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Contents

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For Mieko

Preface

The activities associated with the genome center around the readout, processing, maintenance and transfer of the information encoded in the DNA sequence. In eukaryotes, the corresponding processes like gene expression and RNA processing, as well as DNA repair, replication, recombination and genome segregation take place in the environment of the nucleus. It provides a complex dynamic organization that serves to establish two apparently contradicting functions: On the one hand the genome has to be protected from uncontrolled modifications that would compromise its function, and it has to be reliably replicated and segregated during cell division and meiosis. On the other hand it has to be remarkably plastic to allow for a dynamic (re)organization so that the cell is able to adopt different functional states.

To understand how this is accomplished, findings from research in genomics, chromatin, epigenetics and nuclear organization have to be integrated. This need is addressed in the present book by combining complementary and interconnected contributions from renowned experts in these different fields of research. Issues that are directly related to DNA sequence and epigenetic information are discussed in Chapters 1, 2, 4 and 15. Chromatin organization and dynamics are covered from the scale of a single nucleosome to that of whole chromosomes in Chapters 2–6, 8, 9, 15, 17–20. The architecture of the nucleus and its subcompartments are discussed in relation to genome function in Chapters 7–10, 12 and 17. Within this framework, the central genome activities are treated in dedicated chapters for transcription, RNA processing and non-coding RNAs (Chapters 10–14), DNA replication and repair (Chapters 15, 16) as well as genome segregation and recombination during cell division and meiosis (Chapters 18, 19). Finally, using two exemplary cases, protein complex assembly during DNA repair and chromatin folding, it is discussed how quantitative models are applied to describe and predict functional genome features (Chapter 20).

Bringing together results from these different research areas in one book has been a highly rewarding experience for me. It has provided me with new insight on how the genome structure and its nuclear environment are interconnected with its functions, and hopefully the readers of the book will share this view. I am most grateful to all authors for their excellent contributions, and I wish to thank my colleagues from the DKFZ and BioQuant, the members of my laboratory and the editorial staff from Wiley-VCH for their advice and help in preparing this book.

Heidelberg, July 2011

Karsten Rippe

List of Contributors

Geneviève Almouzni

Institut Curie

Research Center

UMR218 CNRS

26 rue d’Ulm

75248 Paris cedex 05

France

Edouard Bertrand

Institut de Génétique Moléculaire de

Montpellier

CNRS UMR 5535

1919, route de Mende

34293 Montpellier Cedex 5

France

François-Michel Boisvert

Wellcome Trust Centre for Gene

Regulation and Expression, College of Life Sciences

University of Dundee

Dundee DD1 5EH

United Kingdom

Peter R. Cook

University of Oxford

Sir William Dunn School of Pathology

South Parks Road

Oxford OX1 3RE

United Kingdom

Armelle Corpet

Institut Curie

Research Center

UMR218 CNRS

26 rue d’Ulm

75248

Paris cedex 05

France

Thomas Cremer

LMU Biozentrum

Department Biology II (Anthropology and Human Genetics)

