Human Chromosomes Fourth Edition Springer Science+Business Media, LLC Human Chromosomes Fourth Edition Orlando J. Miller Wayne State University School of Medicine Eeva Therman Professor Emeritus, University of Wisconsin-Madison With108 Illustrations,9 inFull Color Springer Orlando].Miller EevaTherman CenterforMolecularMedicineand Genetics Laboratoryof Genetics Wayne State University School of Medicine Universityof Wisconsin 3216 Scott Hali Genetics Building 540 East CanfieldAvenue Madison,WI 53706,USA Detroit, MI 48201,USA [email protected] Coverillustration:Ametaphase spread (front cover) and a karyotype (back cover) after in situ hybridization and detection of multiplex probes. Red and green bars represent regions that hybridized to fragments inonly one probe pool, and yellow bars represent regions that hybridizedequally to fragments in both probe pools.Mixed colorsare due to overrepresen tation of fragments from one pool. Regions that failto hybridize to fragments ineither pool show background DAPI blue fluorescence. (Reproduced from Mulleret al., Toward a multi colorchromosomebarcodeforthe entirehuman karyotypebyfluorescence insituhybridiza tion, Hum Genet 100, fig.3,page 273,copyright Springer-Verlag 1997.) LibraryofCongressCataloging-in-PublicationData Miller,Orlando). Humanchromosornes/Orlando]. Miller,EevaTherman.-4thed. p.cm. Includesbibliographicalreferencesand index. ISBN978-0-387-95046-4 ISBN978-1-4613-0139-4(eBook) DOI 10.1007/978-1-4613-0139-4 1. Humanchromosomes. 2. Humancytogenetics. 3. Humanchromosomeabnormalities. 1. Therman,Eeva. II. Tttle. QH431 .T436 2000 611'.01816-dc21 00-044007 Printedon acid-free paper. ©2001 SpringerScience+BusinessMediaNewYork Originallypublishedby Springer-VerlagNewYork,Inc in 2001 Softcoverreprintofthehardcover4thedition 2001 AIIrights reserved.This work may not be translatedor copiedinwhole or in part without the written permission of the publisher(Springer-Verlag New York, Inc., 175Fifth Avenue,New York, NY 10010, USA),exceprforbnefexcerptsinconnectionwith reviewsorscholarlyanalysis.Use inconnectionwith any form ofinformationstorageand retrieval,electronicadaptation,computersoftware,orbysimilaror dissimilarmethodologynow knownorhereafterdevelopedisforbidden. Theuseofgeneraldescriptivenames,tradenames,trademarks,etc.,inthis publication,eveniftheformer are not especially identified, is not to be taken as a sign that such names, asunderstood by theTrade Marksand MerchandiseMarksAct,may accordinglybe used freely byanyone. Productioncoordinatedby ChernowEditorial Services,lnc.,and managedby FrancineMcNeill;manu facturing supervisedbyJeffreyTaub. Typesetby Best-Set Typesetterl.td.,HongKong. 9 8 765 4 3 2 1 ISBN978-0-387-95046-4 Preface Thisbook presentsacomprehensive introduction to the principles of human cytogenetics and provides examples of their applications, especially those thatare importantindiagnosticand preventivemedicine.Theauthors have each worked in human cytogenetics for more than 40 years and have witnessed first handtheenormousstridesmade inthe fieldduringthis time.Themany advances made since the third edition of this book reflect the rapidly growingapplication of molecular biological techniques and concepts by human cytogeneticists. Insertion of transposable elements, genomic imprinting, and expansion of tri nucleotide repeats are only a fewof the important cytogenetic mechanisms that have been discoveredand shown to playarole inproducingdisease phenotypes. Molecular cytogenetic methods have taken center stage in cancer studies with the demonstration that cancers arise by chromosomal mechanisms such asgene amplification, oncogene activation by chromosome rearrangement, ectopic recombination leading to loss of heterozygosity, and multiple mechanisms leading to genome destabilization. v Preface We presentacomprehensive and relatively brief overview of the principles of cytogenetics, including the important new disease mechanisms previously men tioned.Examplesarechosen that illustrate these principlesandtheirapplication, thus preparing the reader to understand the new developments that constantly appear in the laboratory, the clinic,and the current literature of this very active field.At many points in the book, importantunsolved problems in cytogenetics are mentioned with suggestions of how a solution might be sought, which acts as a stimulus to the reader to come up with his or her own suggestions. The bookshould be particularlyuseful for physicianswho want to keep up with new developments in this fieldand students interested in a career in medical genet icsor geneticcounseling.Itcouldeasilyserve asatext foraone-semestercollege or graduate-level course in human cytogenetics, or,with some supplementation, a course in general cytogenetics. In this edition, the text has been extensively reorganized and almost com pletelyrewritten to incorporateessential insights from cell and moleculargenet ics, along with other advances in cytogenetics, and to present them in a systematicway.Examples