Base Editors: Methods and Protocols

ISBN-13: 9781071628782 / Angielski / Twarda / 2023 / 235 str.

Sangsu Bae; Beomjong Song

Opis

This volume explores base editors (BEs), an invaluable CRISPR-based genome editing tool with a wide variety of versatile applications. Beginning with an overview of BEs, their diverse variants, and computational tools, the book continues with experimental applications of BEs for disease modeling in mammalian cells and generating mutagenic mice, therapeutic base editing strategies, which covers delivery methods of BE-encoded DNA plasmids, mRNAs, or ribonucleoproteins through viruses or non-viral lipid nanoparticles, and lastly, the use of BEs in plants and bacteria. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Base Editors: Methods and Protocols serves as an ideal guide for researchers looking to use base editors to continue their studies in an array of fields.

Spis treści

Part I: Overview of BEs, Diverse Variants of BEs, and Computational Tools for Bes

 

1. Introduction and Perspectives of DNA Base Editors

            Beomjong Song and Sangsu Bae

 

2. Web-Based Computational Tools for Base Editors

            Gue-Ho Hwang and Sangsu Bae

 

3. Prediction of Base Editing Efficiencies and Outcomes Using DeepABE and DeepCBE

            Jinman Park and Hui Kwon Kim

 

4. Profiling Genome-Wide Specificity of dCpf1 Cytidine Base Editors Using Digenome-Seq

            Daesik Kim

 

Part II: Application of BEs for Disease Modeling

 

5. Base Editing of Human Hematopoietic Stem Cells

            Jing Zeng, Gabriele Casirati, My Anh Nguyen, Pietro Genovese, and Daniel E. Bauer

 

6. A/C Simultaneous Conversion Using the Dual Base Editor in Human Cells

            Xiaohui Zhang, Yuting Guan, and Dali Li

 

7. Functional Analysis of Variants in BRCA1 Using CRISPR Base-Editors

            Ji-Eun See and Yongsub Kim

 

8. Use of the Representative Base Editing Tool Target-AID to Introduce Pathogenic Mutations into Mice

            Hiroki Sasaguri

 

9. Targeted Mutagenesis in Mice Using a Base Editor

            Tae Yeong Jeong, Soo-Yeon Lim, Je Kyung Seong, and Kyoungmi Kim

 

Part III: Therapeutic Base Editing Strategies

 

10. Heterologous Expression and Purification of a CRISPR-Cas9-Based Adenine Base Editor

            Seu-Na Lee, Hong-Su Jang, and Jae-Sung Woo

 

11. Delivering Base Editors In Vivo by Adeno-Associated Virus Vectors

            Colin K.W. Lim, Angelo J. Miskalis, Pablo Perez-Pinera, and Thomas Gaj

 

12. The Delivery of ABE mRNA to the Adult Murine Liver by Lipid Nanoparticles (LNPs)

            Dong Yang and Chun-Qing Song

 

13. Ex Vivo Base Editing Therapy with Chemically-Derived Hepatic Progenitors

            Yohan Kim, Jaemin Jeong, and Dongho Choi

 

14. Application of Base Editor-Mediated Genome Editing in Mouse Retina

            Jun Wu, Chang Sik Cho, Dong Hyun Jo, and Jeong Hun Kim

 

Part IV: Use of BEs in Plants and Bacteria

 

15. High-Throughput Base-Editing-Mediated Artificial Evolution Streamlines Trait Gene Identification in Rice

            Fang Yan, Man Yu, Meixia Wang, and Huanbin Zhou

 

16. Heritable Virus-Induced Genome Editing (VIGE) in Nicotiana attenuate

            Hyeonjin Kim, Youngbin Oh, Eunae Park, Moonyoung Kang, Yuri Choi, and Sang-Gyu Kim

 

17. Cytosine Base Editing in Bacteria

            Ye Liu, Yang Liu, Ping Zheng, Yu Wang, and Meng Wang