CHROMOSOMES: ORGANIZATION AND FUNCTION Chromosomes Organization and Function Adrian T. Sumner North Berwick, United Kingdom © 2003 by Blackwell Science Ltd a Blackwell Publishing company 350 Main Street, Malden, MA 02148-5018, USA 108 Cowley Road, Oxford OX4 1JF, UK 550 Swanston Street, Carlton South, Melbourne,Victoria 3053, Australia Kurfürstendamm 57, 10707 Berlin, Germany The right of Adrian Sumner to be identified as the Author of this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher. First published 2003 Library of Congress Cataloging-in-Publication Data Sumner, A.T. (Adrian Thomas), 1940– Chromosomes: organization and function/Adrian T. Sumner. p. cm. Includes bibliographical references and index. ISBN 0-632-05407-7 (pbk.: alk. paper) 1. Chromosomes. I. Title. QH600.S863 2003 572.8¢7 – dc21 2002066646 A catalogue record for this title is available from the British Library. Set in 9.5/12 pt Bembo by SNP Best-set Typesetter Ltd., Hong Kong Printed and bound in the United Kingdom by MPG Books Ltd, Bodmin, Cornwall For further information on Blackwell Publishing, visit our website: http://www.blackwellpublishing.com Contents Preface, ix Chapter 4: Assembly of chromatin, 44 4.1 Introduction, 44 Chapter 1: Why study chromosomes? 1 4.2 The nucleosome fibre, 44 1.1 Early studies of chromosomes, 1 4.3 Packing nucleosomes into solenoids, 54 1.2 The origin of genetics, and the 4.4 Yet more packing, 55 chromosome theory of inheritance, 1 4.5 Other ways to pack DNA, 55 1.3 The chemical nature of genes and 4.6 Summary, 56 chromosomes, 2 Websites, 56 1.4 The position of chromosomes in an age of molecular biology, 3 Chapter 5: The chromosomes in Website, 4 interphase, 57 5.1 Interphase nuclei: sites of chromosome Chapter 2: Mitosis, meiosis and the cell activity, 57 cycle, 5 5.2 How are the chromosomes arranged in 2.1 The necessity for accuracy in the cell the nucleus? 58 cycle, 5 5.3 Where do replication and transcription 2.2 The mitotic cycle, 6 take place? 62 2.3 Essentials of mitosis, 11 5.4 The nuclear matrix, 64 2.4 Other cell-cycle events must be 5.5 Other nuclear structures, 66 co-ordinated with mitosis, 15 5.6 Interphase nuclei are highly organized 2.5 Meiosis, 15 and dynamic, 68 2.6 Accuracy is ensured in cell division, 23 Website, 69 Chapter 3: DNA, the genetic code, 24 Chapter 6: Structure of mitotic and 3.1 Stability and variability of DNA, 24 meiotic chromosomes, 70 3.2 The amount of DNA in nuclei, and the 6.1 Chromosomes of dividing and interphase C-value paradox, 24 cells compared, 70 3.3 Repetitive DNA – sequences with a 6.2 Making a mitotic chromosome, 71 function, or just junk? 25 6.3 Loops and scaffolds, 72 3.4 DNA replication, 31 6.4 Chromosome condensation – the final 3.5 5-Methylcytosine – epigenetic stages, 75 modification of DNA, 32 6.5 Biochemistry of condensation, 78 3.6 DNA damage and repair, 35 6.6 The periphery of the chromosome, 79 3.7 DNA is dynamic, 43 6.7 Meiotic and mitotic chromosomes Websites, 43 compared, 82 vi Contents 6.8 There is still much to be learnt about Chapter 11: The nucleolus and the chromosome structure, 83 nucleolus organizer regions (NORs), 133 Chapter 7: Constitutive 11.1 The importance of nucleoli and heterochromatin, 84 NORs, 133 7.1 What is heterochromatin? 84 11.2 The ribosomal genes, 133 7.2 Where is constitutive heterochromatin on 11.3 Silver staining of NORs and nucleoli – the chromosomes? 85 what does it mean? 136 7.3 What is constitutive heterochromatin 11.4 The nucleolus in interphase, 137 made of ? 85 11.5 What happens to the nucleolus during 7.4 What does heterochromatin do? 91 cell division? 138 7.5 Applications of heterochromatin 11.6 What else does the nucleolus do? 141 staining, 95 7.6 Heterochromatin today, 96 Chapter 12: Centromeres, kinetochores Websites, 96 and the segregation of chromosomes, 143 Chapter 8: Sex chromosomes and sex 12.1 What are centromeres and determination, 97 kinetochores? 143 8.1 What are sex chromosomes? 97 12.2 How are centromeres constructed? 143 8.2 The evolution of sex chromosomes, 97 12.3 How are kinetochores made? 149 8.3 Sex chromosome systems and mechanisms 12.4 Proteins of the centromere and of sex determination, 99 kinetochore, 149 8.4 Dosage compensation: coping with 12.5 Holocentric chromosomes, 155 different numbers of X chromosomes in 12.6 Kinetochores are essential for the the two sexes, 102 functioning of chromosomes, 156 8.5 Sex chromosomes at meiosis and gametogenesis, 106 Chapter 13: Telomeres, 159 8.6 Sex chromosomes: different means, the 13.1 What is a telomere? 159 same ends, 108 13.2 Telomeric DNA, 159 Websites, 108 13.3 How do telomeres maintain chromosome length? 