INTRODUCTION TO GENETIC ANALYSIS

Transcription

1 INTRODUCTION TO GENETIC ANALYSIS Ninth Edition Anthony J. F. Griffiths University of British Columbia Susan R. Wessler University of Georgia Richard C. Lewontin Harvard University Sean B. Carroll Howard Hughes Medical Institute University of Wisconsin IS W. H. Freeman and Company New York

2 in Brief Preface xiii Preface xiii i The Genetic Approach to Biology PART 1 TRANSMISSION GENETICS Single-Gene Inheritance Independent Assortment of Genes Mapping Eukaryote Chromosomes by Recombination The Genetics of Bacteria and Their Viruses Gene Interaction PART II FROM DNA TO PHENOTYPE 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 PART III MUTATION, VARIATION, AND EVOLUTION The Dynamic Genome Mutation, Repair, and Recombination Large-Scale Chromosomal Changes Population Genetics Quantitative Genetics Evolutionary Genetics J_ 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 PART IV TECHNIQUES Gene Isolation and Manipulation 715 PART I TRANSMISSION GENETICS J2j Single-Gene Inheritance 31 A Brief Guide to Model Organisms Appendix A: Genetic Nomenclature Genes and Chromosomes Single-Gene Inheritance Patterns 37 Appendix B: Bioinformatics Resources for Genetics and Genomics Glossary Answers to Selected Problems Index 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

3 VI 2.4 Discovering Genes by Observing Segregation Ratios 57 Discovering a gene active in the development of flower color 57 Discovering a gene for wing development 58 Discovering a gene for spore production 58 The results of gene discovery 59 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 62 Model Organism Box Drosophila 63 X-linked inheritance Human Pedigree Analysis 66 Autosomal recessive disorders 66 Autosomal dominant disorders 68 Autosomal polymorphisms 69 X-linked recessive disorders 71 X-linked dominant disorders 73 Y-linked inheritance 73 Calculating risks in pedigree analysis 74 ^ Independent Assortment of Genes Mendel's Law of Independent Assortment Working with Independent Assortment 94 Predicting progeny ratios 94 Using the chi-square test on monohybrid and dihybrid ratios 97 Synthesizing pure lines 99 Hybrid vigor The Chromosomal Basis of Independent Assortment 102 Independent assortment in diploid organisms 103 Independent assortment in haploid organisms 103 Independent assortment of combinations of autosomal and X-linked genes 105 Recombination 106 Model Organism Box Neurospora Polygenic Inheritance Organelle Genes: Inheritance Independent of the Nucleus Patterns of inheritance in organelles 112 Cytoplasm ic segregation 114 Cytoplasmic mutations in humans 116 Mapping Eukaryote Chromosomes by Recombination 129 Diagnostics of Linkage 131 Using recombinant frequency to recognize linkage 131 How crossovers produce recombinants for linked genes 133 Linkage symbolism and terminology 134 Evidence that crossing over is a breakage-and-rejoining process 134 Evidence that crossing over takes place at the fourchromatid stage 135 Multiple crossovers can include more than two chromatids Mapping by Recombinant Frequency 137 Map units 137 Three-point testcross 140 Deducing gene order by inspection 142 Interference 143 Using ratios as diagnostics Mapping with Molecular Markers 146 Single nucleotide polymorphisms 147 Mapping by using SNP haplotypes 149 Simple sequence length polymorphisms Centromere Mapping with Linear Tetrads Using the Chi-Square Test for Testing Linkage Analysis Using Lod Scores to Assess Linkage in Human Pedigrees Accounting for Unseen Multiple Crossovers 159 A mapping function 160 The Perkins formula 162

