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Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing

Journal Article · · Trends in Biotechnology
 [1];  [2];  [2];  [3]
  1. Univ. of Colorado, Boulder, CO (United States); Univ. of Colorado, Boulder, CO (United States)
  2. Univ. of Colorado, Boulder, CO (United States)
  3. Univ. of Colorado, Boulder, CO (United States); Technical Univ. of Denmark, Lyngby (Denmark)
CRISPR technology is a universal tool for genome engineering that has revolutionized biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered Cas proteins, have rapidly expanded the functions and applications of CRISPR/Cas systems. The structures of Cas proteins are complex, containing multiple functional domains. These protein domains are evolutionarily conserved polypeptide units that generally show independent structural or functional properties. Here, we propose using protein domains as a new way to classify protein engineering strategies for these proteins and discuss common ways to engineer key domains to modify the functions of CRISPR/Cas systems.
Research Organization:
Univ. of Colorado, Boulder, CO (United States)
Sponsoring Organization:
USDOE; USDOE Office of Science (SC)
Grant/Contract Number:
SC0018368
OSTI ID:
1852615
Alternate ID(s):
OSTI ID: 1765405
Journal Information:
Trends in Biotechnology, Journal Name: Trends in Biotechnology Journal Issue: 3 Vol. 39; ISSN 0167-7799
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

References (92)

A Singular System with Precise Dosing and Spatiotemporal Control of CRISPR‐Cas9 journal May 2019
CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii journal June 2016
Off-target challenge for base editor-mediated genome editing journal April 2019
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA journal February 2014
Development and Applications of CRISPR-Cas9 for Genome Engineering journal June 2014
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System journal October 2015
Structure and Engineering of Francisella novicida Cas9 journal February 2016
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA journal May 2016
Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene journal February 2018
An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance journal April 2018
Transcriptional repression of endogenous genes in BmE cells using CRISPRi system journal August 2019
Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum journal June 2020
Diversity, classification and evolution of CRISPR-Cas systems journal June 2017
Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9 journal March 2016
Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a journal April 2017
Multiple Input Sensing and Signal Integration Using a Split Cas12a System journal April 2020
Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG journal July 2019
HIT-Cas9: A CRISPR/Cas9 Genome-Editing Device under Tight and Effective Drug Control journal December 2018
Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production journal January 2019
Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells journal February 2017
Precision Control of CRISPR-Cas9 Using Small Molecules and Light journal January 2019
A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription journal September 2017
CRISPRi and CRISPRa Screens in Mammalian Cells for Precision Biology and Medicine journal September 2017
Orthogonal Genetic Regulation in Human Cells Using Chemically Induced CRISPR/Cas9 Activators journal January 2017
Target Specificity of Cas9 Nuclease via DNA Rearrangement Regulated by the REC2 Domain journal May 2018
High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System journal November 2014
Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease journal July 2014
Engineered CRISPR-Cas9 nucleases with altered PAM specificities journal June 2015
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects journal January 2016
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy journal September 2017
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage journal October 2017
Evolved Cas9 variants with broad PAM compatibility and high DNA specificity journal February 2018
RNA-guided editing of bacterial genomes using CRISPR-Cas systems journal January 2013
Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition journal November 2015
Applications of CRISPR technologies in research and beyond journal September 2016
Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion journal February 2017
Highly efficient RNA-guided base editing in mouse embryos journal February 2017
Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion journal March 2017
Engineered Cpf1 variants with altered PAM specificities journal June 2017
A highly specific SpCas9 variant is identified by in vivo screening in yeast journal January 2018
Partial DNA-guided Cas9 enables genome editing with reduced off-target activity journal January 2018
CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum journal May 2017
CRISPR–Cas9-based photoactivatable transcription systems to induce neuronal differentiation journal September 2017
Off-Targeting of Base Editors: BE3 but not ABE induces substantial off-target single nucleotide variants journal April 2019
Structural insights into a high fidelity variant of SpCas9 journal January 2019
Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity journal April 2018
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance journal June 2018
Directed evolution of CRISPR-Cas9 to increase its specificity journal August 2018
Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information journal February 2019
Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9 journal April 2019
Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria journal August 2019
Synthetic chimeric nucleases function for efficient genome editing journal December 2019
CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window journal August 2018
Search-and-replace genome editing without double-strand breaks or donor DNA journal October 2019
Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing journal February 2019
Continuous evolution of SpCas9 variants compatible with non-G PAMs journal February 2020
Prime genome editing in rice and wheat journal March 2020
A split CRISPR–Cpf1 platform for inducible genome editing and gene activation journal August 2019
Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches journal March 2020
A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells journal August 2018
Treatment of a metabolic liver disease by in vivo genome base editing in adult mice journal October 2018
Allele-specific gene editing prevents deafness in a model of dominant progressive hearing loss journal July 2019
CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging journal October 2018
Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9 journal July 2019
Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING) journal January 2018
Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis journal April 2018
Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system journal August 2019
Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium journal May 2016
Direct observation of the formation of a CRISPR–Cas12a R-loop complex at the single-molecule level journal January 2020
Epigenetic editing by CRISPR/dCas9 in Plasmodium falciparum journal December 2018
Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity journal September 2019
Expressing Transgenes That Exceed the Packaging Capacity of Adeno-Associated Virus Capsids journal February 2016
Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase journal November 2016
Developing Heritable Mutations in Arabidopsis thaliana Using a Modified CRISPR/Cas9 Toolkit Comprising PAM-Altered Cas9 Variants and gRNAs journal June 2019
Increasing the efficiency of CRISPR-Cas9-VQR precise genome editing in rice journal August 2017
Expanding the base editing scope in rice by using Cas9 variants journal October 2018
Live-cell CRISPR imaging in plants reveals dynamic telomere movements journal July 2017
Minimal PAM specificity of a highly similar SpCas9 ortholog journal October 2018
Multiplex Genome Engineering Using CRISPR/Cas Systems journal January 2013
Rationally engineered Cas9 nucleases with improved specificity journal December 2015
Kinetics of dCas9 target search in Escherichia coli journal September 2017
Engineered CRISPR-Cas9 nuclease with expanded targeting space journal August 2018
RNA-guided DNA insertion with CRISPR-associated transposases journal June 2019
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants journal March 2020
CRISPR–Cas9 Structures and Mechanisms journal May 2017
Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system journal March 2018
Efficient disruption of bcr-abl gene by CRISPR RNA-guided FokI nucleases depresses the oncogenesis of chronic myeloid leukemia cells journal May 2019
Perfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high-fidelity SpCas9 nucleases journal October 2017
Comparison and optimization of CRISPR/dCas9/gRNA genome-labeling systems for live cell imaging journal March 2018
Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion journal May 2018
CRISPR-cas gene-editing as plausible treatment of neuromuscular and nucleotide-repeat-expansion diseases: A systematic review journal February 2019
High‐throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae journal May 2017

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