INTRODUCTION TO GENETIC ANALYSIS

Transcription

1 INTRODUCTION TO GENETIC ANALYSIS Ninth Edition Anthony). F. Griffiths Susan R. Wessler Richard C. Lewontin Sean B. Carroll New York

2 by W. H. Freeman and Company

3 Preface xiii Preface xiii 1 The Genetic Approach to Biology 1 PART I TRANSMISSION GENETICS 2 Single-Gene Inheritance 31 3 Independent Assortment of Genes 89 4 Mapping Eukaryote Chromosomes by Recombination The Genetics of Bacteria and Their Viruses Gene Interaction 221 PART II FROM DNA TO PHENOTYPE _ 7 DNA: Structure and Replication RNA: Transcription and Processing Proteins and Their Synthesis Regulation of Gene Expression in Bacteria and Their Viruses Regulation of Gene Expression in Eukaryotes The Genetic Control of Development Genomes and Genomics 453 PART III MUTATION, VARIATION, AND EVOLUTION 14 The Dynamic Genome Mutation, Repair, and Recombination Large-Scale Chromosomal Changes Population Genetics Quantitative Genetics Evolutionary Genetics 679 PART IV TECHNIQUES 20 Gene Isolation and Manipulation 000 A Brief Guide to Model Organisms 000 Appendix A: Genetic Nomenclature 000 Appendix B: Bioinformatics Resources for Genetics and Genomics 000 Answers to Selected Problems 000 Glossary 000 Index The Genetic Approach to Biology Genetics and the Questions of Biology The Molecular Basis of Genetic Information 5 Specifying the amino acid sequence of a protein 6 Gene regulation The Program of Genetic Investigation 9 The necessity of variation 9 Starting with variation: Forward genetics 10 Starting with DNA: Reverse genetics Methodologies Used in Genetics 14 An Overview 14 Detecting specific molecules of DNA, RNA, and protein Model Organisms 17 Lessons from the first model organisms 17 The need for a variety of model organisms Genes, the Environment, and the Organism 21 Model I: Genetic determination 21 Model II: Environmental determination 22 Model III: Genotype-environment interaction 23 The use of genotype and phenotype 23 Developmental noise 24 Three levels of development 26 PART I TRANSMISSION GENETICS Single-Gene Inheritance Genes and Chromosomes Single-Gene Inheritance Patterns 37 Mendel's law of equal segregation The Chromosomal Basis of Single-Gene Inheritance Patterns 42 Single-gene inheritance in haploids 46 The molecular basis of single-gene segregation and expression 50

4 2.4 Discovering Genes by Observing Model Organism Box Neurospora 107 Segregation Ratios Polygenic Inheritance 110 Discovering a gene active in the development 3.5 Organelle Genes: Inheritance Independent of flower color 57 of the Nucleus 112 Discovering a gene for wing development 58 Patterns of inheritance in organelles 112 Discovering a gene for spore production 58 Cytoplasmic segregation 114 The results of gene discovery 59 Cytoplasmic mutations in humans 116 Forward genetics 60 Predicting progeny proportions or parental genotypes by applying the principles of single-gene influence Sex-Linked Single-Gene Inheritance Patterns 61 Sex chromosomes 61 Sex-linked patterns of inheritance Wit al Model Organism Box Drosophila 63 ' X-linked inheritance 63 4 Mapping Eukaryote Chromosomes 2.6 Human Pedigree Analysis 66 by Recombination 129 Autosomal recessive disorders Diagnostics of Linkage 131 Autosomal dominant disorders 68 Using recombinant frequency to recognize linkage 131 Autosomal polymorphisms 69 How crossovers produce recombinants for linked X-linked recessive disorders 71 genes 133 X-linked dominant disorders 73 Linkage symbolism and terminology 134 Y-linked inheritance 73 Evidence that crossing over is a breakage-and-rejoining Calculating risks in pedigree analysis 74 process 134 Evidence that crossing over takes place at the four- F chromatid stage 135 Progeny seeds.s.r Total d21,7 e', ` Ai M ( v. ' Multiple crossovers can include more than two chromatids 136 ' I 4.2 Mapping by Recombinant Frequency 137 ` Map units 137 Three-point testcross Independent Assortment of Genes 89 Interference 143 Deducing gene order by inspection Mendel's Law of Independent Assortment 90 Using ratios as diagnostics Working with Independent Assortment Mapping with Molecular Markers 146 Predicting progeny ratios 94 Single nucleotide polymorphisms 147 Using the chi-square test on monohybrid Mapping by using SNP haplotypes 149 and dihybrid ratios 97 Simple sequence length polymorphisms 151 Synthesizing pure lines Centromere Mapping with Linear Hybrid vigor 101 Tetrads The Chromosomal Basis of Independent 4.5 Using the Chi-Square Test for Testing Linkage Assortment 102 Analysis 155 Independent assortment in diploid organisms Using Lod Scores to Assess Linkage in Human Independent assortment in haploid organisms 103 Pedigrees 158 Independent assortment of combinations of autosomal 4.7 Accounting for Unseen Multiple Crossovers 159 and X-linked genes 105 A mapping function 160 Recombination 106 The Perkins formula 162

