|
Contents |
6 |
|
|
Contributors |
8 |
|
|
Chapter 1: Double-Strand Break Repair and Its Application to Genome Engineering in Plants |
10 |
|
|
1 DSB Induction as a Tool for Genome Manipulation in Plants |
11 |
|
|
2 Mechanisms of DSB Repair Involving Homologous Sequences |
12 |
|
|
3 The Chromosomal Site of the Template Makes a Difference |
15 |
|
|
4 Extrachromosomal Templates |
17 |
|
|
5 Factors Involved in Homologous Recombination |
19 |
|
|
6 DSB Repair via Nonhomologous End Joining |
21 |
|
|
7 From Gene Engineering to Genome Engineering: Inducing More Than One DSB at a Time |
24 |
|
|
References |
26 |
|
|
Chapter 2: Engineering Meganuclease for Precise Plant Genome Modification |
30 |
|
|
1 Introduction |
30 |
|
|
2 Engineering of Meganucleases for New Sequence Specificity |
31 |
|
|
2.1 Yeast High-Throughput Screening Assay |
32 |
|
|
2.2 Principle of the Two-Step Semi-rational Approach |
33 |
|
|
3 Meganuclease Scaffold Optimization |
35 |
|
|
3.1 Improvement of the Meganuclease Activity |
35 |
|
|
3.2 Improvement of the Meganuclease Specificity |
36 |
|
|
3.2.1 Obligatory Heterodimer |
36 |
|
|
3.2.2 Single-Chain Molecule |
37 |
|
|
3.2.3 Fusion HE-TALE |
37 |
|
|
4 Factors Influencing the Meganuclease Activity In Vivo |
38 |
|
|
4.1 Meganucleases Are Sensitive to Chromatin Compaction |
38 |
|
|
4.2 Meganucleases Are Sensitive to CpG Methylation |
38 |
|
|
4.3 Identification of Host Factors Regulating Homologous Gene Targeting |
40 |
|
|
4.4 Increased Targeted Mutagenesis Frequency by Co-factors |
40 |
|
|
5 Precise Plant Genome Modification with Meganucleases |
41 |
|
|
6 Future Perspectives |
43 |
|
|
References |
44 |
|
|
Chapter 3: High Efficient Genome Modification by Designed Zinc Finger Nuclease |
48 |
|
|
1 Introduction |
48 |
|
|
2 Making and Testing ZFNs |
49 |
|
|
3 Targeted Mutagenesis by ZFNs |
53 |
|
|
4 Targeted Chromosomal Deletions and Inversions by ZFNs |
54 |
|
|
5 Gene Replacement and Gene Stacking by ZFNs |
54 |
|
|
6 Donor and/or ZFN Delivery |
55 |
|
|
7 Cytotoxicity and Off-Targeting by ZFNs |
56 |
|
|
8 Somatic Versus Germinal Modifications by ZFNs |
56 |
|
|
9 Genetic Approaches to Facilitate High Frequency Genome Modifications |
57 |
|
|
10 Future Perspective |
58 |
|
|
References |
58 |
|
|
Chapter 4: Engineered TAL Effector Proteins: Versatile Reagents for Manipulating Plant Genomes |
63 |
|
|
1 Genome Editing Using TAL Effector Nuclease Technology |
68 |
|
|
2 Methods to Engineer Novel TAL Effector Arrays |
70 |
|
|
3 Modifying Genes Using TAL Effector Fusion Proteins |
71 |
|
|
4 Optimizing TAL Effector Architecture |
73 |
|
|
5 Factors Affecting DNA Binding |
75 |
|
|
6 Conclusions |
77 |
|
|
References |
78 |
|
|
Chapter 5: Oligo-Mediated Targeted Gene Editing |
81 |
|
|
1 Introduction |
81 |
|
|
1.1 Gene Repair Oligonucleotide Structure |
83 |
|
|
1.2 Delivery |
84 |
|
|
1.3 RTDS Mechanism/Process |
84 |
|
|
1.4 Application of RTDS |
85 |
|
|
1.4.1 Targeting Acetohydroxyacid Synthase |
85 |
|
|
1.4.2 Targeting Green Fluorescent Protein Transgenics |
86 |
|
|
2 Materials and Methods |
86 |
|
|
2.1 Oil Seed Rape AHAS |
86 |
|
|
2.2 BFP to GFP Conversion in Arabidopsis |
89 |
|
|
3 Results |
89 |
|
|
3.1 Chromosomal Conversion |
89 |
|
|
3.1.1 Oil Seed Rape AHAS |
89 |
|
|
3.1.2 BFP to GFP Conversion in Arabidopsis |
92 |
|
|
4 Discussion |
93 |
|
|
References |
95 |
|
|
Chapter 6: Gene Targeting in Crop Species with Effective Selection Systems |
98 |
|
|
1 Introduction |
99 |
|
|
2 General Background on Gene Targeting |
100 |
|
|
3 Gene Targeting with Effective Selection Systems |
105 |
|
|
4 Gene Targeting with Gene-Specific Selection |
106 |
|
|
5 Gene Targeting with Positive–Negative Selection |
106 |
|
|
5.1 Knockout and Knockin Targeting |
109 |
|
|
5.2 Toward the Development of Desired Subtle and Localized Mutageneses |
112 |
|
|
6 Future Prospects |
114 |
|
|
References |
115 |
|
|
Chapter 7: Recombinase Technology for Precise Genome Engineering |
119 |
|
|
1 Introduction |
120 |
|
|
2 Recombinase Types and Catalysis |
121 |
|
|
3 Application: Excision |
124 |
|
|
4 Application: Molecular Switches |
127 |
|
|
5 Application: Transgene Insertion Site Resolution |
128 |
|
|
6 Application: Integration |
129 |
|
|
7 Application: Recombinase-Mediated Cassette Exchange |
132 |
|
|
8 Application: Megabase Modifications/Chromosome Level Engineering |
136 |
|
|
9 Conclusion: Benefits of Site-Specific Recombinase Technology and Future Directions |
140 |
|
|
References |
141 |
|
|
Chapter 8: Developing CRISPR Technology in Major Crop Plants |
151 |
|
|
1 Introduction |
151 |
|
|
2 Development of CRISPR Technology |
152 |
|
|
2.1 The CRISPR/Cas Defense System |
152 |
|
|
2.2 CRISPR Genome Engineering |
153 |
|
|
2.3 Maximizing the Specificity of CRISPR |
155 |
|
|
3 CRISPR Technology in Plants |
156 |
|
|
3.1 Improving CRISPR Technology in Plants |
156 |
|
|
3.2 Examples of Applications to Crop Plants |
159 |
|
|
3.2.1 Rice |
159 |
|
|
3.2.2 Wheat |
161 |
|
|
3.2.3 Maize |
161 |
|
|
4 Perspective and Conclusions |
161 |
|
|
4.1 Developing CRISPR as a New Plant Breeding Technique for Next Generation Crop Improvement |
161 |
|
|
4.2 Developing CRISPR for Regulating Plant Genomes |
162 |
|
|
References |
163 |
|
|
Index |
166 |
|