John Wiley & Sons Genetic Theory and Analysis Cover GENETIC THEORY AND ANALYSIS Understand and apply what drives change of characteristic genetic trait.. Product #: 978-1-118-08692-6 Regular price: $85.89 $85.89 Auf Lager

Genetic Theory and Analysis

Finding Meaning in a Genome

Miller, Danny E. / Miller, Angela L. / Hawley, R. Scott

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2. Auflage November 2023
304 Seiten, Softcover
Wiley & Sons Ltd

ISBN: 978-1-118-08692-6
John Wiley & Sons

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GENETIC THEORY AND ANALYSIS

Understand and apply what drives change of characteristic genetic traits and heredity

Genetics is the study of how traits are passed from parents to their offspring and how the variation in those traits affects the development and health of the organism. Investigating how these traits affect the organism involves a diverse set of approaches and tools, including genetic screens, DNA and RNA sequencing, mapping, and methods to understand the structure and function of proteins. Thus, there is a need for a textbook that provides a broad overview of these methods.

Genetic Theory and Analysis meets this need by describing key approaches and methods in genetic analysis through a historical lens. Focusing on the five basic principles underlying the field--mutation, complementation, recombination, segregation, and regulation--it identifies the full suite of tests and methodologies available to the geneticist in an age of flourishing genetic and genomic research. This second edition of the text has been updated to reflect recent advances and increase accessibility to advanced undergraduate students.

Genetic Theory and Analysis, 2nd edition readers will also find:
* Detailed treatment of subjects including mutagenesis, meiosis, complementation, suppression, and more
* Updated discussion of epistasis, mosaic analysis, RNAi, genome sequencing, and more
* Appendices discussing model organisms, genetic fine-structure analysis, and tetrad analysis

Genetic Theory and Analysis is ideal for both graduate students and advanced undergraduates undertaking courses in genetics, genetic engineering, and computational biology.

Preface xi

Introduction xiii

1 Mutation 1

1.1 Types of Mutations 1

Muller's Classification of Mutants 2

Nullomorphs 2

Hypomorphs 4

Hypermorphs 5

Antimorphs 6

Neomorphs 8

Modern Mutant Terminology 10

Loss-of-Function Mutants 10

Dominant Mutants 10

Gain-of-Function Mutants 11

Separation-of-Function Mutants 11

DNA-Level Terminology 11

Base-Pair-Substitution Mutants 11

Base-Pair Insertions or Deletions 12

Chromosomal Aberrations 12

1.2 Dominance and Recessivity 13

The Cellular Meaning of Dominance 13

The Cellular Meaning of Recessivity 15

Difficulties in Applying the Terms Dominant and Recessive to Sex-Linked Mutants 16

The Genetic Utility of Dominant and Recessive Mutants 17

1.3 Summary 17

References 17

2 Mutant Hunts 20

2.1 Why Look for New Mutants? 20

Reason 1: To Identify Genes Required for a Specific Biological Process 21

Reason 2: To Isolate more Mutations in a Specific Gene of Interest 31

Reason 3: To Obtain Mutants for a Structure-Function Analysis 32

Reason 4: To Isolate Mutations in a Gene So Far Identified only by Computational Approaches 32

2.2 Mutagenesis and Mutational Mechanisms 32

Method 1: Ionizing Radiation 33

Method 2: Chemical Mutagens 33

Alkylating Agents 34

Crosslinking Agents 35

Method 3: Transposons 35

Identifying Where Your Transposon Landed 37

Why not Always Screen With TEs? 40

Method 4: Targeted Gene Disruption 40

RNA Interference 40

CRISPR/Cas9 41

TALENs 42

So Which Mutagen Should You Use? 43

2.3 What Phenotype Should You Screen (or Select) for? 44

2.4 Actually Getting Started 45

Your Starting Material 45

Pilot Screen 45

What to Keep? 45

How many Mutants is Enough? 46

Estimating the Number of Genes not Represented by Mutants in Your New Collection 46

2.5 Summary 48

References 48

3 Complementation 51

3.1 The Essence of the Complementation Test 51

3.2 Rules for Using the Complementation Test 55

The Complementation Test Can be Done Only When Both Mutants are Fully Recessive 55

The Complementation Test Does Not Require that the Two Mutants Have Exactly the Same Phenotype 56

The Phenotype of a Compound Heterozygote Can be More Extreme than that of Either Homozygote 56

3.3 How the Complementation Test Might Lie to You 57

Two Mutations in the Same Gene Complement Each Other 57

A Mutation in One Gene Silences Expression of a Nearby Gene 57

Mutations in Regulatory Elements 59

3.4 Second-Site Noncomplementation (Nonallelic Noncomplementation) 59

Type 1 SSNC (PoisonousInteractions): The Interaction is Allele Specific at Both Loci 60