161 Chapter 9: Imprinting, 109 13.4 How do telomeres protect chromosome 9.1 What is imprinting? 109 ends? 165 9.2 Which organisms show imprinting? 109 13.5 Telomeres and the spatial organization of 9.3 How does imprinting work? 112 nuclei, 166 9.4 What is imprinting for? 115 13.6 Telomeres, ageing and cancer, 167 Websites, 116 Websites, 170 Chapter 10: Euchromatin and the Chapter 14: Lampbrush longitudinal differentiation chromosomes, 171 of chromosomes, 117 14.1 What are lampbrush chromosomes? 171 10.1 What is euchromatin? 117 14.2 Lampbrush chromosome 10.2 Euchromatin and chromosome banding structure, 172 in mammals, 117 14.3 What have we learnt from oocyte 10.3 Longitudinal differentiation of lampbrush chromosomes? 178 chromosomes in non-mammals, 130 14.4 Lampbrush Y chromosomes in Drosophila 10.4 The how and why of longitudinal spermatocytes, 179 differentiation, 132 Websites, 180 Contents vii Chapter 15: Polytene chromosomes, 182 17.2 Numerical chromosome defects – errors 15.1 What are polytene chromosomes? 182 in cell division, 206 15.2 Polytene chromosomes in Diptera, 183 17.3 Diseases produced by chromosome 15.3 Polytene chromosomes and macronucleus deletions and duplications, 212 formation in ciliates, 188 17.4 Chromosome breakage syndromes – 15.4 Mammalian polytene chromosomes, 190 failures in DNA repair, 213 15.5 Polytene chromosomes in plants, 191 17.5 Fragile sites and triplet repeat 15.6 Mechanisms of polytenization, 192 diseases, 216 15.7 What is the point of polytene 17.6 Diseases of imprinting, 220 chromosomes? 193 17.7 DNA methylation and disease, 220 Websites, 193 17.8 Telomeres and disease, 222 17.9 Cancer – anything and everything can Chapter 16: Chromosomes, the karyotype go wrong with chromosomes, 223 and evolution, 194 Websites, 227 16.1 Chromosomes and evolution, 194 16.2 Constraints on chromosome size, shape Chapter 18: Chromosome and number, 194 engineering and artificial 16.3 Types of chromosome change during chromosomes, 228 evolution, 195 18.1 Engineering chromosomes – an ancient 16.4 Chromosome changes and technique, 228 speciation, 203 18.2 What is an artificial chromosome? 230 16.5 Nucleotypic effects, 204 18.3 How to make artificial 16.6 Chromosomal change is a concomitant chromosomes, 232 of evolution, 205 18.4 Artificial chromosomes – the future, 237 Chapter 17: Chromosomes and disease, 206 References, 239 17.1 The significance of chromosomal disease, 206 Index, 275 Preface Several years ago, with the tidal wave of mole- to guide the reader to further, related informa- cular biology threatening to engulf and obliter- tion. I have also included a substantial amount of ate the rest of biology, it might have seemed that tabular material, which I believe is the most the study of chromosomes was something to be satisfactory way of dealing with the vast amount left to a few old-fashioned scientists to occupy of data now available on some topics.We are sup- them harmlessly until they retired. In fact, posed to be living in an electronic age, and nothing could be further from the truth, and where appropriate I have referred to websites, but recently there has been an upsurge in chromo- only when they supplement or complement the some studies, stimulated by these advances in material in this book. Access to additional chro- molecular biology but accompanied by the real- mosomal websites can be obtained through ization that the arrangement of biological mole- www.chromosome.net/index.htm cules could not, on its own, explain all biological This book could never have been written phenomena. In fact, it has long been known that without the help of numerous scientists who not the behaviour of chromosomes at mitosis and only spared the time to discuss various points and meiosis determines the nature of inheritance, and to send me numerous reprints of their work but, it is becoming clear that the disposition of chro- perhaps more importantly, offered their encour- mosomes in interphase nuclei is also important agement, and convinced me that this book would for their functioning. Many chromosomal sub- really meet a need. I am also very grateful for structures such as heterochromatin, nucleoli, cen- access to the library at the MRC Human tromeres and telomeres are being studied Genetics Unit in Edinburgh. Many people have intensively, as well as chromosomal phenomena generously supplied illustrations for the book such as imprinting. With the immense reduction and, although they are acknowledged individu- in mortality from infectious disease in Western ally in the figure legends, I should like to thank societies, genetic diseases have become much them again here.