4 VII 4.8 Using Recombination-Based Maps in Conjunction with Physical Maps 163 ^ The Genetics of Bacteria and Their Viruses Working with Microorganisms Bacterial Conjugation 185 Discovery of conjugation 185 Model Organism Box Escherichia coli 185 Discovery of the fertility factor (F) 187 Hfr strains 188 Mapping of bacterial chromosomes 192 F plasmids that carry genomic fragments 195 Rplasmids Bacterial Transformation 198 Chromosome mapping using transformation Bacteriophage Genetics 199 Infection of bacteria by phages 200 Mapping phage chromosomes by using phage crosses Transduction 204 Discovery of transduction 204 Generalized transduction 205 Specialized transduction 207 Mechanism of specialized transduction Physical Maps and Linkage Maps Compared Inferring Gene Interactions 235 Defining the set of genes by using the complementation test 235 Analyzing double mutants of random mutations Penetrance and Expressivity 247 PART II FROM DNA TO PHENOTYPE _7_ DNA: Structure and Replication DNA: The Genetic Material 266 Discovery of transformation 266 Hershey-Chase experiment The DNA Structure 269 DNA structure before Watson and Crick 270 The double helix Semiconservative Replication 275 Meselson-Stahl experiment 276 The replication fork 277 DNA polymerases Overview of DNA Replication The Replisome: A Remarkable Replication Machine 281 Unwinding the double helix 283 Assembling the replisome: Replication initiation Replication in Eukarydtic Organisms 284 The eukaryotic replisome 284 Eukaryotic origins of replication 285 DNA replication and the yeast cell cycle 286 Replication origins in higher eukaryotes Telomeres and Telomerase: Replication Termination 287 Telomeres, cancer, and aging 288 6^ Gene Interaction Interactions Between the Alleles of a Single Gene: Variations on Dominance 223 Complete dominance and recessiveness 223 Incomplete dominance 225 Codominance 225 Recessive lethal alleles 227 Model Organism Box Mouse Interaction of Genes in Pathways 230 Biosynthetic pathways in Neurospora 230 Gene interaction in other types of pathways 233 8_ RNA: Transcription and Processing RNA 297 Early experiments suggest an RNA intermediate 297 Properties of RNA 297 Classes of RNA Transcription 300 Overview: DNA as transcription template 300 Stages of transcription Transcription in eukaryotes 304 Transcription initiation in eukaryotes 306 Elongation, termination, and pre-mrna processing in eukaryotes 307

5 VIII 8.4 Functional RNAs 309 Small nuclear RNAs (snrnas): The mechanism of exon splicing 310 Self-splicing introns and the RNA world 312 Small interfering RNAs (sirnas) Proteins and Their Synthesis Protein Structure Colinearity of Gene and Protein The Genetic Code 325 Overlapping versus nonoverlapping codes 325 Number of letters in the codon 326 Use of suppressors to demonstrate a triplet code 326 Degeneracy of the genetic code 328 Cracking the code 328 Stop codons trna: The Adapter 330 Codon translation by trna 331 Degeneracy revisited Ribosomes 333 Ribosome features 334 Translation initiation, elongation, and termination 336 Nonsense suppressor mutations The Proteome 340 Alternative splicing generates protein isoforms 340 Posttranslational events 340 1C Regulation of Gene Expression in Bacteria and Their Viruses Gene Regulation 353 The basics of prokaryotic transcriptional regulation: Genetic switches 354 A first look at the lac regulatory circuit Discovery of the lac System: Negative Control 358 Genes controlled together 358 Genetic evidence for the operator and repressor 359 Genetic evidence for allostery 361 Genetic analysis of the lac promoter 362 Molecular characterization of the Lac repressor and the lac operator 363 Polar mutations Catabolic Repression of the lac Operon: 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: The Arabinose Operon Metabolic Pathways and Additional Levels of Regulation: Attenuation 369 Transcription of the trp operon is regulated at two steps Bacteriophage Life Cycles: More Regulators, Complex Operons 372 Molecular anatomy of the genetic switch 375 Sequence-specific binding of regulatory proteins to DNA Alternative Sigma Factors Regulate Large Sets of Genes 378 "\\ Regulation of Gene Expression in Eukaryotes Transcriptional Regulation in Eukaryotes: An Overview 386 Model Organism Box Yeast Lessons from Yeast: the GAL System 390 Gal4 regulates multiple genes through upstream activation sequences 391 The Gal4 protein has separable DNA-binding and activation domains 392 Gal4 activity is physiologically regulated 392 Gal4 functions in most eukaryotes 393 Activators recruit the transcriptional machinery Dynamic Chromatin and Eukaryotic Gene Regulation 394 Chromatin-remodeling proteins and gene activation 395 Histones and chromatin remodeling Mechanism of Enhancer Action 398 The (3-interferon enhanceosome 398 The control of yeast mating type: Combinatorial interactions 399 DNA-binding proteins combinatorially regulate the expression of cell-type-specific genes 399!

