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El. knyga: Genome Editing Tools and Gene Drives: A Brief Overview

, (Lupane State University, Zimbabwe), , , , , , (Lupane State University, Zimbabwe), ,
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"This book succinctly reviews and describes genome editing tools such as ZFNs, CRISPR, megaTALs and TALENs. It covers the history, principles, applications and the advantages and disadvantages of each tool. The book provides an approachable outline enhancing science education in schools and universities by demystifying genome editing technologies"--

This book succinctly reviews and describes genome editing tools such as ZFNs, CRISPR, megaTALs and TALENs. It covers the history, principles, applications and the advantages and disadvantages of each tool. The book provides an approachable outline enhancing science education in schools and universities by demystifying genome editing technologies.

Genome editing methods are becoming routine tools for molecular and cell biologists. Such tools include ZFNs, CRISPR, megaTALs and TALENs. These tools are revolutionizing the creation of precisely manipulated genomes to modify the characteristics of organisms or cells. Additionally, gene drives have altered the way we understand inheritance laws. They give us the ability to have total control of the inheritance of traits of choice and importance. This succinct volume summarizes the history, principles, and applications – as well as the advantages and disadvantages – of each of these tools and various kinds of gene drives. The book is part of a program to produce books helpful to students and faculties of science at colleges and universities. This volume in the Pocket Guides to Biomedical Sciences series will help demystify these technologies. The book fills the gap between established conventional methods and the novel and exciting newly introduced tools of genome editing and gene drives. It will help young scientists understand the emerging genome editing tools and gene drives thereby promoting related research and adoption.

Key Features

  • The book extensively reviews the current genome editing tools and gene drives.

  • Clarifies their targeting mechanisms and specificity of genome editing tools.

  • Details many different types of natural and synthetic gene drives.

  • Highlights concerns with gene drives and genome editing tools.

Related Titles

Brown, T. A. Genomes 4 (ISBN 978-0-8153-4508-4)

Soh, J., et al. Genome Annotation (ISBN 978-1-4398-4117-4)

Samuelsson, T. The Human Genome in Health and Disease: A Story in Four Letters (ISBN 978-0-8153-4591-6)

Recenzijos

**Description** This volume describes genome editing tools (molecular methods for the targeted alteration of DNA sequences) and gene drives (mechanisms that propagate specific genes well in excess of the rate expected by chance). True to its name, it is a very brief but effective treatment of these important topics. This is a stand-alone paperback book without any supporting website or video backup. At just 100 pages in length, this book very briefly introduces four approaches to genome editing and six approaches to implementing gene drives. The book is divided into 13 chapters that range in length from two to 12 pages. The book is part of the Pocket Guides to Biomedical Science.

**Purpose** In the preface, the 13 authors describe their principal motivation for writing the book as a desire to introduce modern methods of genome editing and gene drives to African scientists and students. Indeed, all of the authors are African and are currently affiliated with universities in Zimbabwe. This book will easily fulfill the goal of helping inform African researchers and students, but its utility goes well beyond that. This book is broadly useful to any biology student or researcher new to the fields of genome editing or gene drives.

**Audience** While the authors are motivated by a desire to smooth the way for the use of genomic tools in Africa, their writing is so clear and concise that many audiences will find the book useful. Undergraduate students will find the concise descriptions of genomic and gene drives methods useful as they learn about these approaches. New graduate student researchers and professionals exploring genomic tools will likewise find the focused writing helpful in gaining a solid initial understanding of the topics covered. The authors have written accurately and effectively about their topics and provide practical examples of applications as well as discussions of the pros and cons of methods.

**Features** All chapters in this book are brief. The opening chapter gives a quick orientation to genome editing. This is followed by five chapters on genome editing approaches. Descriptions of four genome editing methods, zinc finger nucleases, TALENs, MegaTALs, and CRISPR, are followed by a chapter that offers a convenient comparison of the methods. The remaining six chapters describe various methods for applying gene drives. Each chapter contains a discussion of applications and describes the pros and cons of the method. The book also contains a helpful glossary, a long list of references cited, and a good index.



