Advanced Genetic Analysis Finding Meaning in a Genome

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ISBN: 9781405103367 | 1405103361
Cover: Paperback
Copyright: 1/31/2003

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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 author's 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. Basic principles - Focuses students attention on the 'how' and 'why' of the essential analytical tools. Vibrant, accessible style provides an easy guide through difficult genetic concepts and techniques. Text boxes highlight key questions and timely examples. Boxes of key information in each chapter, chapter summaries and extensive references - prompt the student to synthesise and reinforce the chapter material. Special reference section addressing a range of model organisms to help provide a particularly relevant context for students' research interests.

Preface

Introduction

xiv

Mutation

(30)

Types of mutations

(10)

Muller's classification of mutants

(7)

Modern mutant terminology

(1)

DNA-level terminology

(1)

Dominance and recessivity

(3)

Dominance and recessivity at the level of the cell

(1)

Difficulties in applying the terms ``dominant'' and ``recessive'' to sex-linked mutants

(1)

The genetic utility of dominant and recessive mutants

(17)

Summary

(1)

Gallery of model organisms

(1)

Our favorite organism: Drosophila melanogaster

(3)

Our second favorite organism: Saccharomyces cerevisiae

(1)

Our third favorite organism: Caenorhabditis elegans

(2)

Our new favorite organism: zebrafish

(2)

Phage lambda

(2)

Phage T4

(2)

Arabidopsis thaliana

(1)

Mus musculus (the mouse)

(3)

Mutant hunts

(24)

Why look for new mutants?

(6)

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

(3)

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

(3)

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

(1)

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

(1)

Mutagenesis and mutational mechanisms

(8)

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

(1)

Method 2: Chemical mutagens

(2)

Method 3: Transposons as mutagens

(2)

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

(2)

What phenotype should you screen (or select) for?

(1)

Actually getting started

(8)

Your starting material

(1)

Pilot screens

(1)

Keeping too many, keeping too few

(1)

How many mutants is enough?

(2)

Summary

A screen for embryonic lethal mutations in Drosophila

(1)

The balancer chromosome

(2)

A screen for sex-linked lethal mutations in Drosophila

(9)

Making phenocopies by RNAi and co-suppression

(6)

Reviews of mutant isolation schemes and techniques in various organisms

(4)

The complementation test

(27)

The essence of the complementation test

(3)

Rules for using the complementation test

(2)

How might the complementation test lie to you?

(1)

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

(18)

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

(8)

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

(6)

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

(1)

Summary of SSNC

(2)

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

(3)

A successful screen for dominant enhancers

(2)

Summary

A more rigorous definition of the complementation test

(1)

An example of using the complementation test in yeast

(1)

Transformation rescue is a variant of the complementation test

(1)

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

(3)

Pairing-dependent complementation: transvection

(5)

Synthetic lethality and genetic buffering

(15)

Suppression

(25)

A basic definition of genetic suppression

(1)

Intragenic suppression (pseudo-reversion)

(5)

Intragenic revertants can mediate translational suppression

(2)

Intragenic suppression as a result of compensatory mutants

(2)

Extragenic suppression

(1)

Transcriptional suppression

(2)

Suppression at the level of gene expression

(1)

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

(1)

Suppression of nonsense mutants by messenger stabilization in C. elegans

(1)

Translational suppression

(3)

Simplicity: tRNA suppressors in E. coli

(2)

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

(1)

Suppression of a frameshift mutation using a mutant tRNA gene

(1)

Suppressing a nonsense codon using unaltered tRNAs

(1)

Suppression by post-translational modification

(1)

Extragenic suppression as a result of protein-protein interaction

(6)

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

(5)

Extragenic suppression as a result of ``lock-and-key'' conformational suppression

100

(1)

Suppression without physical interaction

100

(5)

Bypass suppression

101

(1)

``Push me, pull you'' bypass selection by counterbalancing of opposite activities

102

(1)

Extra-copy suppression as a form of bypass suppression

103

(2)

Suppression of dominant mutations

105

(1)

Designing your own screen for suppressor mutations

105

(2)

Summary and a warning

106

Intragenic suppression of antimorphic mutations that produce a poisonous protein

(15)

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

102

(5)

Determining when and where genes function

107

(20)

Epistasis: ordering gene function in pathways

107

(11)

Ordering gene function in a biosynthetic pathway

108

(1)

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

109

(2)

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

111

(7)

How might an epistasis experiment mislead you?

118

(1)

Mosaic analysis: where does a given gene act?

118

(9)

Tissure transplantation studies

119

(1)

Loss of the unstable ring X chromosome

120

(3)

Mitotic recombination

123

(1)

Genetically controllable mitotic recombination: the FLP-FRT system

124

(2)

Summary

126

(1)

Genetic fine-structure analysis

127

(24)

Intragenic mapping (then)

127

(7)

The first efforts towards finding structure within a gene

127

(2)

The unit of recombination and mutation is the base pair

129

(5)

Intragenic mapping (now)

134

(1)

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

135

(3)

The formal analysis of intragenic complementation

136

(2)

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

138

(1)

A genetic and functional dissection of the HIS4 gene in yeast

138

(1)

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

139

(3)

Genetic and functional dissection of the cut gene in Drosophila

139

(3)

Pairing-dependent intragenic complementation

142

(9)

Genetic and functional dissection of the yellow gene in Drosophila

142

(1)

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

143

(2)

Genetic and functional dissection of BX-C in Drosophila

145

(1)

Summary

146

(1)

Genetic and functional dissection of the rudimentary gene in Drosophila

147

(4)

Meiotic recombination

151

(49)

An introduction to meiosis

151

(9)

A cytological description of meiosis

158

(2)

A more detailed description of meiotic prophase

160

(1)

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

160

(2)

The classical analysis of recombination

162

(5)

Measuring the frequency of recombination

167

(26)

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

167

(1)

Map lengths and recombination frequency

168

(3)

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

171

(11)

Statistical estimation of recombination frequencies (LOD scores)

182

(10)

The actual distribution of exchange events

192

(1)

Practicalities of mapping

193

(1)

The mechanism of recombination

193

(7)

Gene conversion

193

(2)

Previous models

195

(3)

The currently accepted mechanism of recombination: the DSBR model

198

(1)

Summary

199

The molecular biology of synapsis

155

(1)

Do specific chromosomal sites mediate pairing?

156

(7)

Crossingover in compound X chromosomes

163

(3)

Does any sister chromatid exchange occur during meiosis?

166

(11)

Using tetrad analysis to determine linkage

177

(1)

Mapping centromeres in fungi with unordered tetrads

177

(23)

Meiotic chromosome segregation

200

(19)

Types and consequences of failed segregation

201

(1)

The origin of spontaneous nondisjunction

202

(2)

The centromere

204

(9)

The isolation and analysis of the S. cerevisiae centromere

204

(3)

The isolation and analysis of the Drosophila centromere

207

(6)

Segregational mechanisms

213

(6)

How chiasmata ensure segregation

213

(1)

Achiasmate segregation

214

(4)

Summary

218

Identifying genes that encode centromere-binding proteins in yeast

206

(6)

The concept of the epigenetic centromere in Drosophila and humans

212

(5)

Achiasmate heterologous segregation in Drosophila females

217

(2)

Epilogue

219

(1)

References

220

(16)

Partial author index

236

(2)

Subject index

238

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Advanced Genetic Analysis Finding Meaning in a Genome

Summary

Author Biography

Table of Contents

Supplemental Materials