4.7 Article

In Vivo Rapid Investigation of CRISPR-Based Base Editing Components in Escherichia coli (IRI-CCE): A Platform for Evaluating Base Editing Tools and Their Components

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells

Ibrahim C. Kurt et al.

Summary: This study presents two base editor architectures that can efficiently induce targeted C-to-G base transversions, with reduced levels of unwanted mutations. These new base editors hold promise for optimizing C-to-G base editors for both research and therapeutic applications.

NATURE BIOTECHNOLOGY (2021)

Article Biotechnology & Applied Microbiology

Tomato protoplasts as cell target for ribonucleoprotein (RNP)-mediated multiplexed genome editing

Alessandro Nicolia et al.

Summary: This study demonstrates the feasibility of using PEG-mediated RNPs for multiplexing genome editing in tomato protoplasts, showing high efficiency in editing outcomes. This highlights the potential application of RNPs in multiplexing genome editing in plant breeding.

PLANT CELL TISSUE AND ORGAN CULTURE (2021)

Article Biochemistry & Molecular Biology

First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts

Sapna Badhan et al.

Summary: The current genome editing system CRISPR/Cas9 has been proven effective in plant applications, with the DNA-free editing showing promise in achieving targeted mutagenesis in chickpea. By selecting drought tolerance-related genes 4CL and RVE7 for editing in chickpea protoplast, this study demonstrated high efficiency in editing the RVE7 gene, providing insights into gene functions under drought stress in chickpea.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemistry & Molecular Biology

Necessity for Validation of Effectiveness of Selected Guide RNA In Silico for Application of CRISPR/Cas9

Dong-Hwan Kim et al.

Summary: The study emphasizes the importance of selecting appropriate guide RNAs in CRISPR/Cas9 gene editing to improve efficiency. By designing three high-scoring gRNAs targeting the qRbp7 gene and using Sanger sequencing and ICE analysis to predict efficiency, the researchers were able to confirm the actual mutation rates. The data demonstrates a rapid and reliable method for evaluating the efficiency of selected gRNAs, crucial for successful gene editing in future applications.

MOLECULAR BIOTECHNOLOGY (2021)

Review Biochemistry & Molecular Biology

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

Dibyajyoti Pramanik et al.

Summary: The central dogma of molecular biology involves transferring genetic information from DNA to RNA to proteins, which is crucial for gene regulation in plants. Precisely manipulating these processes can accelerate crop improvement to meet the growing global population's demands.

MOLECULAR PLANT (2021)

Article Biochemical Research Methods

Precision genome editing using cytosine and adenine base editors in mammalian cells

Tony P. Huang et al.

Summary: Genome editing technology, specifically base editing, holds great promise in treating genetic diseases with high efficiency and precision. Current base editors have shown high editing efficiencies in cell cultures and in vivo experiments, with new variants continuously being developed.

NATURE PROTOCOLS (2021)

Article Multidisciplinary Sciences

Efficient CRISPR-mediated base editing in Agrobacterium spp.

Savio D. Rodrigues et al.

Summary: Agrobacterium spp. are important plant pathogens that can be genetically modified using CRISPR-mediated base editing to introduce targeted point mutations, improving the efficiency and functionality of the strains for plant transformation and gene editing. The method developed in this study has shown high efficiency and potential for future advancements in engineering Agrobacterium strains.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

CRISPR/Cas9-Mediated Generation of Pathogen-Resistant Tomato against Tomato Yellow Leaf Curl Virus and Powdery Mildew

Dibyajyoti Pramanik et al.

Summary: This study successfully targeted the SlPelo and SlMlo1 genes using the CRISPR/Cas9 system to create tomato varieties with enhanced resistance to viruses and fungi. The results demonstrate the efficiency of the CRISPR/Cas9 system in the rapid development of pathogen-resistant tomato varieties.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemistry & Molecular Biology

High-efficiency andmultiplex adenine base editing in plants using new TadA variants

Daqi Yan et al.