**Assessment** This is a highly useful book that, in its brief 100 pages, captures the essence of four contemporary approaches to genome editing and six ways in which methods of gene drives can be applied to captive and natural populations. The brevity of this book and its comparative lack of research data set it apart from other books covering the same topics. This book is for those who are new to genome editing and gene drives. Without getting bogged down in research details, readers with a biology background who are unfamiliar with the methods discussed will come away with a working understanding of the methods and approaches described.

- Mark F. Sanders, PhD (UC Davis College of Biological Sciences)

Preface xiii
Acknowledgments xv
Authors xvii
Abbreviations xix
1 Genome Editing
1(8)
History
1(1)
Principle
2(1)
Applications of Genome Editing
3(3)
Concerns with Genome Editing
6(3)
2 Zinc Finger Nucleases
9(14)
History of Zinc Finger Nucleases
9(1)
Target Cells (Prokaryotic Cells and Eukaryotic Cells)
10(1)
Efficiency
10(1)
Specificity
10(1)
Monitoring Editing Specificity
11(1)
Error Rate
12(1)
Versions of ZFNs
12(1)
Construct
12(4)
Procedure
16(1)
ZFN-Mediated Genome Editing
17(1)
Applications of ZFNs
17(1)
Gene Disruption
17(1)
Gene Disruption in Model Organisms
17(2)
Gene Disruption in Mammalian Somatic Cells
19(1)
More Complex Types of Disruption
19(1)
Homology-Based Genome Editing
20(1)
Gene Correction (Allele Editing)
20(1)
Gene Addition in Human ES and iPS Cells
20(1)
Gene Addition in Plants
20(1)
Other Practical Applications of ZFNs
21(1)
Advances in Therapy Using ZFNs
22(1)
Advantages of ZFNs
22(1)
Disadvantages of ZFNs
22(1)
3 TALENs
23(4)
History
23(1)
Principle
23(1)
Procedure
23(1)
Efficiency
24(1)
Applications of TALENs
25(1)
Advantages of TALENs
26(1)
Disadvantages of TALENs
26(1)
4 MegaTALs
27(4)
Introduction and History
27(1)
Ease of Use
27(1)
Efficiency
28(1)
Specificity
28(1)
Versions of Meganucleases
28(1)
Construct
28(1)
Principle Behind MegaTALs
28(1)
Applications of MegaTALs
29(1)
Advantages and Disadvantages
29(2)
5 CRISPR
31(14)
History
31(1)
Versions of CRISPR
32(3)
Mechanism of the CRISPR System
35(1)
Genome Editing Using CRISPR
36(3)
Applications of CRISPR
39(1)
Other Applications of CRISPR in Crops and Livestock
40(1)
Other Applications of CRISPR in Humans
41(1)
Advantages
41(1)
Disadvantages
42(1)
How to Counter Off-Target Effects
43(2)
6 Comparison of ZFNs, TALENs, CRISPR, and MegaTALs
45(6)
Mechanism of Action
45(3)
Nucleases
48(1)
DNA Target Recognition
48(1)
Recognition Site
48(1)
Specificity and Simplicity
48(1)
Targeting Constraints
49(1)
Ease of Engineering
49(1)
Immunogenicity
49(1)
Ease of Ex Vivo Delivery
49(1)
Ease of In Vivo Delivery
49(1)
Cost Effectiveness
50(1)
Speed
50(1)
Efficiency of Gene Editing
50(1)
Biology at the Breakpoint
50(1)
7 Gene Drives
51(12)
Introduction
51(1)
History of and Principle behind Gene Drives
52(1)
Classifications of Gene Drives
