Construct design for CRISPR/Cas-based genome editing in plants

PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants

(2021) Sebastian M. Siegner et al.   BMC BIOINFORMATICS

Genome engineering for crop improvement and future agriculture

(2021) Caixia Gao   CELL

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

(2021) Daqi Yan et al.   Molecular Plant

Efficient gene targeting in Nicotiana tabacum using CRISPR/SaCas9 and temperature tolerant LbCas12a

(2021) Teng‐Kuei Huang et al.   PLANT BIOTECHNOLOGY JOURNAL

Highly efficient multiplex editing: One‐shot generation of 8x Nicotiana benthamiana and 12x Arabidopsis mutants

(2021) Johannes Stuttmann et al.   PLANT JOURNAL

Novel CRISPR/Cas applications in plants: from prime editing to chromosome engineering

(2021) Teng-Kuei Huang et al.   TRANSGENIC RESEARCH

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

(2021) Jonathan Y. Hsu et al.   Nature Communications

Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins

(2021) Liwei Chen et al.   Nature Communications

CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants

(2021) Changtian Pan et al.   CURRENT OPINION IN PLANT BIOLOGY

High-efficiency prime editing with optimized, paired pegRNAs in plants

(2021) Qiupeng Lin et al.   NATURE BIOTECHNOLOGY

Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems

(2021) Yingxiao Zhang et al.   Nature Communications

Improved plant cytosine base editors with high editing activity, purity, and specificity

(2021) Qiurong Ren et al.   PLANT BIOTECHNOLOGY JOURNAL

Design of Guide RNA for CRISPR/Cas Plant Genome Editing

(2020) G. A. Gerashchenkov et al.   MOLECULAR BIOLOGY

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors

(2020) Jordan L. Doman et al.   NATURE BIOTECHNOLOGY

Targeted base editing in rice with CRISPR/ScCas9 system

(2020) Meixia Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Gene editing in plants: assessing the variables through a simplified case study

(2020) Jay Shockey   PLANT MOLECULAR BIOLOGY

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

(2020) Fatima Naim et al.   PLoS One

Comparison of CRISPR-Cas9/Cas12a Ribonucleoprotein Complexes for Genome Editing Efficiency in the Rice Phytoene Desaturase (OsPDS) Gene

(2020) Raviraj Banakar et al.   Rice

Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

(2020) Zhaohui Zhong et al.   Rice

Targeted mutagenesis in Arabidopsis thaliana using CRISPR‐Cas12b/C2c1

(2020) Fan Wu et al.   Journal of Integrative Plant Biology

Plant Prime Editors Enable Precise Gene Editing in Rice Cells

(2020) Xu Tang et al.   Molecular Plant

Precise Modifications of Both Exogenous and Endogenous Genes in Rice by Prime Editing

(2020) Huiyuan Li et al.   Molecular Plant

Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System

(2020) Wen Xu et al.   Molecular Plant

Design and analysis of CRISPR–Cas experiments

(2020) Ruth E. Hanna et al.   NATURE BIOTECHNOLOGY

Prime genome editing in rice and wheat

(2020) Qiupeng Lin et al.   NATURE BIOTECHNOLOGY

Engineering herbicide resistance via prime editing in rice

(2020) Haroon Butt et al.   PLANT BIOTECHNOLOGY JOURNAL

The application of a heat‐inducible CRISPR/Cas12b (C2c1) genome editing system in tetraploid cotton ( G.hirsutum ) plants

(2020) Qiongqiong Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Precision genome engineering in rice using prime editing system

(2020) Kai Hua et al.   PLANT BIOTECHNOLOGY JOURNAL

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity

(2020) Yi Yu et al.   Nature Communications

Multiplexed CRISPR technologies for gene editing and transcriptional regulation

(2020) Nicholas S. McCarty et al.   Nature Communications

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

(2020) Ibrahim C. Kurt et al.   NATURE BIOTECHNOLOGY

Glycosylase base editors enable C-to-A and C-to-G base changes

(2020) Dongdong Zhao et al.   NATURE BIOTECHNOLOGY

Targeted, efficient sequence insertion and replacement in rice

(2020) Yuming Lu et al.   NATURE BIOTECHNOLOGY

CRISPR/Cas9-Based Gene Editing Using Egg Cell-Specific Promoters in Arabidopsis and Soybean

(2020) Na Zheng et al.   Frontiers in Plant Science

A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants

(2020) Juan M. Debernardi et al.   NATURE BIOTECHNOLOGY

Predicting the efficiency of prime editing guide RNAs in human cells

(2020) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Applications of CRISPR–Cas in agriculture and plant biotechnology