An Example of Type 1 SSNC Involving the Alpha- and Beta-Tubulin Genes in Yeast 60

An Example of Type 1 SSNC Involving the Actin Genes in Yeast 62

Type 2 SSNC (Sequestration): The Interaction is Allele Specific at One Locus 66

An Example of Type 2 SSNC Involving the Tubulin Genes in Drosophila 66

An Example of Type 2 SSNC in Drosophila that Does Not Involve the Tubulin Genes 69

An Example of Type 2 SSNC in the Nematode Caenorhabditis elegans 71

Type 3 SSNC (Combined Haploinsufficiency): The Interaction is Allele-Independent at Both Loci 72

An Example of Type 3 SSNC Involving Two Motor Protein Genes in Flies 72

Summary of SSNC in Model Organisms 72

SSNC in Humans (Digenic Inheritance) 73

Pushing the Limits: Third-Site Noncomplementation 74

3.5 An Extension of SSNC: Dominant Enhancers 74

A Successful Screen for Dominant Enhancers 75

3.6 Summary 76

References 77

4 Meiotic Recombination 81

4.1 An Introduction to Meiosis 81

A Cytological Description of Meiosis 88

A More Detailed Description of Meiotic Prophase 89

4.2 Crossing Over and Chiasmata 92

4.3 The Classical Analysis of Recombination 93

4.4 Measuring the Frequency of Recombination 96

The Curious Relationship Between the Frequency of Recombination and Chiasma Frequency 97

Map Lengths and Recombination Frequency 97

The Mapping Function 99

Tetrad Analysis 100

Statistical Estimation of Recombination Frequencies 101

Two-Point Linkage Analysis 101

What Constitutes Statistically Significant Evidence for Linkage? 104

An Example of LOD Score Analysis 105

Multipoint Linkage Analysis 105

Local Mapping via Haplotype Analysis 106

The Endgame 108

The Actual Distribution of Exchange Events 109

The Centromere Effect 110

The Effects of Heterozygosity for Aberration Breakpoints on Recombination 110

Practicalities of Mapping 110

4.5 The Mechanism of Recombination 111

Gene Conversion 111

Early Models of Recombination 112

The Holliday Model 112

The Meselson-Radding Model 114

The Currently Accepted Mechanism of Recombination: The Double-Strand Break Repair Model 114

Class I Versus Class II Recombination Events 116

4.6 Summary 117

References 118

5 Identifying Homologous Genes 126

5.1 Homology 126

Orthologs 127

Paralogs 127

Xenologs 128

5.2 Identifying Sequence Homology 128

Nucleotide-Nucleotide BLAST (blastn) 129

An Example Using blastn 129

Translated Nucleotide-Protein BLAST (blastx) 131

An Example Using blastx 131

Protein-Protein BLAST (blastp) 132

An Example Using blastp 132

Translated BLASTx (tblastx) and Translated BLASTn (tblastn) 133

5.3 How Similar is Similar? 133

5.4 Summary 134

References 134

6 Suppression 136

6.1 Intragenic Suppression 137

Intragenic Suppression of Loss-of-Function Mutations 137

Intragenic Suppression of a Frameshift Mutation by the Addition of a Second, Compensatory Frameshift Mutation 138

Intragenic Suppression of Missense Mutations by the Addition of a Second and Compensatory Missense Mutation 140

Intragenic Suppression of Antimorphic Mutations that Produce a Poisonous Protein 141

6.2 Extragenic Suppression 141

6.3 Transcriptional Suppression 141

Suppression at the Level of Gene Expression 142

A CRISPR Screen for Suppression of Inhibitor Resistance in Melanoma 142

Suppression of Transposon-Insertion Mutants by Altering the Control of mRNA Processing 143

Suppression of Nonsense Mutants by Messenger Stabilization 143

6.4 Translational Suppression 144

tRNA-Mediated Nonsense Suppression 144

The Numerical and Functional Redundancy of tRNA Genes Allows Suppressor Mutations to be Viable 146

tRNA-Mediated Frameshift Suppression 146

6.5 Suppression by Post-Translational Modification 147

6.6 Conformational Suppression: Suppression as a Result of Protein-Protein Interaction 147

Searching for Suppressors that Act by Protein-Protein Interaction in Eukaryotes 148

