CRISPR Biology and Applications

“An excellent compendium of all things CRISPR from some of the leading minds in the field. With thorough coverage from every angle and beautifully detailed illustrations, this book is not to be missed!”

Jennifer A. Doudna,
Professor of Chemistry, Biochemistry & Molecular Biology, UC Berkeley; Founder, Innovative Genomics Institute; Nobel Laureate and coinventor of CRISPR technology

“This journey through CRISPR biology and several of its breakthrough applications offers an exciting glimpse into one of the most beautiful and compelling fields in the life sciences.”

David R. Liu,
Director of the Merkin Institute at the Broad Institute of MIT and Harvard; Professor of Chemistry and Chemical Biology at Harvard University; coinventor of base editing and prime editing

“A must read! The CRISPR topics, written by world-leading experts, span from the fascinating mechanistic underpinnings to the ingenious applications. One can read from start to finish or pick and choose themes. Either way, the book delivers utterly enjoyable learning!”

Bonnie Bassler,
Squibb Professor and Chair, Princeton University Department of Molecular Biology; Howard Hughes Medical Institute Investigator

CRISPR-Cas systems have revolutionized the science of gene editing and their possible applications continue to expand, from basic research to potentially groundbreaking medical and commercial uses.

Led by a distinguished team of editors, CRISPR: Biology and Applications explores the subject matter needed to delve into this fascinating area. Topics covered include:

• Classification and molecular mechanisms of CRISPR-Cas systems
• CRISPR-Cas evolution, regulation, expression, and function
• Uses for gene editing and modulation of gene expression
• CRISPR-based antimicrobials and phage resistance for medical and industrial purposes

Written by internationally renowned authors, CRISPR: Biology and Applications serves as both an introductory guide for those new to the field and an authoritative reference for seasoned researchers whose work touches this evolving and headline- making science.

ABOUT THE EDITORS

Rodolphe Barrangou is the Todd R. Klaenhammer Distinguished Professor in the Department of Food, Bioprocessing and Nutrition Sciences at North Carolina State University; a member of the AAM, NAS, NAE, and NAI; a cofounder of Intellia Therapeutics, Locus Biosciences, Ancilia Biosciences, CRISPR Biotechnologies, and TreeCo; and Editor- in-Chief of The CRISPR Journal.

Erik J. Sontheimer is the Pillar Chair in Biomedical Research and Professor in the RNA Therapeutics Institute at the University of Massachusetts Chan Medical School; an Associate Editor of RNA; a member of the AAM; a cofounder of Intellia Therapeutics; and a Scientific Advisory Board member at Tessera Therapeutics.

Luciano A. Marraffini is the Kayden Family Professor and Head of the Laboratory of Bacteriology at The Rockefeller University; a Howard Hughes Medical Institute Investigator; a member of the AAM, AAAS, and NAS; and a cofounder of Intellia Therapeutics, CRISPR Biotechnologies, and Eligo Biosciences.

Contributors Vii

Preface xi

S E C T I O N I

Diversity of CRISPR‐Cas Systems 1

1 CRISPR-Cas Systems: Core Features and Common Mechanisms 3
Rodolphe Barrangou, Luciano A. Marraffini, and Erik J. Sontheimer

2 Evolutionary Classification of CRISPR-Cas Systems 13
Kira S. Makarova, Yuri I. Wolf, and Eugene V. Koonin

3 Molecular Mechanisms of Type I CRISPR-Cas Systems 39
John van der Oost

4 Molecular Mechanisms of Type II CRISPR‐Cas Systems 53
Tautvydas Karvelis and Virginijus Siksnys

5 Mechanism of Type III CRISPR‐Cas Immunity 71
Luciano A. Marraffini

6 Type V CRISPR‐Cas Systems 85
Morgan Quinn Beckett, Anita Ramachandran, and Scott Bailey

7 CRISPR-Cas13: Biology, Mechanism, and Applications of RNA-Guided, RNA-Targeting CRISPR Systems 99
Omar O. Abudayyeh and Jonathan S. Gootenberg

S E C T I O N II

CRISPR‐Cas Biology 121 8 CRISPR-Cas, Horizontal Gene Transfer, and the Flexible (Pan) Genome 123
Uri Gophna

9 Evasion Tactics Manifested by Bacteriophages against Bacterial Immunity 131
Jenny Y. Zhang, Sutharsan Govindarajan, and Joseph Bondy-Denomy

10 Regulation of CRISPR‐Cas Expression and Function 145
Leah M. Smith, Aroa Rey Campa, and Peter C. Fineran

S E C T I O N III

CRISPR‐Based Technologies and Applications 163

11 Genome Editing with CRISPR‐Cas Systems 165
Peter Lotfy and Patrick D. Hsu

12 Genetic and Epigenetic Modulation of Gene Expression by CRISPR-dCas Systems 195
Jasprina N. Noordermeer, Crystal Chen, and Lei S. Qi

13 CRISPR Screens 213
Jonathan D. D’Gama, Joseph S. Park, and Matthew K. Waldor

14 CRISPR‐Based Antimicrobials 233
Justen Russell and David Bikard

15 Exploiting CRISPR‐Cas Systems To Provide Phage Resistance in Industrial Bacteria 249
Rodolphe Barrangou and Avery Roberts

16 Recording Biological Information with CRISPR‐Cas Systems 267
Mariia Y. Cherepkova, Tanmay Tanna, and Randall J. Platt

Afterword 281

Index 283

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