Advanced genetic analysis : finding meaning in a genome / R. Scott Hawley and Michelle Y. Walker.

Format:

Book

Author/Creator:

Hawley, R. Scott.

Contributor:

Walker, Michelle Y.

Language:

English

Subjects (All):

Genetics--Research--Methodology.

Genetics.

Genetic Techniques.

Genetics--Research.

Medical Subjects:

Genetics.

Genetic Techniques.

Physical Description:

xv, 239 pages : illustrations ; 25 cm

Place of Publication:

Malden, MA : Blackwell Pub., 2003.

Summary:

Advanced Genetic Analysis brings a state-of-the-art, exciting new approach to genetic analysis. Focusing on the underlying principles of modern genetic analysis, this book provides the "how" and "why" of the essential analytical tools needed. The authors' vibrant, accessible style provides an easy guide to difficult genetic concepts, from mutation and gene function to gene mapping and chromosome segregation. Throughout, a balanced range of model organisms and timely examples are used to illustrate the theoretical basics.

Contents:

Chapter 1 Mutation 1

1.1 Types of mutations 1

1.1.1 Muller's classification of mutants 2

1.1.3 DNA-level terminology 10

1.2 Dominance and recessivity 11

1.2.1 Dominance and recessivity at the level of the cell 12

1.2.2 Difficulties in applying the terms "dominant" and "recessive" to sex-linked mutants 13

1.3 The genetic utility of dominant and recessive mutants 14

1.1 Our favorite organism: Drosophila melanogaster 15

1.2 Our second favorite organism: Saccharomyces cerevisiae 18

1.3 Our third favorite organism: Caenorhabditis elegans 19

1.4 Our new favorite organism: zebrafish 21

1.5 Phage lambda 23

1.6 Phage T4 25

1.7 Arabidopsis thaliana 27

1.8 Mus musculus (the mouse) 28

Chapter 2 Mutant hunts 31

2.1 Why look for new mutants? 32

2.1.1 Reason 1: To identify genes required for a specific biological process 32

2.1.2 Reason 2: To isolate more mutations in a specific gene of interest 35

2.1.3 Reason 3: To obtain mutations tools for structure-function analysis 38

2.1.4 Reason 4: To isolate mutations in a gene so far identified only by molecular approaches 38

2.2 Mutagenesis and mutational mechanisms 38

2.2.1 Method 1: Ionizing radiation (usually X-rays and gamma-rays) 39

2.2.2 Method 2: Chemical mutagens 40

2.2.3 Method 3: Transposons as mutagens 42

2.2.4 Method 4: Targeted gene disruption (a variant on transposon mutagenesis) 44

2.3 What phenotype should you screen (or select) for? 46

2.4 Actually getting started 47

2.4.1 Your starting material 47

2.4.2 Pilot screens 47

2.4.3 Keeping too many, keeping too few 48

2.4.4 How many mutants is enough? 48

Box 2.1 A screen for embryonic lethal mutations in Drosophila 33

Box 2.2 The balancer chromosome 34

Box 2.3 A screen for sex-linked lethal mutations in Drosophila 36

Box 2.4 Making phenocopies by RNAi and co-suppression 45

Box 2.5 Reviews of mutant isolation schemes and techniques in various organisms 51

Chapter 3 The complementation test 55

3.1 The essence of the complementation test 55

3.2 Rules for using the complementation test 58

3.3 How might the complementation test lie to you? 60

3.4 Second-site non-complementation (SSNC) (non-allelic non-complementation) 61

3.4.1 Type 1 SSNC (poisonous interactions): the interaction is allele-specific at both loci 62

3.4.2 Type 2 SSNC (sequestration): the interaction is allele-specific at one locus 70

3.4.3 Type 3 SSNC (combined haplo-insufficiency): the interaction is allele-independent at both loci 76

3.4.4 Summary of SSNC 77

3.5 An extension of second-site non-complementation: dominant enhancers 79

3.5.1 A successful screen for dominant enhancers 79

Box 3.1 A more rigorous definition of the complementation test 56

Box 3.2 An example of using the complementation test in yeast 57

Box 3.3 Transformation rescue is a variant of the complementation test 58

Box 3.4 One method for determining whether or not a dominant mutation is an allele of a given gene, or how to make dominants into recessives by pseudo-reversion 59

Box 3.5 Pairing-dependent complementation: transvection 62

Box 3.6 Synthetic lethality and genetic buffering 67

Chapter 4 Suppression 82

4.1 A basic definition of genetic suppression 82

4.2 Intragenic suppression (pseudo-reversion) 83

4.2.1 Intragenic revertants can mediate translational suppression 84

4.2.2 Intragenic suppression as a result of compensatory mutants 86

4.3 Extragenic suppression 88

4.4 Transcriptional suppression 88

4.4.1 Suppression at the level of gene expression 88

4.4.2 Suppression of transposon insertion mutants by altering the control of mRNA processing 89

4.4.3 Suppression of nonsense mutants by messenger stabilization in C. elegans 89

4.5 Translational suppression 90

4.5.1 Simplicity: tRNA suppressors in E. coli 90

4.5.2 The numerical and functional redundancy of tRNA genes allowing suppressor mutations to be viable 92

4.5.3 Suppression of a frameshift mutation using a mutant tRNA gene 93

4.5.4 Suppressing a nonsense codon using unaltered tRNAs 93

4.6 Suppression by post-translational modification 93

4.7 Extragenic suppression as a result of protein-protein interaction 94

4.7.1 Searching for suppressors that act by protein-protein interaction in eukaryotes 95

4.7.2 Extragenic suppression as a result of "lock-and-key" conformational suppression 100

4.8 Suppression without physical interaction 100

4.8.1 Bypass suppression 101

4.8.2 "Push me, pull you" bypass selection by counterbalancing of opposite activities 102