5 4.8 Using Recombination-Based Maps in Conjunction 6.3 Inferring Gene Interactions 235 with Physical Maps 163 Defining the set of genes by using the complementation test The Genetics of Bacteria and Their Analyzing double mutants of random mutations 239 Viruses Penetrance and Expressivity Working with Microorganisms Bacterial Conjugation 185 PART II FROM DNA TO PHENOTYPE Discovery of conjugation 185 Model Organism Box Escherichia coli DNA: Structure and Replication 265 Discovery of the fertility factor (F) DNA: The Genetic Material 266 Hfr strains 188 Discovery of transformation 266 Mapping of bacterial chromosomes 192 Hershey-Chase experiment 268 F plasmids that carry genomic fragments The DNA Structure 269 R plasmids 196 DNA structure before Watson and Crick Bacterial Transformation 198 The double helix 272 Chromosome mapping using transformation Semiconservative Replication Bacteriophage Genetics 199 Meselson-Stahl experiment 276 Infection of bacteria by phages 200 The replication fork 277 Mapping phage chromosomes by using DNA polymerases 278 phage crosses Overview of DNA Replication Transduction The Replisome: A Remarkable Replication Discovery of transduction 204 Machine 281 Generalized transduction 205 Unwinding the double helix 283 Specialized transduction 207 Assembling the replisome: Replication initiation 284 Mechanism of specialized transduction Replication in Eukaryotic Organisms Physical Maps and Linkage Maps The eukaryotic replisome 284 Compared 209 Eukaryotic origins of replication Gene Interaction RNA 297 DNA replication and the yeast cell cycle 286 Replication origins in higher eukaryotes Telomeres and Telomerase: Replication Termination 287 Telomeres, cancer, and aging 288 U 8 RNA: Transcription and Processing Interactions Between the Alleles of a Single Gene: Early experiments suggest an RNA intermediate 297 Variations on Dominance 223 Properties of RNA 297 Complete dominance and recessiveness 223 Classes of RNA 298 Incomplete dominance Transcription 300 Codominance 225 Overview: DNA as transcription template 300 Recessive lethal alleles 227 Stages of transcription 301 Model Organism Box Mouse Transcription in eukaryotes Interaction of Genes in Pathways 230 Transcription initiation in eukaryotes 306 Biosynthetic pathways in Neurospora 230 Elongation, termination, and pre-mrna processing Gene interaction in other types of pathways 233 in eukaryotes 307

6 8.4 Functional RNAs 309 Molecular characterization of the Lac repressor Small nuclear RNAs (snrnas): The mechanism of exon and the lac operator 363 splicing 310 Polar mutations 363 Self-splicing introns and the RNA world Catabolic Repression of the lac Operon: Small interfering RNAs (sirnas) 312 Positive Control 364 The basics of catabolite repression of the lac operon: Choosing the best sugar to metabolize 364 The structures of target DNA sites 365 A summary of the lac operon Dual Positive and Negative Control: 5" The Arabi nose Operon Metabolic Pathways and Additional Levels 9 Proteins and Their Synthesis 319 of Regulation: Attenuation Protein Structure 321 Transcription of the trp operon is regulated at 9.2 Colinearity of Gene and Protein 324 two steps The Genetic Code Bacteriophage Life Cycles: More Regulators, Complex Operons 372 Overlapping versus nonoverlapping codes 325 Molecular anatomy of the genetic switch 375 Number of letters in the codon 326 Sequence-specific binding of regulatory proteins Use of suppressors to demonstrate a triplet code 326 to DNA 376 Degeneracy of the genetic code Alternative Sigma Factors Regulate Large Sets Cracking the code 328 of Genes 378 Stop codons trna: The Adapter Regulation of Gene Expression in Codon translation by trna 331 Eukaryotes 385 Degeneracy revisited Transcriptional Regulation in Eukaryotes: 9.5 Ribosomes 333 An Overview 386 Ribosome features 334 Model Organism Box Yeast 390 Translation initiation, elongation, and 11.2 Lessons from Yeast: the GAL System 390 termination 336 Gal4 regulates multiple genes through upstream Nonsense suppressor mutations 339 activation sequences The Proteome 340 The Gal4 protein has separable DNA-binding and Alternative splicing generates protein isoforms 340 activation domains 392 Posttranslational events 340 Gal4 activity is physiologically regulated 392 Gal4 functions in most eukaryotes Regulation of Gene Expression in Bacteria Activators recruit the transcriptional machinery 393 and Their Viruses Dynamic Chromatin and Eukaryotic Gene Regulation Gene Regulation 353 Chromatin-remodeling proteins and gene The basics of prokaryotic transcriptional regulation: activation 395 Genetic switches 354 Histones and chromatin remodeling 396 A first look at the lac regulatory circuit Mechanism of Enhancer Action Discovery of the lac System: Negative Control 358 The B -interferon enhanceosome 398 Genes controlled together 358 The control of yeast mating type: Combinatorial Genetic evidence for the operator and repressor 359 interactions 399 Genetic evidence for allostery 361 DNA-binding proteins combinatorially regulate the Genetic analysis of the lac promoter 362 expression of cell-type-specific genes 399

