Genome Stability and Human Diseases SUBCELLULAR BIOCHEMISTRY SERIES EDITOR J. ROBIN HARRIS, University of Mainz, Mainz, Germany ASSISTANT EDITORS P.J. QUINN, King’s College London, London, U.K. Recent Volumes in this Series Vo l u m e 3 3 Bacterial Invasion into Eukaryotic Cells Tobias A. Oelschlaeger and Jorg Hacker Vo l u m e 3 4 Fusion of Biological Membranes and Related Problems Edited by Herwig Hilderson and Stefan Fuller Vo l u m e 3 5 Enzyme-Catalyzed Electron and Radical Transfer Andreas Holzenburg and Nigel S. Scrutton Vo l u m e 3 6 Phospholipid Metabolism in Apoptosis Edited by Peter J. Quinn and Valerian E. Kagan Vo l u m e 3 7 Membrane Dynamics and Domains Edited by P.J. Quinn Vo l u m e 3 8 Alzheimer’s Disease: Cellular and Molecular Aspects of Amyloid beta Edited by R. Harris and F. Fahrenholz Vo l u m e 3 9 Biology of Inositols and Phosphoinositides Edited by A. Lahiri Majumder and B.B. Biswas Vo l u m e 4 0 Reviews and Protocols in DT40 Research Edited by Jean-Marie Buerstedde and Shunichi Takeda Vo l u m e 4 1 Chromatin and Disease Edited by Tapas K. Kundu and Dipak Dasgupta Vo l u m e 4 2 Inflammation in the Pathogenesis of Chronic Diseases Edited by Randall E. Harris Vo l u m e 4 3 Subcellular Proteomics Edited by Eric Bertrand and Michel Faupel Vo l u m e 4 4 Peroxiredoxin Systems Edited by Leopold Flohd J. Robin Harris Vo l u m e 4 5 Calcium Signalling and Disease Edited by Ernesto Carafoli and Marisa Brini Vo l u m e 4 6 Creatine and Creatine Kinase in Health and Disease Edited by Gajja S. Salomons and Markus Wyss Vo l u m e 4 7 Molecular Mechanisms of Parasite Invasion Edited by Barbara A. Burleigh and Dominique Soldati-Favre Vo l u m e 4 8 The Coronin Family of Proteins Edited by Christoph S. Clemen, Ludwig Eichinger and Vasily Rybakin Vo l u m e 4 9 Lipids in Health and Disease Edited by Peter J. Quinn and Xiaoyuan Wang Vo l u m e 5 0 Genome Stability and Human Diseases Edited by Heinz Peter Nasheuer Heinz Peter Nasheuer Editor Genome Stability and Human Diseases 123 Editor Heinz Peter Nasheuer National University of Ireland, Galway Galway Ireland ISBN 978-90-481-3470-0 e-ISBN 978-90-481-3471-7 DOI 10.1007/978-90-481-3471-7 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2009941695 ©SpringerScience+BusinessMediaB.V.2010 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) This review book is dedicated to Dr. Teresa Wang the Klaus-Bensch Professor of Pathology Stanford University, California, to celebrate her life-long achievements in the fields of Genome Stability and Cell Cycle Regulation Preface Since the discovery of the DNA structure by Crick, Franklin, Watson and Wilkins in 1953 and even before researchers have been highly interested in the molecular basis of the inheritance of genes and of genetic disorders (Franklin and Gosling, 1953; Watson and Crick, 1953a, b; Wilkins et al., 1953a, b). In addition, these publica- tions were the foundation of a new research stream coined “Molecular Biology”. At the same time but remaining nearly unrecognized, cell biologists A. Howard and S. R. Pelc published a nearly as fundamental discovery when they discovered DNA replication as a timely scheduled process between two cell divisions and coined the names G1, S and G2 phase introducing the concept of the eukaryotic cell cycle (Howard and Pelc, 1953). Prior to this, for about half a century, cell biologists had studied mitosis and the remaining was considered as a “black Box” called inter- phase. Further understanding of the structure, assembly and replication of DNA in the nucleus as well as knowing the mechanisms cell cycle regulation has not only yielded numerous Nobel prizes for scientists but ever since also resulted in better understanding of the molecular bases of diseases to introduce more rational treatments including improved treatments of cancer. During her career Teresa Wang was one of the scientists, who with great success has enhanced our understanding of cancer cell biology since the early1970s when the American President Richard Nixon proclaimed the “War on Cancer”. It was nearly at the same time when Teresa Wang started her career at Stanford University where her main research focus has been in the fields of cell growth, cell division and genome stability. She contributed numerous milestones to the field such as cloning and expressing the first human replicative DNA polymerase, study regulation of replication proteins in the cell cycle, in dependence of proliferation and after DNA damage to name a few. During her research career, she has served as a role model for a huge number of life scientists, who work in her group but also interacted with her at all stages of their research career. A