have been chosen that not only emphasize the under lying principles but also illustrate the growing clinical importance of molecular cytogenetics.Mostof the tables and the majority ofthe figuresare new,andvir tually all are based on studies of human chromosomes. We are grateful to the colleaguesand copyrightholderswhohave generously permittedtheuseoftheir published and unpublished figures and tables. Detroit, Michigan OrlandoJ Miller Madison, Wisconsin EevaTherman vi Contents Preface v l Origins and Directions of Human Cytogenetics Origins:Cytology,Genetics,and DNA Chemistry 2 The Midwives of Human Cytogenetics 3 The Birthof Clinical Cytogenetics 4 The LyonHypothesis 6 Adolescence:The Chromosome Banding Era 6 Somatic Cell Genetics and Chromosome Mapping 7 Maturity:The Molecular Era 8 References 10 2 The Mitotic Cell Cycle 13 The Cell Cycle:Interphase,Mitosis,and Cytokinesis 14 Cell Cycle Progression:Cyclins and Cyclin-Dependent Kinases 16 vii Contents Cell Cycle Checkpoints 19 Prophase 20 Prometaphase, Centrosomes, and the Mitotic Spindle 22 Metaphase,Anaphase, and Telophase 22 Nondisjunction, Lossof Chromosomes, and Mosaicism 24 References 25 3 DNA Replication and Chromosome Reproduction 29 Replication IsSemiconservative 29 The Chemistry of Replication 31 Initiation at Many Sites:Origins of Replication 33 Replication IsPrecisely Ordered:Replication Banding 35 The Control of DNA Replication 38 Replication of Chromosome Ends:Telomerase and Cell Aging 40 Postreplication Steps:DNA Methylation and Chromatin Assembly 41 References 42 4 General Features of Mitotic Chromosomes 45 Metaphase Chromosomes 45 The Chromosome Complement and Karyotype 47 DNA Content and DNA-Based Flow Cytometric Karyotypes 48 Centromeres and Kinetochores 49 Telomeres 54 Nucleolus Organizers and Ribosomal RNA Genes 55 Constitutive and Facultative Heterochromatin 56 References 56 5 The Chemistry and Packaging of Chromosomes 61 DNA Content and the Estimated Numberof BasePairs in the Genome 62 Histone Proteins and the Nucleosome 62 The Chromosome Scaffold and Chromatin Loops 63 Chromosome Domains in the Interphase Nucleus 67 The NuclearMatrix:Replication and Transcription Complexes 68 Locus Control Regions and Functional Domains 70 Euchromatin and Heterochromatin:Regulation of Gene Function 71 Histone Modifications, DNA Methylation, and Chromosome Condensation 72 References 74 viii Contents 6 Chromosome Bands 79 Q-banding 80 C-banding 81 G-banding, R-banding, and T-banding 83 High-Resolution and Replication Banding 84 Banding with Other Fluorochromesand Nonfluorochromes 85 Antibody Banding 87 Nuclease Banding 88 InSitu Hybridization Banding 89 Nomenclature of Banded Chromosomes and Abnormal Karyotypes 89 References 92 7 Molecular Correlates of Chromosome Bands 95 GC- and AT-RichIsochores 95 Llnrnethylated CpG Clusters and Housekeeping and Tissue-SpecificGenes 98 Interspersed Repetitive DNA Sequences and Transposable Elements 99 Tandernly Repetitive Elements:Telomeres, Centromeres, and Satellite DNAs 100 Chromosomal Proteins and Chromatin Conformation 101 Functional Significance of Chromosome Bands 103 References 103 8 In Situ Hybridization 107 InSitu Hybridization of Repetitive and Unique DNA Sequences 108 Fluorescence InSitu Hybridization 109 Replication Timing by FISH 114 Cloned, PCR-Generated, and InSitu-Generated Probes 114 Chromosome-, Region-, and Band-Specific Painting Probes 116 MulticolorFISH,Spectral Karyotyping, and BarCodes 117 High-Resolution (Interphase and Fiber) FISH 118 Comparative Genomic Hybridization 121 References 121 9 Main Features of Meiosis 125 Prophase I: Leptotene, Zygotene, Pachytene, Diplotene, and Diakinesis 127 ix Contents Chiasmata and Genetic Recombination 132 Metaphase I,Anaphase I,Telophase I,Interkinesis, and Meiosis II 133 Female Meiosis:Dictyotene Arrest, Metaphase IIArrest, and Apoptosis 134 Male Meiosis 135 Segregation Distortion and Meiotic Drive 136 Meiotic Behavior of Three Homologous Chromosomes 137 References I38 lO Details of Meiosis 141 The Switch from Mitosis to Meiosis 141 Pairing of Homologous Chromosomes 142 The Synaptonemal Complex and Recombination Nodules 142 Nonrandom Distribution of Meiotic Recombination Sites 145 Molecular Mechanisms of Meiotic Recombination 146 Meiotic DNA Damage Checkpoint 149 Absence of a Spindle"Assembly Checkpoint in Female Meiosis: Role in Nondisjunction? 151 References 151 l l Meiotic Abnormalities: Abnormal Numbers of Chromosomes 157 Incidence of Nondisjunction in Meiosis and Gametes 159 Incidence of Nondisjunction in Spontaneous Abortions,Stillborns, and Liveborns 161 Causes of Meiotic Nondisjunction 164 Maternal Age, Recombination, and Mechanisms of Nondisjunction 164 Parental Origin of Aneuploid Gametes 168 The Origin of Diploid Gametes and Polyploidy 169 Aneuploidy of Somatic (Mitotic) Origin:Mosaicism 170 References 171 l 2 Abnormal Phenotypes Due to Autosomal Aneuploidy or Polyploidy 175 Trisomy 2I and Down Syndrome 176 Trisomy 18and Edwards Syndrome 178 Trisomy 13and Patau Syndrome 178 x