4.8.3 Extra-copy suppression as a form of bypass suppression 103

4.9 Suppression of dominant mutations 105

4.10 Designing your own screen for suppressor mutations 105

Box 4.1 Intragenic suppression of antimorphic mutations that produce a poisonous protein 87

Box 4.2 Bypass suppression of a telomere defect in the yeast S. pombe 102

Chapter 5 Determining when and where genes function 107

5.1 Epistasis: ordering gene function in pathways 107

5.1.1 Ordering gene function in a biosynthetic pathway 108

5.1.2 The use of epistasis in non-biosynthetic pathways: determining if two genes act in the same or different pathways 109

5.1.3 The real value of epistasis analysis is in the dissection of regulatory hierarchies 111

5.1.4 How might an epistasis experiment mislead you? 118

5.2 Mosaic analysis: where does a given gene act? 118

5.2.1 Tissure transplantation studies 119

5.2.2 Loss of the unstable ring X chromosome 120

5.2.3 Mitotic recombination 123

5.2.4 Genetically controllable mitotic recombination: the FLP-FRT system 124

Chapter 6 Genetic fine-structure analysis 127

6.1 Intragenic mapping (then) 127

6.1.1 The first efforts towards finding structure within a gene 127

6.1.2 The unit of recombination and mutation is the base pair 129

6.2 Intragenic mapping (now) 134

6.3 Intragenic complementation meets intragenic recombination: the basis of fine-structure analysis 135

6.3.1 The formal analysis of intragenic complementation 136

6.4 An example of fine-structure analysis for a eukaryotic gene encoding a multifunctional protein 138

6.4.1 A genetic and functional dissection of the HIS4 gene in yeast 138

6.5 Fine-structure analysis of genes with complex regulatory elements in eukaryotes 139

6.5.1 Genetic and functional dissection of the cut gene in Drosophila 139

6.6 Pairing-dependent intragenic complementation 142

6.6.1 Genetic and functional dissection of the yellow gene in Drosophila 142

6.6.2 The influence of the zeste gene on pairing-dependent complementation at the white locus in Drosophila 143

6.6.3 Genetic and functional dissection of BX-C in Drosophila 145

Box 6.1 Genetic and functional dissection of the rudimentary gene in Drosophila 147

Chapter 7 Meiotic recombination 151

7.1 An introduction to meiosis 151

7.1.1 A cytological description of meiosis 158

7.1.2 A more detailed description of meiotic prophase 160

7.2 Crossingover and chiasmata: recombination involves the physical interchange of genetic material and ensures homolog separation 160

7.3 The classical analysis of recombination 162

7.4 Measuring the frequency of recombination 167

7.4.1 The curious relationship between the frequency of recombination and chiasma frequency (and why it matters) 167

7.4.2 Map lengths and recombination frequency 168

7.4.3 Determining the fraction of bivalents with zero, one, two, or more exchanges (tetrad analysis) 171

7.4.4 Statistical estimation of recombination frequencies (LOD scores) 182

7.4.5 The actual distribution of exchange events 192

7.4.6 Practicalities of mapping 193

7.5 The mechanism of recombination 193

7.5.1 Gene conversion 193

7.5.2 Previous models 195

7.5.3 The currently accepted mechanism of recombination: the DSBR model 198

Box 7.1 The molecular biology of synapsis 155

Box 7.2 Do specific chromosomal sites mediate pairing? 156

Box 7.3 Crossingover

in compound X chromosomes 163

Box 7.4 Does any sister chromatid exchange occur during meiosis? 166

Box 7.5 Using tetrad analysis to determine linkage 177

Box 7.6 Mapping centromeres in fungi with unordered tetrads 177

Chapter 8 Meiotic chromosome segregation 200

8.1 Types and consequences of failed segregation 201

8.2 The origin of spontaneous nondisjunction 202

8.3 The centromere 204

8.3.1 The isolation and analysis of the S. cerevisiae centromere 204

8.3.2 The isolation and analysis of the Drosophila centromere 207

8.4 Segregational mechanisms 213

8.4.1 How chiasmata ensure segregation 213

8.4.2 Achiasmate segregation 214

Box 8.1 Identifying genes that encode centromere-binding proteins in yeast 206

Box 8.2 The concept of the epigenetic centromere in Drosophila and humans 212

Box 8.3 Achiasmate heterologous segregation in Drosophila females 217.

Notes:

Includes bibliographical references (pages [220]-235) and indexes.

ISBN:

1405103361

OCLC:

49795681