7 Enhancer-blocking insulators 401 Model Organism Box Caenorhabditis 11.5 Genomic Imprinting 402 elegans 442 But what about Dolly and other cloned mammals? 404 mirna control of developmental timing in C. elegans 11.6 Chromatin Domains and Their Inheritance 404 and other species 444 Mating type switching and gene silencing The Many Roles of Individual Toolkit Genes 445 Heterochromatin and euchromatin compared 405 From flies to fingers, feathers, and floor plates 445 Position-effect variegation in Drosophila reveals 12.7 Development and Disease 446 genomic neighborhoods 406 Polydactyly 446 Genetic analysis of PEV reveals proteins necessary for Holoprosencephaly 447 heterochromatin formation 407 Cancer as a developmental disease 447 Silencing an entire chromosome: X-chromosome inactivation 409 The inheritance of epigenetic marks and chromatin structure 410 Gala UAS T Pt Migl Mig1 site ----\ GAL1 OFF 13 Genomes and Genomics The Genomics Revolution The Genetic Control of Development Creating the Sequence Map of a Genome 456 Turning sequence reads into a sequence 12.1 The Genetic Approach to Development 416 map 456 Model Organism Box Drosophila 418 Establishing a genomic library of clones The Genetic Toolkit for Drosophila Sequencing a simple genome by using the whole- Development 418 genome shotgun approach 459 Classification of genes by developmental function 419 Using the whole-genome shotgun approach to Homeotic genes and segmental identity 420 create a draft sequence of a complex genome 460 Organization and expression of Hox genes 421 Using the ordered-clone approach to sequence a The homeobox 423 complex genome 461 Clusters of Hox genes control development in most Filling sequence gaps 462 animals Bioinformatics: Meaning from Genomic 12.3 Defining the Entire Toolkit 427 Sequence 463 The anteroposterior and dorsoventral axes 428 The nature of the information content of DNA 463 Expression of toolkit genes 428 Deducing the protein-encoding genes from 12.4 genomic sequence 464 Spatial Regulation of Gene Expression in Development The Structure of the Human Genome 468 Maternal gradients and gene activation Comparative Genomics 470 Drawing stripes: Integration of gap-protein inputs 434 Of mice and humans 471 Making segments different: Integration of Hox Comparative genomics of chimpanzees and humans 472 inputs Posttranscriptional Regulation of Gene Expression Conserved and ultraconserved noncoding in Development 439 elements 472 RNA splicing and sex determination in Comparative genomics of non-pathogenic and pathogenic E. coli 473 Drosophila 439 Regulation of mrna translation and cell lineage in 13.6 Functional Genomics and Reverse Genetics 475 C. elegans 441 Ome, Sweet Ome 475 Translational control in the early embryo 441 Reverse genetics 479