Summary: The study investigated the activities of three evolved E. coli adenosine deaminase TadA variants in transgenic rice, revealing that TadA8e outperformed TadA8.17 and TadA8.20. The newly generated variant TadA9, with V82S/Q154R mutations, showed broad compatibility and efficient editing in various CRISPR systems. These novel ABEs have great potential in the development of plant base editors and crop molecular breeding.

MOLECULAR PLANT (2021)

Article Multidisciplinary Sciences

Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules

Arik Shams et al.

Summary: Proteins evolve through modular rearrangement, and the MISER technique allows for comprehensive deletions of proteins. The study found that Cas9 can tolerate large single deletions, which can be stacked together to engineer minimal, DNA-binding effector proteins.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors

Zhixin Lei et al.

Summary: Detect-seq, a new method for evaluating CBE specificity, enables sensitive detection of genome-wide off-target sites induced by CBEs. Unexpected off-target edits, with high editing ratio, were found to be prevalent, challenging the common belief that CBEs do not induce proximal off-target mutations.

NATURE METHODS (2021)

Article Biochemistry & Molecular Biology

Development of a base editor for protein evolution via in situ mutation in vivo

Wenliang Hao et al.

Summary: The development of a base editor in Bacillus subtilis allows for efficient protein evolution in vivo. The base editor can introduce mutations with high efficiency, regulate conversion efficiency by changing culture conditions, and is applicable for constructing mutant protein libraries in vivo.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing

Yaojun Tong et al.

Summary: The researchers have developed a CRISPR-based prime editing toolkit for high-fidelity genome engineering in E. coli, allowing for substitutions, deletions, and insertions. While efficiency drops with increased fragment sizes, deletions up to 97 bp and insertions up to 33 bp have been successful under optimal conditions.

NATURE COMMUNICATIONS (2021)

Article Microbiology

Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in Bacillus subtilis and Paenibacillus polymyxa

Man Su Kim et al.

Summary: The development of a multiplex genome editing system using CBE has shown high editing efficiencies for multiple genes in Bacillus subtilis, providing a powerful tool for uncovering hidden antibiotics in Bacillus and Paenibacillus species.

FRONTIERS IN MICROBIOLOGY (2021)

Review Biochemistry & Molecular Biology

Agroinfiltration Mediated Scalable Transient Gene Expression in Genome Edited Crop Plants

Maninder Kaur et al.

Summary: Agrobacterium-mediated transformation is a commonly used method for transferring foreign genes into target plants. The combination of agroinfiltration and the breakthrough discovery of CRISPR/Cas9 offers targeted and efficient genome editing capabilities.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemistry & Molecular Biology

GO: a functional reporter system to identify and enrich base editing activity

Alyna Katti et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Are the current gRNA ranking prediction algorithms useful for genome editing in plants?

Fatima Naim et al.

PLOS ONE (2020)

Article Biology

Multiplex genome editing using a dCas9-cytidine deaminase fusion in Streptomyces

Yawei Zhao et al.

SCIENCE CHINA-LIFE SCIENCES (2020)

Article Agricultural Engineering

Efficient genome editing of rubber tree (hevea brasiliensis) protoplasts using CRISPR/Cas9 ribonucleoproteins

Yueting Fan et al.

INDUSTRIAL CROPS AND PRODUCTS (2020)

Article Biochemical Research Methods

A multiplex guide RNA expression system and its efficacy for plant genome engineering

Youngbin Oh et al.

PLANT METHODS (2020)

Article Biotechnology & Applied Microbiology

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

Michelle F. Richter et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemistry & Molecular Biology

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

Mandana Arbab et al.

Review Biotechnology & Applied Microbiology

Development and Application of CRISPR/Cas in Microbial Biotechnology

Wentao Ding et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Biotechnology & Applied Microbiology

CRISPR-Assisted Multiplex Base Editing System inPseudomonas putidaKT2440

Jun Sun et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors

Andrew V. Anzalone et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemistry & Molecular Biology

Development of multiplex genome editing toolkits for citrus with high efficacy in biallelic and homozygous mutations

Xiaoen Huang et al.

PLANT MOLECULAR BIOLOGY (2020)

Article Multidisciplinary Sciences

DNA capture by a CRISPR-Cas9-guided adenine base editor

Audrone Lapinaite et al.