Actin and Fimbrin in Yeast 148

Mediator Proteins and RNA Polymerase II in Yeast 150

"Lock-and-key" Conformational Suppression 152

Suppression of a Flagellar Motor Mutant in E. coli 152

Suppression of a Mutant Transporter Gene in C. elegans 152

Suppression of a Telomerase Mutant in Humans 153

6.7 Bypass Suppression: Suppression Without Physical Interaction 154

"Push me, Pull You" Bypass Suppression 155

Multicopy Bypass Suppression 156

6.8 Suppression of Dominant Mutations 157

6.9 Designing Your Own Screen for Suppressor Mutations 157

6.10 Summary 158

References 158

7 Epistasis Analysis 163

7.1 Ordering Gene Function in Pathways 163

Biosynthetic Pathways 164

Nonbiosynthetic Pathways 165

7.2 Dissection of Regulatory Hierarchies 167

Epistasis Analysis Using Mutants with Opposite Effects on the Phenotype 167

Hierarchies for Sex Determination in Drosophila 169

Epistasis Analysis Using Mutants with the Same or Similar Effects on the Final Phenotype 170

Using Opposite-Acting Conditional Mutants to Order Gene Function by Reciprocal Shift Experiments 170

Using a Drug or Agent that Stops the Pathway at a Given Point 170

Exploiting Subtle Phenotypic Differences Exhibited by Mutants that Affect the Same Signal State 172

7.3 How Might an Epistasis Experiment Mislead You? 172

7.4 Summary 173

References 173

8 Mosaic Analysis 175

8.1 Tissue Transplantation 176

Early Tissue Transplantation in Drosophila 176

Tissue Transplantation in Zebrafish 177

8.2 Mitotic Chromosome Loss 178

Loss of the Unstable Ring-X Chromosome 179

Other Mechanisms of Mitotic Chromosome Loss 179

Mosaics Derived from Sex Chromosome Loss in Humans and Mice (Turner Syndrome) 180

8.3 Mitotic Recombination 181

Gene Knockout Using the FLP/FRT or Cre-Lox Systems 182

8.4 Tissue-Specific Gene Expression 184

Gene Knockdown Using RNAi 184

Tissue-Specific Gene Editing Using CRISPR/Cas9 185

8.5 Summary 187

References 188

9 Meiotic Chromosome Segregation 191

9.1 Types and Consequences of Failed Segregation 192

9.2 The Origin of Spontaneous Nondisjunction 193

MI Exceptions 194

MII Exceptions 194

9.3 The Centromere 195

The Isolation and Analysis of the Saccharomyces cerevisiae Centromere 195

The Isolation and Analysis of the Drosophila Centromere 198

The Concept of the Epigenetic Centromere in Drosophila and Humans 200

Holocentric Chromosomes 201

9.4 Chromosome Segregation Mechanisms 202

Chiasmate Chromosome Segregation 202

Segregation Without Chiasmata (Achiasmate Chromosome Segregation) 203

Achiasmate Segregation in Drosophila Males 203

Achiasmate Segregation in D. melanogaster Females 204

Achiasmate Segregation in S. cerevisiae 205

Achiasmate Segregation in S. pombe 207

Achiasmate Segregation in Silkworm Females 207

9.5 Meiotic Drive 207

Meiotic Drive Via Spore Killing 207

An Example in Schizosaccharomyces pombe 207

An Example in D. melanogaster 208

Meiotic Drive Via Directed Segregation 208

9.6 Summary 210

References 210

Appendix A: Model Organisms 215

Appendix B: Genetic Fine-Structure Analysis 228

Appendix C: Tetrad Analysis 250

Glossary 262

Index 275
Danny E. Miller, MD, PhD is an Assistant Professor in the Department of Pediatrics, Division of Genetic Medicine and Laboratory Medicine & Pathology at the University of Washington in Seattle, WA, USA. He is the recipient of the 2017 Larry Sandler Memorial Award, the 2018 Lawrence E. Lamb Prize for Medical Research, and a 2022 National Institutes of Health Director's Early Independence Award. Dr Miller is a leader in the field of long-read sequencing technology and the use of new technology to evaluate individuals with unsolved genetic disorders.

Angela L. Miller is a Research Coordinator at the University of Washington in Seattle, WA, USA, with a background in journalism, visual communications, and molecular biology. She has published several peer-reviewed papers and has won multiple national awards for her work as a journal art director.

R. Scott Hawley, PhD is an Investigator at the Stowers Institute for Medical Research, Kansas City, MO, USA. He is a member of the National Academy of Sciences and former President of the Genetics Society of America, with faculty positions at the University of Kansas Medical Center and the University of Missouri-Kansas City. During his distinguished career, Dr. Hawley has mentored hundreds of trainees, received numerous genetics awards, written six textbooks, and published extensively on meiosis.

D. E. Miller, University of Washington, Seattle, WA; A. L. Miller, University of Washington, Seattle, WA; R. S. Hawley, Stowers Institute for Medical Research, Kansas City, MO