8 PART III MUTATION, VARIATION, u. Postreplication repair: Mismatch repair 536 AND EVOLUTION Error-prone repair: Translesion DNA Synthesis The Dynamic Genome 487 Repair of double-strand breaks The Mechanism of Meiotic Crossing Over Discovery of Transposable Elements in Maize 488 McClintock's experiments: the Ds element 488 Programmed double-strand breaks initiate meiotic recombination 542 Model Organism Box Maize 489 Genetic analyses of tetrads provide clues to the Autonomous and nonautomous elements 491 mechanism of recombination 543 Transposable elements: Only in maize? 492 The double-strand break model for meiotic 14.2 Transposable Elements in Prokaryotes 492 recombination 544 Bacterial insertion sequences 492 Prokaryotic transposons 493 Mechanism of transposition Transposable Elements in Eukaryotes 496 Class I: Retrotransposons 496 DNA transposons 499 Utility of DNA transposons for gene discovery Cancer: An Important Phenotypic Consequence of Mutations 546 How cancer cells differ from normal cells 546 Mutations in cancer cells 547 rt~l ~ ~ f 14.4 The Dynamic Genome: More Transposable Elements Than Ever Imagined Large-Scale Chromosomal Changes 555 Large genomes are largely transposable elements 504 Transposable elements in the human genome 505 The grasses: LTR retrotransposons thrive in large genomes 507 Safe havens Mutation, Repair, and Recombination 513 W ~ Changes in Chromosome Number 557 Aberrant euploidy 557 Aneuploidy 565 The concept of gene balance Changes in Chromosome Structure 572 Deletions 574 Duplications Phenotypic Consequences of DNA Mutations 514 Inversions 580 Types of point mutation 515 Reciprocal translocations 583 The molecular consequences of point mutations in a coding region 516 Robertsonian translocations 584 The molecular consequences of point mutations in a Applications of inversions and translocations 586 noncoding region 517 Q Rearrangements and cancer The Molecular Basis of Spontaneous Identifying chromosome mutations by genomics 588 Mutations Overall Incidence of Human Chromosome Luria and Delbrück fluctuation test 518 Mutations 588 Mechanisms of spontaneous mutations 520 Spontaneous mutations in humans: Trinucleotide repeat diseases The Molecular Basis of Induced Mutations 525 I Mechanisms of mutagenesis 526 The Ames test: Evaluating mutagens in our environment Population Genetics Biological Repair Mechanisms Variation and Its Modulation 604 Direct reversal of damaged DNA 532 Observations of variation 604 Base-excision repair 532 Protein polymorphisms 606 Nucleotide-excision repair 534 DNA structure and sequence polymorphism 609

9 17.2 Effect of Sexual Reproduction on Variation Locating Genes 664 Meiotic segregation and genetic equilibrium 613 Marker-gene segregation 666 Heterozygosity 616 Quantitative linkage analysis 666 Random mating 616 Statistical Appendix 669 Inbreeding and assortative mating 618 Measures of central tendency Sources of Variation 620 Measures of dispersion: The variance 670 Variation from mutation 620 Measures of relation 671 Variation from recombination 620 Variation from migration Evolutionary Genetics Selection Darwinian Evolution 680 Two forms of selection A Synthesis of Forces: Variation and Divergence Measuring fitness differences 625 of Populations 683 How selection works Multiple Adaptive Peaks 685 Rate of change in gene frequency 628 Exploration of adaptive peaks Balanced Polymorphism Genetic Variation 689 Overdominance and underdominance 629 Heritability of variation 689 Balance between mutation and selection 630 Variation within and between populations Random Events Mutation and Molecular Evolution 690 The signature of purifying selection on DNA Quantitative Genetics Relating Genetic to Functional Change: Protein Evolution Genes and Quantitative Traits 640 The signature of positive selection on DNA 18.2 Some Basic Statistical Notions 642 sequences 693 Statistical distributions 642 Morphological evolution 694 Statistical measures 643 Gene inactivation Genotypes and Phenotypic Distribution Regulatory Evolution 697 The critical difference between quantitative Regulatory evolution in humans 699 and Mendelian traits The Origin of New Genes 699 Gene number and quantitative traits 645 Polyploidy Norm of Reaction and Phenotypic Duplications 700 Distribution 646 I mported DNA Determining Norms of Reaction Genetic Evidence of Common Ancestry Domesticated plants and animals 647 in Evolution 703 Studies of natural populations 649 Comparing the proteomes among distant species 705 Results of norm-of-reaction studies 649 Comparing the proteomes among near neighbors: 18.6 The Heritability of a Quantitative Character 651 Human-mouse comparative genomics 706 Familiality and heritability The Process of Speciation 707 Phenotypic similarity between relatives 652 Genetics of species isolation Quantifying Heritability 654 Methods of estimating H The meaning of H Narrow heritability 659 Estimating the components of genetic variance 661 Artificial selection 662 The use of h 2 in breeding 663

10 PART IV TECHNIQUES A forward analysis to identify a human disease gene Gene Isolation and Manipulation 715 A forward analysis to identify a gene important to corn 20.1 Generating Recombinant Molecules 716 domestication 738 Type of donor DNA Detecting Human Disease Alleles: Cutting genomic DNA 717 Molecular Genetic Diagnostics 739 Attaching donor and vector DNA Genetic Engineering 741 Amplification inside a bacterial cell 720 Genetic engineering in Saccharomyces cerevisiae 741 Entry of recombinant molecules into the Genetic engineering in plants 742 bacterial cell 723 Genetic engineering in animals 745 Recovery of amplified recombinant molecules 723 Human gene therapy 749 Making genomic and cdna libraries 724 Finding a specific clone of interest 724 A Brief Guide to Model Organisms DNA Amplification in Vitro: The Polymerase Appendix A: Genetic Nomenclature 775 Chain Reaction 731 Appendix B: Bioinformatics Resources for Genetics 20.3 Determining the Base Sequence of a DNA and Genomics 776 Segment 732 Glossary Forward Genetic Analysis by Using Positional Answers to Selected Problems 803 Cloning 735 Index 815