6 IX Enhancer-blocking insulators Genomic Imprinting 402 But what about Dolly and other cloned mammals? Chromatin Domains and Their Inheritance 404 Mating-type switching and gene silencing 404 Heterochromatin and euchromatin compared 405 Position-effect variegation in Drosophila reveals genomic neighborhoods 406 Genetic analysis of PEV reveals proteins necessary for heterochromatin formation 407 Silencing an entire chromosome: X-chromosome inactivation 409 The inheritance of epigenetic marks and chromatin structure 410 Model Organism Box Caenorhabditis elegans 442 mirna control of developmental timing in C. elegans and other species The Many Roles of Individual Toolkit Genes 445 From flies to fingers, feathers, and floor plates Development and Disease 446 Polydactyly 446 Holoprosencephaly 447 Cancer as a developmental disease 447 2^5 Genomes and Genomics The Genetic Control of Development The Genetic Approach to Development 416 Model Organism Box Drosophila The Genetic Toolkit for Drosophila Development 418 Classification of genes by developmental function 419 Homeotic genes and segmental identity 420 Organization and expression of Hox genes 421 The homeobox 423 Clusters of Hox genes.control development in most animals Defining the Entire Toolkit 427 The anteroposterior and dorsoventral axes 428 Expression of toolkit genes Spatial Regulation of Gene Expression in Development 432 Maternal gradients and gene activation 432 Drawing stripes: Integration of gap-protein inputs 434 Making segments different: Integration of Hox inputs Posttranscriptional Regulation of Gene Expression in Development 439 RNA splicing and sex determination in Drosophila 439 Regulation of mrna translation and cell lineage in C. elegans 441 Translational control in the early embryo The Genomics Revolution Creating the Sequence Map of a Genome 456 Turning sequence reads into a sequence map 456 Establishing a genomic library of clones 459 Sequencing a simple genome by using the wholegenome shotgun approach 459 Using the whole-genome shotgun approach to create a draft sequence of a complex genome 460 Using the ordered-clone approach to sequence a complex genome 461 Filling sequence gaps Bioinformatics: Meaning from Genomic Sequence 463 The nature of the information content of DNA 463 Deducing the protein-encoding genes from genomic sequence The Structure of the Human Genome Comparative Genomics 470 Of mice and humans 471 Comparative genomics of chimpanzees and humans 472 Conserved and ultraconserved noncoding elements 472 Comparative genomics of non-pathogenic and i pathogenic coli Functional Genomics and Reverse Genetics 475 Ome, Sweet Ome 475 Reverse genetics 479

7 XII PART IV TECHNIQUES 20 Gene Isolation and Manipulation Generating Recombinant Molecules 716 Type of donor DNA 717 Cutting genomic DNA 717 Attaching donor and vector DNA 719 Amplification inside a bacterial cell 720 Entry of recombinant molecules into the bacterial cell 723 Recovery of amplified recombinant molecules 723 Making genomic and cdna libraries 724 Finding a specific clone of interest DNA Amplification in Vitro: The Polymerase Chain Reaction Determining the Base Sequence of a DNA Segment Forward Genetic Analysis by Using Positional Cloning 735 A forward analysis to identify a human disease gene 737 A forward analysis to identify a gene important to corn domestication Detecting Human Disease Alleles: Molecular Genetic Diagnostics Genetic Engineering 741 Genetic engineering in Saccharomyces cerevisiae 741 Genetic engineering in plants 742 Genetic engineering in animals 745 Human gene therapy 749 A Brief Guide to Model Organisms 759 Appendix A: Genetic Nomenclature 775 Appendix B: Bioinformatics Resources for Genetics and Genomics 776 Glossary 779 Answers to Selected Problems 803 Index 815