Principles of Genome Analysis and Genomics

With the first draft of the human genome project in the public domain and full analyses of model genomes now available, the subject matter of 'Principles of Genome Analysis and Genomics' is even 'hotter' now than when the first two editions were published in 1995 and 1998. In the new edition of this very practical guide to the different techniques and theory behind genomes and genome analysis, Sandy Primrose and new author Richard Twyman provide a fresh look at this topic. In the light of recent exciting advancements in the field, the authors have completely revised and rewritten many parts of the new edition with the addition of five new chapters. Aimed at upper level students, it is essential that in this extremely fast moving topic area the text is up to date and relevant. Completely revised new edition of an established textbook. Features new chapters and examples from exciting new research in genomics, including the human genome project. Excellent new co-author in Richard Twyman, also co-author of the new edition of hugely popular Principles of Gene Manipulation. Accompanying web-page to help students deal with this difficult topic at www.blackwellpublishing.com/primrose

Richard Twyman is a Visiting Fellow at the Department of Biology, University of York.

Preface

v

Abbreviations

vi

Setting the scene: the new science of genomics

1

(9)

Introduction

1

(1)

Physical mapping of genomes

1

(2)

Sequencing whole genomes

3

(2)

Benefits of genome sequencing

5

(1)

Outline of the rest of the book

6

(2)

Terminology

8

(1)

Keeping up to date

8

(1)

Suggested reading

8

(1)

Useful websites

9

(1)

The organization and structure of genomes

10

(24)

Introduction

10

(1)

Genome size

10

(1)

Sequence complexity

11

(2)

Introns and exons

13

(3)

Genome structure in viruses and prokaryotes

16

(2)

The organization of organelle genomes

18

(1)

The organization of nuclear DNA in eukaryotes

19

(14)

Suggested reading

33

(1)

Useful websites

33

(1)

Subdividing the genome

34

(13)

Introduction

34

(1)

Fragmentation of DNA with restriction enzymes

34

(2)

Separating large fragments of DNA

36

(1)

Isolation of chromosomes

37

(2)

Chromosome microdissection

39

(1)

Vectors for cloning DNA

39

(1)

Yeast artificial chromosomes

40

(2)

P1-derived and bacterial artificial chromosomes as alternatives to yeast artificial chromosomes

42

(2)

Retrofitting

44

(1)

Choice of vector

45

(1)

Suggested reading

45

(1)

Useful website

46

(1)

Assembling a physical map of the genome

47

(24)

Introduction

47

(1)

Restriction enzyme fingerprinting

47

(2)

Marker sequences

49

(10)

Hybridization assays

59

(5)

Physical mapping without cloning

64

(5)

Integration of different mapping methods

69

(1)

Suggested reading

70

(1)

Useful websites

70

(1)

Sequencing methods and strategies

71

(23)

Basic DNA sequencing

71

(2)

Modifications of chain-terminator sequencing

73

(2)

Automated DNA sequencing

75

(1)

DNA sequencing by capillary array electrophoresis

76

(1)

Basecalling and sequence accuracy

77

(1)

High-throughput sequencing

77

(1)

Sequencing strategies

78

(7)

Alternative DNA sequencing methodologies

85

(7)

Suggested reading

92

(1)

Useful websites

93

(1)

Genome annotation and bioinformatics

94

(19)

Introduction

94

(1)

Traditional routes to gene identification

94

(3)

Databases

97

(1)

Overview of sequence analysis

97

(2)

Detecting open-reading frames

99

(1)

Software programs for finding genes

99

(3)

Using homology to find genes

102

(3)

Analysis of non-coding RNA and extragenic DNA

105

(1)

Identifying the function of a new gene

105

(2)

Secondary databases of functional domains

107

(1)

Gene ontology

108

(1)

Analyses not based on homology

108

(3)

Genome annotation

111

(1)

Molecular phylogenetics

111

(1)

Suggested reading

112

(1)

Useful websites

112

(1)

Comparative genomics

113

(20)

Introduction

113

(1)

Orthologues, paralogues and gene displacement

113

(1)

Protein evolution by exon shuffling

113

(1)

Comparative genomics of prokaryotes

114

(7)

Comparative genomics of organelles

121

(2)

Comparative genomics of eukaryotes

123

(7)

Other aspects of comparative genomics

130

(2)

Suggested reading

132

(1)

Useful websites

132

(1)

Protein structural genomics

133

(13)

Introduction

133

(1)

Determining gene function by sequence comparison

133

(1)

Determining gene function through conserved protein structure

134

(2)

Approaches to protein structural genomics

136

(8)

Suggested reading

144

(1)

Useful website

145

(1)

Global expression profiling

146

(27)

Introduction

146

(1)

Traditional approaches to expression profiling

146

(2)

Global analysis of RNA expression

148

(15)

Global analysis of protein expression

163

(8)

Suggested reading

171

(1)

Useful websites

172

(1)

Comprehensive mutant libraries

173

(14)

Introduction

173

(1)

High-throughput systematic gene knockout

173

(2)

Genome-wide random mutagenesis

175

(11)

Suggested reading

186

(1)

Useful websites

186

(1)

Mapping protein interactions

187

(13)

Introduction

187

(1)

Methods for protein interaction analysis

187

(2)

Library-based methods for screening protein interactions

189

(1)

Interactions

189

(7)

Informatics tools and resources for protein interaction data

196

(3)

Suggested reading

199

(1)

Useful websites

199

(1)

Applications of genome analysis and genomics

200

(30)

Introduction

200

(1)

Theme 1: Understanding genetic diseases of humans

200

(9)

Theme 2: Understanding responses to drugs (pharmacogenomics)

209

(2)

Theme 3: Getting to grips with bacterial pathogenicity

211

(7)

Theme 4: Getting to grips with quantitative traits

218

(5)

Theme 5: The impact of genomics on agriculture

223

(2)

Theme 6: Developmental genomics

225

(3)

Suggested reading

228

(2)

References

230

(25)

Index

255

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Principles of Genome Analysis and Genomics

Summary

Author Biography

Table of Contents

Supplemental Materials