
Nezha S. Benabdallah and
 Wendy A. Bickmore
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
Prenucleosomes and Active Chromatin
Mai T. Khuong, Jia Fei, Haruhiko Ishii, and James T. Kadonaga
HIPMap: A High-Throughput Imaging Method for Mapping Spatial Gene Positions
Sigal Shachar, Gianluca Pegoraro, and Tom Misteli
Genome Organization and Chromosome Architecture
Giorgio Bernardi
Genome Stability

A System to Study Aneuploidy In Vivo
Sarah J. Pfau and Angelika Amon
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
21st Century Genetics: Mass Spectrometry of Yeast Telomerase
Kah Wai Lin and Virginia A. Zakian
From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer Genomes
Cheng-Zhong Zhang and David Pellman
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
Germ Cells and Early Development

Mechanism and Reconstitution In Vitro of Germ Cell Development in Mammals
Kazuki Kurimoto and Mitinori Saitou
Erase-Maintain-Establish: Natural Reprogramming of the Mammalian Epigenome
Milena Leseva, Barbara B. Knowles, Daniel M. Messerschmidt, and Davor Solter
Regulation of Reprogramming and Cellular Plasticity through Histone Exchange and Histone Variant Incorporation
Xavier Gaume and Maria-Elena Torres-Padilla
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
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
Monitoring Dynamics of DNA Methylation at Single-Cell Resolution during Development and Disease
Yonatan Stelzer and Rudolf Jaenisch
Perturbing Chromatin Structure to Understand Mechanisms of Gene Expression
Caroline R. Bartman and Gerd A. Blobel
Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers
Verena M. Link, David Gosselin, and Christopher K. Glass
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
Dissecting the Rev-erbα Cistrome and the Mechanisms Controlling Circadian Transcription in Liver
Bin Fang and Mitchell A. Lazar
Modulating the Genomic Programming of Adipocytes
Anne Loft, Søren Fisker Schmidt, and Susanne Mandrup
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
Regulation of RORγt in Inflammatory Lymphoid Cell Differentiation
Wendy Huang and Dan R. Littman

How Transcription Networks Evolve and Produce Biological Novelty
Isabel Nocedal and Alexander D. Johnson
The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane
Itamar Harel and Anne Brunet
Transposable Elements, Polydactyl Proteins, and the Genesis of Human-Specific Transcription Networks
Didier Trono
Dorcas Cummings Lecture

Svante Pääbo
Conversations at the Symposium

Geneviève Almouzni

Angelika Amon

Julius Brennecke

Emmanuelle Charpentier

Job Dekker

Titia de Lange

Jennifer Doudna

Denis Duboule

Ron Evans

Anne Ferguson-Smith

Edith Heard

David Kingsley

Arnold Levine

Susan Lindquist

Dan Littman

Richard Morimoto

David Page

Wolf Reik

Bing Ren

Ueli Schibler

Davor Solter

Alexander Tarakhovsky

Joanna Wysocka

Rick Young
Author Index
Subject Index