SCIENCE (2020)

Article Biochemical Research Methods

CRISPR-dCas9 Mediated Cytosine Deaminase Base Editing in Bacillus subtilis

Sili Yu et al.

ACS SYNTHETIC BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Efficient genome editing using CRISPR-Cas9 RNP delivery into cabbage protoplasts via electro-transfection

Myoung Hui Lee et al.

PLANT BIOTECHNOLOGY REPORTS (2020)

Article Chemistry, Multidisciplinary

Programmable adenine deamination in bacteria using a Cas9-adenine-deaminase fusion

Ya Zhang et al.

CHEMICAL SCIENCE (2020)

Article Biotechnology & Applied Microbiology

CRISPR-Cas9D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii

Qi Li et al.

BIOTECHNOLOGY AND BIOENGINEERING (2019)

Article Biotechnology & Applied Microbiology

Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum

Yu Wang et al.

BIOTECHNOLOGY AND BIOENGINEERING (2019)

Review Biochemistry & Molecular Biology

Genome Editing in Agriculture: Technical and Practical Considerations

Julia Jansing et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biotechnology & Applied Microbiology

Continuous evolution of base editors with expanded target compatibility and improved activity

B. W. Thuronyi et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

Yaojun Tong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Expanding C-T base editing toolkit with diversified cytidine deaminases

Tian-Lin Cheng et al.

NATURE COMMUNICATIONS (2019)

Article Biotechnology & Applied Microbiology

Continuous evolution of base editors with expanded target compatibility and improved activity

Benjamin W. Thuronyi et al.

NATURE BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

MACBETH: Multiplex automated Corynebacterium glutamicum base editing method

Yu Wang et al.

METABOLIC ENGINEERING (2018)

Review Biochemistry & Molecular Biology

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands

Jason D. Salter et al.

TRENDS IN BIOCHEMICAL SCIENCES (2018)

Article Microbiology

Deaminase-mediated multiplex genome editing in Escherichia coli

Satomi Banno et al.

NATURE MICROBIOLOGY (2018)

Article Biotechnology & Applied Microbiology

Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A

Yuan Zong et al.

NATURE BIOTECHNOLOGY (2018)

Review Genetics & Heredity

Base editing: precision chemistry on the genome and transcriptome of living cells

Holly A. Rees et al.

NATURE REVIEWS GENETICS (2018)

Article Genetics & Heredity

EditR: A Method to Quantify Base Editing from Sanger Sequencing

Mitchell G. Kluesner et al.

CRISPR JOURNAL (2018)

Article Multidisciplinary Sciences

Programmable base editing of A.T to G.C in genomic DNA without DNA cleavage

Nicole M. Gaudelli et al.

NATURE (2017)

Article Plant Sciences

An Efficient Visual Screen for CRISPR/Cas9 Activity in Arabidopsis thaliana

Florian Hahn et al.

FRONTIERS IN PLANT SCIENCE (2017)

Article Multidisciplinary Sciences

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

Alexis C. Komor et al.

NATURE (2016)

Review Biochemistry & Molecular Biology

The APOBEC Protein Family: United by Structure, Divergent in Function

Jason D. Salter et al.

TRENDS IN BIOCHEMICAL SCIENCES (2016)

Article Multidisciplinary Sciences

Internal guide RNA interactions interfere with Cas9-mediated cleavage

Summer B. Thyme et al.

NATURE COMMUNICATIONS (2016)

Article Biochemical Research Methods

EcoFlex: A Multifunctional MoClo Kit for E-coli Synthetic Biology

Simon J. Moore et al.

ACS SYNTHETIC BIOLOGY (2016)

Article Biochemical Research Methods

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

Michael E. Lee et al.

ACS SYNTHETIC BIOLOGY (2015)

Article Biochemical Research Methods

A Golden Gate Modular Cloning Toolbox for Plants

Carola Engler et al.

ACS SYNTHETIC BIOLOGY (2014)

Article Multidisciplinary Sciences

A Modular Cloning System for Standardized Assembly of Multigene Constructs

Ernst Weber et al.

PLOS ONE (2011)