Grosshadernerstrasse 2

82152

Planegg-Martinsried

Germany

and

Munich Center for Integrated

Protein Science Munich

81377 Munich

Germany

Mekonnen Lemma Dechassa

Howard Hughes Medical Institute and Colorado State University

Department of Biochemistry and Molecular Biology

Fort Collins

CO 80523-1870

USA

Job Dekker

University of Massachusetts Medical School

Program in Gene Function and Expression

Program in Systems Biology

Department of Biochemistry and Molecular Pharmacology

364 Plantation Street

Worcester

MA 01605

USA

Berina Eppink

Erasmus Medical Center

Department of Cell Biology and Genetics

3000 DR Rotterdam

The Netherlands

Jeroen Essers

Erasmus Medical Center

Department of Cell Biology and Genetics

3000 DR Rotterdam

The Netherlands

Katalin Fejes Tóth

California Institute of Technology

1200 E California Blvd, MC 156-29

Pasadena, CA 91125

USA

Kieran Finan

University of Oxford

Sir William Dunn School of Pathology

South Parks Road

Oxford OX1 3RE

United Kingdom

Carina Frauer

Center for Integrated Protein Science

Ludwig Maximilians University Munich

Department of Biology

82152 Planegg-Martinsried

Germany

Ron Hancock

Université Laval

Département de Médecine Moléculaire et Centre de Recherche en Cancérologie

9 rue MacMahon

Québec G1R2J6

Canada

Gregory Hannon

Howard Hughes Medical Institute,

Cold Spring Harbor Laboratory

Watson School of Biological Sciences

1 Bungtown Road

Cold Spring Harbor

NY 11724

USA

Dieter W. Heermann

University of Heidelberg

Institute for Theoretical Physics

Philosophenweg 19

69120 Heidelberg

Germany

and

The Jackson Laboratory

Bar Harbor

ME 04609

USA

Saskia Hutten

Wellcome Trust Centre for Gene

Regulation and Expression, College of Life Sciences

University of Dundee

Dundee DD1 5EH

United Kingdom

Mark Kaganovich

Stanford University School of Medicine

Department of Genetics

Stanford, CA 94305

USA

Roland Kanaar

Erasmus Medical Center

Department of Cell Biology and Genetics

3000 DR Rotterdam

The Netherlands

and

Erasmus Medical Center

Department of Radiation Oncology

3000 DR Rotterdam

The Netherlands

Nancy Kleckner

Harvard University

Department of Molecular and Cellular Biology

Cambridge, MA 02138

USA

Angus I. Lamond

Wellcome Trust Centre for Gene

Regulation and Expression, College of Life Sciences

University of Dundee

Dundee DD1 5EH

United Kingdom

Heinrich Leonhardt

Center for Integrated Protein Science Ludwig Maximilians University Munich

Department of Biology

82152 Planegg-Martinsried

Germany

Gernot Längst

Universität Regensburg

Biochemie III

Universitätsstrasse 31

93053 Regensburg

Germany

Karolin Luger

Howard Hughes Medical Institute and Colorado State University

Department of Biochemistry and Molecular Biology

Fort Collins, CO 80523-1870

USA

Martijn S. Luijsterburg

Department of Toxicogenetics

Leiden University Medical Center

2300 RC Leiden

The Netherlands

and

Karolinska Institutet

Department of Cell and Molecular Biology

17177

Stockholm

Sweden

John F. Marko

Northwestern University

Department of Molecular Biosciences and

Department of Physics and Astronomy

Evanston, IL 60208

USA

John S. Mattick

Institute for Molecular Bioscience

The University of Queensland

Brisbane QLD 4072

Australia

Karl Nightingale

Institute of Biomedical Research

University of Birmingham Medical School

Birmingham B15 2TT

United Kingdom

Karsten Rippe

Deutsches Krebsforschungszentrum (DKFZ) & BioQuant

Research Group Genome Organization and Function

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

Eric C. Schirmer

University of Edinburgh

The Wellcome Trust Centre for Cell Biology

Edinburgh EH9 3JR

United Kingdom

Ute Schmidt

Institut de Génétique Moléculaire de Montpellier

CNRS UMR 5535

1919, route de Mende

34293 Montpellier Cedex 5

France

Michael Snyder

Stanford University School of Medicine

Department of Genetics

Stanford, CA 94305

USA

Fabio Spada

Center for Integrated Protein Science Ludwig Maximilians University Munich

Department of Biology

82152 Planegg-Martinsried

Germany

Hilmar Strickfaden

Department of Oncology

University of Alberta Cross Cancer Institute

Edmonton

Alberta T6G 1Z2

Canada

Mariliis Tark-Dame

University of Amsterdam

Swammerdam Institute for Life Sciences

1090 GE Amsterdam

The Netherlands

Vladimir B. Teif

Deutsches Krebsforschungszentrum (DKFZ) & BioQuant

Research Group Genome Organization and Function

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

and

Institute of Bioorganic Chemistry

Belarus National Academy of Sciences

Kuprevich 5/2

220141 Minsk

Belarus

Roel van Driel

University of Amsterdam

Swammerdam Institute for Life Sciences

1090 GE Amsterdam

The Netherlands

Silvana van Koningsbruggen

Wellcome Trust Centre for Gene

Regulation and Expression, College of Life Sciences

University of Dundee

Dundee DD1 5EH

United Kingdom

Beth Weiner

Harvard University

Department of Molecular and Cellular Biology

Cambridge, MA 02138

USA

Belinda J. Westman

Wellcome Trust Centre for Gene

Regulation and Expression

College of Life Sciences

University of Dundee

Dundee DD1 5EH

United Kingdom

Liangran Zhang

Harvard University

Department of Molecular and Cellular Biology

Cambridge, MA 02138

USA

Denise Zickler

Université Paris-Sud

Institut de Génétique et Microbiologie, UMR8621

Orsay

France

Nikolaj Zuleger

University of Edinburgh

The Wellcome Trust Centre for Cell Biology

Edinburgh EH9 3JR

United Kingdom