Essential Genes and Genomes

1. Front Matter

   Pages i-xii

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2. A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9

   • Barbara Mair, Michael Aregger, Amy H. Y. Tong, Katherine S. K. Chan, Jason Moffat

   Pages 1-27

3. CRISPR/Cas9 Screening to Identify Conditionally Essential Genes in Human Cell Lines

   • Kimberly S. Huggler, Nicholas J. Rossiter, Kyle M. Flickinger, Jason R. Cantor

   Pages 29-42

4. Target Identification of Small Molecules Using Large-Scale CRISPR–Cas Mutagenesis Scanning of Essential Genes

   • Bert Kwanten, Jasper Edgar Neggers, Dirk Daelemans

   Pages 43-67

5. Design and Generation of a CRISPR Interference System for Genetic Repression and Essential Gene Analysis in the Fungal Pathogen Candida albicans

   • Lauren Wensing, Rebecca S. Shapiro

   Pages 69-88

6. Identification of Essential Genes Using Sequential CRISPR and siRNA Screens

   • Luke DeHart, Oliver P. Yockey, Jesse Bakke

   Pages 89-107

7. A Simple Method that Combines CRISPR and AID to Quickly Generate Conditional Knockouts for Essential Genes in Various Vertebrate Cell Lines

   • Kohei Nishimura, Tatsuo Fukagawa

   Pages 109-122

8. New Method for Genome-Scale Functional Genomic Study in Bacteria with Superior Performance: CRISPR Interference Screen

   • Xihao Liao, Xin-Hui Xing, Chong Zhang

   Pages 123-141

9. A CRISPR-Based Method for Constructing Conditional Mutations of Essential Genes in Cyanobacteria

   • Ju-Yuan Zhang, Tian-Cai Niu, Gui-Ming Lin, Cheng-Cai Zhang

   Pages 143-157

10. A Method of Transposon Insertion Sequencing in Comprehensively Identifying Vibrio vulnificus Genes Required for Growth in Human Serum

    • Miguel Carda-Diéguez, Carmen Amaro

    Pages 159-178

11. The Use of Tn-Seq and the FiTnEss Analysis to Define the Core Essential Genome of Pseudomonas aeruginosa

    • Bradley E. Poulsen, Anne E. Clatworthy, Deborah T. Hung

    Pages 179-197

12. Analysis of Escherichia coli K1 Virulence Genes by Transposon-Directed Sequencing

    • Alex J. McCarthy, Peter W. Taylor

    Pages 199-213

13. Using Genome Scale Mutant Libraries to Identify Essential Genes

    • Kevin S. Myers, Piyush Behari Lal, Daniel R. Noguera, Timothy J. Donohue

    Pages 215-236

14. Identification and Analysis of Essential Genes in Streptococcus mutans with Transposon Sequencing

    • Alejandro R. Walker, Robert C. Shields

    Pages 237-258

15. The Use of TnSeq to Identify Essential Alphaproteobacterial Genes Reveals Operational Variability in Conserved Developmental and Cell Cycle Systems

    • Gayatri Sharma, Patrick D. Curtis

    Pages 259-271

16. A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus

    • Lorena Ruiz, Francesca Bottacini, Lucie Semenec, Amy Cain, Douwe van Sinderen

    Pages 273-302

17. The Application of Transposon Insertion Sequencing in Identifying Essential Genes in B. fragilis

    • Yaligara Veeranagouda, Hannah M. Wexler

    Pages 303-315

18. Repressible Promoter System to Study Essential Genes in Mycobacteria

    • Francesca Boldrin, Riccardo Manganelli

    Pages 317-332

19. A Single-Cell RNA-Seq-Based Approach for Genome-Wide Identification of Cell Essential Genes

    • Yuqiu Lu, Shaolin Shi

    Pages 333-343

20. Identification of Essential Genes in Caenorhabditis elegans with Lethal Mutations Maintained by Genetic Balancers

    • Shicheng Yu, Chaoran Zheng, Jeffrey Shih-Chieh Chu

    Pages 345-362

This book provides state-of-the-art information on gene essentiality screenings in a wide variety of organisms, i.e. screening for protein-coding genes and other genomic elements that are required by an organism to survive under specific conditions. With a focus on the two techniques that have revolutionized the field, the collection begins with chapters employing CRISPR/Cas9-based approaches followed by Tn-seq-based approaches, but later chapters also delve into other techniques for exploring essential genes, such as bioinformatics methods. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Comprehensive and authoritative, Essential Genes and Genomes: Methods and Protocols is an ideal guide for researchers attempting to strip genetics down to its fundamentals.

• CRISPR/Cas9
• Genome-wide essentiality screening
• Gene essentiality
• Synthetic biology
• Gene targeting technology
• Database of essential genes (DEG)

• Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, USA

  Ren Zhang

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