52(1)
Standard Drive Systems
53(1)
Local Drive Systems
53(1)
Daisy Drive Systems
53(1)
Threshold Drive Systems
53(1)
Combination Drive Systems
53(1)
Natural and Synthetic Gene Drives
53(1)
Suppression Drives
54(1)
Modification Drives
54(1)
Threshold Dependent Drive
54(1)
Threshold-Independent Drive Systems
54(1)
Temporarily Self-Limiting Drives
54(1)
Selfish Genetic Elements
54(1)
Over-Replicators
55(1)
HEGs (Homing Endonuclease Genes)
55(1)
Segregation and Transmission Distorters
55(1)
Sex-Ratio Distorters
55(1)
Toxin--Antidote Based Drives
56(1)
Maternal-Effect Dominant Embryonic Arrest (MEDEA)
56(1)
Genetic Underdominance
56(1)
Transposable Elements
57(1)
Semele System
57(1)
Merea System
57(1)
Medusa System
58(1)
T-Complex or T-Haplotype
58(1)
Translocations
58(1)
Application of Gene Drives
58(1)
Advantages of Gene Drives
59(1)
Disadvantages of Gene Drives
59(1)
Concerns with Gene Drives
60(1)
Regulatory Systems
60(3)
8 Supernumerary B Chromosomes
63(4)
Introduction
63(1)
History
63(1)
Chief Traits of B Chromosomes
64(1)
Target Cells for B Chromosomes
64(1)
Disadvantages of B Chromosomes
64(3)
9 Suppression Drives
67(4)
Mechanism of Suppression Drives
67(1)
Versions
68(1)
A Synthetic CRISPR-Cas9 Gene Drive
68(1)
Construct
68(1)
Applications
68(1)
Examples of Where They Were Used
69(2)
10 Maternal-Effect Dominant Embryonic Arrest {Medea) System
71(2)
11 Heritable Microorganisms: Wolbachia
73(12)
History
73(2)
Target Cells
75(1)
Ease of Use
75(1)
Specificity
75(1)
Error Rate and CI Efficiency
75(1)
Principle
76(1)
Cytoplasmic Incompatibility (CI)
77(1)
Unidirectional and Bidirectional CI
77(1)
Wolbachia Genes Inducing CI
78(1)
Mechanism of CI
78(1)
Procedures
79(1)
Collection of Mosquito Stock
79(1)
Sterilizing Wolbachia from Infected Mosquitoes
79(1)
Infecting Experimental Mosquitoes with Wolbachia
80(1)
Sexing
80(1)
Harvesting Sperm
80(1)
Analysis of Limiting Factor
80(1)
Applications
80(1)
Sterile Insect Technique
80(1)
Gene Drive
81(1)
Wolbachia Causing Disease
81(1)
Advantages
81(1)
Disadvantages
81(2)
Practical Applications of Wolbachia
83(1)
Wolbachia Used to Prevent Disease
83(1)
Deployments of Wolbachia
84(1)
12 CRISPR Gene Drives
85(10)
History
85(1)
Target Cells
85(1)
Ease of Use
85(1)
Efficiency
86(1)
Specificity
87(1)
Error Rate
87(1)
Principle
87(2)
Procedure
89(1)
Mutagenic Chain Reaction (MCR)
90(1)
Mutagenic Chain Reaction Construct
90(1)
Versions
91(1)
Advantages
91(1)
Disadvantages
91(1)
Causes of Failure of CRISPR Gene Drives
91(1)
Applications of CRISPR Gene Drives
92(1)
Examples of How CRISPR Gene Drives Can Be Used
93(1)
Construct
93(2)
13 The Killer-Rescue System
95(4)
History
95(1)
Mechanism
95(1)
Mechanism
95(1)
Efficiency
96(1)
Reliability of the Technology
96(1)
Development
96(1)
Application
96(1)
Pros and Cons
97(1)
Reversibility of the K-R Gene Drive System
97(1)
Comparison of K-R Systems
97(2)
Glossary 99(8)
References 107(20)
Index 127
Reagan Mudziwapasi