number of them contributed to this book. Teresa Wang to whom this book is dedicated was not only an exceptional scientist but was honored with numerous awards including the Klaus-Bensch Professorship of Pathology at Stanford University. Despite her busy university life she also found time to look after her family including her mother, her husband and raising two chil- dren. During my research career at for me an especially sensitive decision-making time I was one of these lucky ones, who spent time in her lab and published some of vii viii Preface my most important discoveries with her. And I can only write in short: “Thank you very much, Teresa, for all your support and help throughout my scientific career.” Galway, Ireland Heinz Peter Nasheuer July 2009 References Franklin, R. E. and Gosling, R. G. (1953) Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleate. Nature,172,156–157. Howard, A. and Pelc, S. R. (1953) Synthesis of deoxyribonucleic acid in normal and irradiated cells and its relation to chromosome breakage. Heredity (Suppl.),6,261–273. Watson, J. D. and Crick, F. H. (1953a) Genetical implications of the structure of deoxyribonucleic acid. Nature,171,964–967. Watson, J. D. and Crick, F. H. (1953b) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature,171,737–738. Wilkins, M. H., Seeds, W. E., Stokes, A. R., and Wilson, H. R. (1953a) Helical structure of crystalline deoxypentose nucleic acid. Nature,172,759–762. Wilkins, M. H., Stokes, A. R., and Wilson, H. R. (1953b) Molecular structure of deoxypentose nucleic acids. Nature,171,738–740. Contents Coming Full Circle: Cyclin-Dependent Kinases as Anti-cancer Drug Targets ................................. 1 Robert P. Fisher Core and Linker Histone Modifications Involved in the DNA Damage Response .............................. 17 Jennifer E. Chubb and Stephen Rea Chromatin Assembly and Signalling the End of DNA Repair Requires Acetylation of Histone H3 on Lysine 56 ............. 43 Thomas Costelloe and Noel F. Lowndes Structure and Function of Histone H2AX ................. 55 David Miguel Susano Pinto and Andrew Flaus The Initiation Step of Eukaryotic DNA Replication ............ 79 Helmut Pospiech, Frank Grosse, and Francesca M. Pisani Non-coding RNAs: New Players in the Field of Eukaryotic DNA Replication .................................. 105 Torsten Krude Function of TopBP1 in Genome Stability ................. 119 Miiko Sokka, Sinikka Parkkinen, Helmut Pospiech, and Juhani E. Syväoja Eukaryotic Single-Stranded DNA Binding Proteins: Central Factors in Genome Stability ......................... 143 Sandra Broderick, Kristina Rehmet, Claire Concannon, and Heinz-Peter Nasheuer DNA Polymerases and Mutagenesis in Human Cancers ......... 165 Emmanuele Crespan, Alessandra Amoroso, and Giovanni Maga DNA Polymerase η, a Key Protein in Translesion Synthesis in Human Cells ................................. 189 Séverine Cruet-Hennequart, Kathleen Gallagher, Anna M. Sokòl, Sangamitra Villalan, Áine M. Prendergast, and Michael P. Carty ix x Contents The Mitochondrial DNA Polymerase in Health and Disease ....... 211 William C. Copeland Centromeres: Assembling and Propagating Epigenetic Function .... 223 Macdara Glynn, Agnieszka Kaczmarczyk, Lisa Prendergast, Nadine Quinn, and Kevin F. Sullivan Nucleotide Excision Repair in Higher Eukaryotes: Mechanism of Primary Damage Recognition in Global Genome Repair ....... 251 N.I. Rechkunova and O.I. Lavrik Nonhomologous DNA End Joining (NHEJ) and Chromosomal Translocations in Humans .......................... 279 Michael R. Lieber, Jiafeng Gu, Haihui Lu, Noriko Shimazaki, and Albert G. Tsai Fluorescence-Based Quantification of Pathway-Specific DNA Double-Strand Break Repair Activities: A Powerful Method for the Analysis of Genome Destabilizing Mechanisms ............ 297 Michael Böhringer and Lisa Wiesmüller Apoptosis: A Way to Maintain Healthy Individuals ............ 307 Chiara Mondello and A. Ivana Scovassi The Use of Transgenic Mice in Cancer and Genome Stability Research ................................... 325 Sarah Conmy and Heinz-Peter Nasheuer Index ..................................... 337 Contributors Alessandra Amoroso Istituto di Genetica Molecolare IGM-CNR, Consiglio Nazionale delle Ricerche, I-27100 Pavia, Italy Michael Böhringer Department of Obstetrics and Gynaecology, University of Ulm, D-89075 Ulm, Germany Sandra Broderick Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland Michael P. Carty Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland, [email protected] Jennifer Chubb Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland Claire Concannon Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland S.