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Tables of Contents for DNA Recombination and Repair
Chapter/Section Title
Page #
Page Count
List of contributors
xv
Abbreviations
xvii
Molecular processing of DNA folding anomalies in Escherichia coli
1
15
David R. F. Leach
Introduction
1
1
Folding anomalies in DNA
1
5
Hairpin DNA
1
1
Pseudo-hairpin DNA and S-DNA
2
2
H-DNA, *H-DNA, and nodule DNA
4
2
Z-DNA
6
1
Quadruplex DNA
6
1
Deletions at direct repeats stimulated by closely spaced inverted repeats
6
2
Duplications and inversions stimulated by closely spaced inverted repeats
8
1
Deletions and amplifications of triplet repeats
9
1
Inhibition of DNA replication and initiation of homologous recombination by SbcCD protein
9
1
Conclusions
10
6
Acknowledgements
11
1
References
12
4
Double-strand break repair and V(D)J recombination
16
22
Belinda K. Singleton
Penny A. Jeggo
Introduction
16
1
V(D)J recombination
16
3
Recognition and cleavage of the signal sequences
17
1
Processing and joining the dsbs
17
2
Mechanisms of DNA double-strand break repair
19
6
Homologous recombination
19
3
Single-strand annealing
22
1
Non-homologous end-joining (NHEJ)
22
3
Identification of the genes involved in NHEJ
25
2
DNA-dependent protein kinase, DNA-PK
25
1
XRCC4 and DNA ligase IV
26
1
Yeast as a model system
27
1
The phenotypes of mammalian mutants defective in NHEJ
27
3
Conclusions
30
8
References
31
7
Translesion replication
38
28
Christopher Lawrence
Roger Woodgate
Introduction
38
2
Tranlesion replication in E. coli
40
10
Translesion replication is usually a strategy of last resort
40
1
Most translesion replication is dependent upon the Umu proteins
41
1
Umu-dependent TR is regulated with exquisite precision
42
3
Formation of the mutasome and translesion replication
45
2
The Umu proteins are generalized elongation factors
47
1
Translesion replication in the absence of Umu proteins
48
2
Translesion replication in yeast
50
5
Genes important for TR and their mutant phenotypes
50
1
Regulation of translesion replication
51
2
Molecular and enzymatic analysis of REV gene function
53
2
The mutagenic properties of DNA damage
55
1
Comparisons, speculations, and TR in humans
56
10
References
58
8
Mismatch repair and cancer
66
33
P. Karran
M. Bignami
Introduction
66
1
Bacterial mismatch repair
67
2
The identification of bacterial mismatch repair genes
67
1
The biochemistry of mismatch repair in Escherichia coli
68
1
Human mismatch repair
69
13
Identification of human mismatch repair genes
69
2
Microsatellite instability and mutator effects in repair-defective human cells
71
7
The biochemistry of the human mismatch repair pathway
78
3
An alternative mismatch repair pathway
81
1
Mismatch repair defects in mouse models
82
2
Mice as models for HNPCC
84
1
Mismatch repair defects and susceptibility to therapeutic agents
84
3
Important areas for the future
87
12
Mismatch repair, transcription-coupled excision repair, and recombinational repair
87
1
Adaptive responses and reduced mismatch repair efficiency
88
1
Epigenetic effects on mismatch repair genes
88
1
Mismatch repair cell-cycle checkpoints and apoptosis
89
1
References
90
9
Enzymology of human nucleotide excision repair
99
39
Hanspeter Naegeli
Introduction
99
1
Human NER factors and general strategies
100
2
The human genetic framework: xeroderma pigmentosum
102
1
The biochemical framework: in vitro reconstitution of human NER activity
103
9
XPA
103
3
RPA
106
1
XPA-HHR23B
107
1
TFIIH
108
2
XPF-ERCC1 and XPG
110
2
RFC, PCNA, DNA Pol ϵ, and DNA ligase I
112
1
The substrate-discrimination problem
112
8
Heterogeneity of DNA damage recognition
113
1
Damaged DNA binding proteins
114
2
Shielding from excision repair
116
1
The damaged DNA binding function of XPA protein
117
2
The role of multiprotein assembly in damage recognition
119
1
Bipartite substrate discrimination in human NER
120
8
Analysis of substrate discrimination using C4' backbone modifications
120
3
Significance of bipartite recognition in mutagenesis and carcinogenesis
123
2
A potential sensor of defective Watson-Crick hybridization
125
1
A potential sensor of defective deoxyribonucleotide chemistry
126
2
Conclusions
128
10
Acknowledgements
129
1
References
129
9
Transcription-coupled and global genome repair in yeast and humans
138
28
Marcel Tijsterman
Richard A. Verhage
Jaap Brouwer
Introduction
138
1
Techniques
139
2
Gene-Specific repair analysis
139
1
Nucleotide-specific repair analysis
139
2
Nucleotide excision repair in vitro
141
1
Transcription-coupled nucleotide excision repair
141
11
General features of RNA polymerase II transcription
144
1
TFIIH: required for RNA pol II transcription and nucleotide excision repair
145
1
Coupling NER to transcription in E. coli: a paradigm for eukaryotes?
146
1
Transcription-coupled repair in humans
146
2
Transcription-coupled repair in the yeast Saccharomyces cerevisiae
148
2
Molecular mechanisms of TCR in eukaryotes
150
2
Global genome nucleotide excision repair
152
5
XP-C and repair of non-transcribed DNA
154
1
Rad7 and Rad16 and repair of non-transcribed DNA
155
2
Connections between NER and other repair pathways
157
9
NER and direct reversal by DNA photolyases
158
1
NER and mismatch repair
158
1
Nucleotide and base excision repair
158
1
Acknowledgements
159
1
References
159
7
The ATM gene and stress response
166
36
Martin F. Lavin
Kum Kum Khanna
Introduction
166
1
Ataxia--telangiectasia
167
2
Cloning of ATM
169
3
Mutation analysis
170
1
ATM cDNA
171
1
Genomic organization of ATM
172
1
The ATM protein
172
3
Detection and importance for radiosensitivity
172
1
Cellular localization
173
2
ATM gene family
175
3
DNA-dependent protein kinase
176
1
Atr (ataxia-telangiectasia and rad3-related)
177
1
Mouse models
178
1
Role of ATM in cell-cycle control
179
7
G1/S-phase checkpoint
179
4
S-phase and G2/M checkpoints
183
2
Cell cycle and radiosensitivity
185
1
Role of ATM in meiosis
186
1
Integrated view of the role of ATM
187
15
References
190
12
p53 and the integrated response to DNA damage
202
31
Paul J. Smith
Christopher J. Jones
Introduction
202
1
DNA damage: induction and processing
202
3
DNA damage induction by anticancer agents
205
4
Alkylating agents
205
1
Antibiotics: parallels with ionizing radiation
206
1
DNA topoisomerase inhibitors
207
2
Cellular responses to stress and the role of p53
209
5
p53 and cycle arrest
210
3
p53 and nucleotide excision repair
213
1
p53 as a damage sensor in replicative senescence
214
6
Replicative senescence and telomeric clocks?
214
1
Telomeres: form and function
215
1
Telomerase
216
1
p53 and replicative senescence
216
1
Nature of the p53-activating signal at senescence and the role of DNA repair pathways?
217
3
Human cancer-prone disorders
220
2
Perspective
220
1
Germline disorders involving dominant proto-oncogenes and dominant tumour suppressor genes
221
1
Conclusions
222
11
References
223
10
Index
233