Reagan Mudziwapasi is a biotechnology researcher, lecturer and entrepreneur. He is a co-founder and Operations Director at EnviroBiotech Solutions Africa, a company that develops biotechnology-based solutions. Reagan has authored several peer-reviewed journals, is a patent holder and has made several inventions and conducted several consultancies. He has contributed to various discussions on biotechnology, entrepreneurship and energy inter alia. Reagan promotes awareness on genetic engineering and its safe and responsible use. He helps marginalized communities and upcoming inventors protect their intellectual property.

Farai Faustos Mashiri

Farai Faustos Mashiri has been an Agricultural Science and Biology educator since 2009 at various institutions in Zimbabwe and recently South Africa. He got his BSc in Agriculture and Natural Resources in 1999 from Africa University and Post Graduate Diploma in Education from Lupane State University. After graduating, his early career engagements included technical work for private enterprises in the Agricultural sector, mainly in aquaculture and horticulture. He is currently undertaking postgraduate studies in Animal Breeding and Biotechnology. His research interests are in Tilapia breeding, genome editing and gene drives. His areas of interest also span the fields of Bioinformatics, Genomics, and Data Analysis using R and Python.

Irvonnie Shoko

Irvonnie Shoko is a founder of Divin Chen Agribusiness Solutions where she offers consultancy and training services in livestock production. She joined Midlands State University in 2019 as a part-time lecturer in Animal Breeding and Physiology. Prior to that, she was a research scientist at SIRDC. During her tenure at SIRDC, she helped the company to set up a robust livestock breeding and production project. She is a graduate of the University of Zimbabwe where she obtained a BSc in Animal Science and an MSc in Biotechnology. She is currently working towards an MSc in Animal Breeding and Biotechnology at Lupane State University. She currently lives in Harare, Zimbabwe with her family. She enjoys empowering communities in agribusiness. When not working, she enjoys nature walks and swimming.

Berlinda Ncube

Berlinda Ncube is a cofounder of Go Science Club where she helps learners come up with science projects. She joined Zezani High School in 2018 as a chemistry teacher. She is a graduate of the National University of Science and Technology where she obtained a BSc Hons in Applied Biology and Biochemistry and Zimbabwe Open University where she obtained a postgraduate Diploma in Education. She is currently working towards obtaining an MSc in Applied Animal Breeding and Biotechnology at Lupane State University. She spends most of her time empowering the Girl Child and enjoys reading novels and surfing the net. She currently lives in Bulawayo, Zimbabwe with her family.

Fortune N. Jomane

Fortune N. Jomane is an animal scientist who specializes in animal breeding and genetics. He holds a BSc in Agriculture (Animal Science), an MSc in Agriculture (Animal Science) and a Ph.D. in Agriculture specializing in Animal Breeding and Genetics. His passion is enhancing animal production through exploiting genetics. He has published several peer-reviewed papers in animal breeding and genetics. He is a senior lecturer and Chairperson of the Department of Animal Science and Rangeland and Lupane State University. He is the secretary for the beef and leather value chain technical assistance project implemented by the Government of Zimbabwe through the Ministry of Industry and Commerce, and the Ministry of Lands, Agriculture, Fisheries, Water and Rural Resettlement.

Dr. Ryman Shoko

Dr. Ryman Shoko is a Senior Lecturer in the Department of Biological Sciences at the Chinhoyi University of Technology. His areas of expertise include molecular biology, proteomics bioinformatics and computational systems biology.

Ringisai Chekera

Ringisai Chekera is an animal scientist who specializes in animal breeding. She holds a BSc in Agriculture (Animal Science) and an MSc in Agriculture (Animal Breeding and Biotechnology). She has a great passion for building the resilience of livestock farmers through the use of various breeding strategies. She has contributed to the Resilience Knowledge Hub as a researcher in a project implemented under the ZRBF project to enhance the resilience of smallholder poultry farmers.

Dr. Rutendo Nyamusamba

Dr. Rutendo Nyamusambas passion lies in development and being a voice for the seemingly voiceless. It is this passion that drives her desire for research. She uses a holistic approach in solving food system challenges. Her research and professional background are strongly rooted in Agronomy and Physiology of field crops focusing on Sustainable Crop Production and Weed Science. She is currently working on the integration of livestock in cropping systems for both commercial and small-scale farmers.

Dr. Nyamusamba has a Ph.D. in Agronomy with a minor in Statistics; an MSc. in Plant Science from South Dakota State University, USA and a BSc. in Agriculture with an Agribusiness specialty from Africa University in Mutare, Zimbabwe. She teaches modules in Weed Science, Plant Physiology, Crop Production, Sustainable Agriculture and Statistics. Occasionally she assists with some specific modules in Agricultural Economics such as Econometrics.

Jemethious Dube

Jemethious Dube has been an agricultural scientist. He holds a diploma in Agriculture from Esigodini College, a BSc in Agriculture Management, a BSc Special Honors Degree in Crop Science and a Masters Degree in Business Administration, all from the Zimbabwe Open University. He also holds a postgraduate diploma in education from Lupane State University. He is studying towards an MSc Crop Science (Plant Breeding) with Lupane State University. His passion for the field saw him attaining. He has vast experience working with financial institutions and non-governmental organizations. He is very passionate about fieldwork.

Moira Amanda Mubani

Moira Amanda Mubani is a very talented and hardworking young scientist. She holds a BSc Honors Degree in Biotechnology and is currently in her final year completing her Master's Degree in Applied Pharmaceutical Science. She is into computational chemistry, where she developed ways of analyzing a substantial amount of data. She uses molecular modeling and bioinformatics to design novel anti-tuberculosis and anticancer drugs. Moira Amanda also works on Ethno-Pharmaceuticals projects where she is involved in cannabis research. Moira has been working at the National Biotechnology Authority (NBA) since October 2019. She was seconded by NBA to work at the African Institute of Biomedical Science and Technology (AiBST) in 2020. At AiBST gained substantial knowledge and experience in Genomics and Bioinformatics technologies. She also on the National Biobank project. Moira was recently seconded to work on the Biobanking project with Dr. Justen Manasa at the University of Zimbabwe innovation hub. This project is key in the establishment of the Zimbabwe Genomics Center. Moira was among the 10 people selected to participate in a hands-on workshop training in advanced genomics technologies organized by the Biomedical Research and Training Institute. This workshop further equipped her with skills in genome sequencing, bioinformatics, big data analysis software and next-generation sequencing in relation to Covid and HIV research. Moira lives in Harare and when she is not at work Moira devotes her time to attending church services and spending quality time with her family.

Mr. Clophas Zibusiso Ncube

Clophas Z. Ncube is an Animal Science and Agribusiness Practitioner. He has over ten years of continuous work experience. He started his professional career by working as a field officer under a USAID-funded project for five years in Victoria Falls and Gwanda districts. Currently, he is working as the national project coordinator of the Green Jobs project for the Food and Agriculture Organisation (FAO) of the United Nations where his main goal is to promote rural youth employment. Prior to this, he was an Agriculture team leader for five years under a USAID-funded project where he was promoting agricultural livelihoods in Gwanda and Bulilima districts. In 2018, he was awarded the Australian awards scholarship to study Agribusiness concentrating on value chains. Mr. Ncube is a holder of a Master of Science Degree in Agribusiness from Africa University in Mutare, Zimbabwe, a BSc in Agricultural Science and a BSc in Agricultural Science Honors Degree in Animal Science. He is currently a student for the Master of Science Degree in Animal Breeding and Biotechnology at Lupane State University. When he is not working or studying, Mr. Ncube enjoys spending time with his family in Bulawayo, Zimbabwe.

Mpumuzi Masuku

Mpumuzi Masuku is a final year student at Lupane State University studying towards a Master of Science Degree in Animal Breeding and Biotechnology. He holds a BSc Honors Degree in Agriculture (Animal Science) from the University of Zimbabwe. He is detail-oriented and values self-actualization immensely. He aims to leverage proven knowledge of research in Animal Breeding, Molecular Biotechnology and Genomics.

Thandanani Moyo

Thandanani Moyo obtained a BSc (Hons) in Applied Biology & Biochemistry from NUST, Zimbabwe. Currently, he is studying towards an MSc in Animal Breeding and Biotechnology at Lupane State University. His research interests are molecular breeding and animal health. He is currently working as a lab Scientist at a diagnostics laboratory.

Charity Chimbo

Charity Chimbo is a Biology and Agriculture Science educator since 2010. She holds a BSc Honors Degree in Agriculture (UZ), Post Graduate Diploma in education (ZOU) and is studying towards an MSc in Animal Breeding and Biotechnology with LSU. Her research interests are in genomics and bioinformatics.
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