(2020) Haocheng Zhu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Precise Genome Modification in Tomato Using an Improved Prime Editing System

(2020) Yuming Lu et al.   PLANT BIOTECHNOLOGY JOURNAL

Base Editing Landscape Extends to Perform Transversion Mutation

(2020) Kutubuddin A. Molla et al.   TRENDS IN GENETICS

A web tool for the design of prime-editing guide RNAs

(2020) Ryan D. Chow et al.   Nature Biomedical Engineering

Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants

(2020) Juan Li et al.   Molecular Plant

Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis

(2019) Baptiste Castel et al.   PLoS One

Target-dependent nickase activities of the CRISPR–Cas nucleases Cpf1 and Cas9

(2019) Becky Xu Hua Fu et al.   Nature Microbiology

Single and multiple gene knockouts by CRISPR–Cas9 in maize

(2019) Nicolas M. Doll et al.   PLANT CELL REPORTS

Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG

(2019) Zhaohui Zhong et al.   Molecular Plant

Cas9-NG greatly expands the targeting scope of genome-editing toolkit by recognizing NG and other atypical PAMs in rice

(2019) Bin Ren et al.   Molecular Plant

Genome engineering in rice using Cas9 variants that recognize NG PAM sequences

(2019) Kai Hua et al.   Molecular Plant

Optimized Cas9 expression systems for highly efficient Arabidopsis genome editing facilitate isolation of complex alleles in a single generation

(2019) Jana Ordon et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis

(2019) Aimee A. Malzahn et al.   BMC BIOLOGY

Plant genome editing using xCas9 with expanded PAM compatibility

(2019) Jingying Li et al.   Journal of Genetics and Genomics

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Assessment of Cas12a‐mediated gene editing efficiency in plants

(2019) Joan Miquel Bernabé‐Orts et al.   PLANT BIOTECHNOLOGY JOURNAL

Engineered xCas9 and SpCas9‐NG variants broaden PAM recognition sites to generate mutations in Arabidopsis plants

(2019) Zengxiang Ge et al.   PLANT BIOTECHNOLOGY JOURNAL

An adenine base editor with expanded targeting scope using SpCas9‐ NG v1 in rice

(2019) Katsuya Negishi et al.   PLANT BIOTECHNOLOGY JOURNAL

Optimizing base editors for improved efficiency and expanded editing scope in rice

(2019) Mugui Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design

(2019) Dong Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strategies to Increase On-Target and Reduce Off-Target Effects of the CRISPR/Cas9 System in Plants

(2019) Zahra Hajiahmadi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Evaluating the Efficiency of gRNAs in CRISPR/Cas9 Mediated Genome Editing in Poplars

(2019) Tobias Bruegmann et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Developing Heritable Mutations in Arabidopsis thaliana Using a Modified CRISPR/Cas9 Toolkit Comprising PAM-Altered Cas9 Variants and gRNAs

(2019) Akihiro Yamamoto et al.   PLANT AND CELL PHYSIOLOGY

Base Editing in Crops: Current Advances, Limitations, and Future Implications

(2019) Rukmini Mishra et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR / dC as9 platforms in plants: strategies and applications beyond genome editing

(2019) Mahdi Moradpour et al.   PLANT BIOTECHNOLOGY JOURNAL

A benchmark of computational CRISPR-Cas9 guide design methods

(2019) Jacob Bradford et al.   PLoS Computational Biology

Bidirectional Promoter-Based CRISPR-Cas9 Systems for Plant Genome Editing

(2019) Qiurong Ren et al.   Frontiers in Plant Science

Multiplex nucleotide editing by high-fidelity Cas9 variants with improved efficiency in rice

(2019) Wen Xu et al.   BMC PLANT BIOLOGY

Efficient induction of haploid plants in wheat by editing of TaMTL using an optimized Agrobacterium-mediated CRISPR system

(2019) Huiyun Liu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Expanding the scope of CRISPR/Cas9‐mediated genome editing in plants using an xCas9 and Cas9‐NG hybrid

(2019) Qingfeng Niu et al.   Journal of Integrative Plant Biology

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Engineering CRISPR/ Lb Cas12a for highly efficient, temperature‐tolerant plant gene editing

(2019) Patrick Schindele et al.   PLANT BIOTECHNOLOGY JOURNAL

Engineered Cas9 variant tools expand targeting scope of genome and base editing in rice

(2019) Dongchang Zeng et al.   PLANT BIOTECHNOLOGY JOURNAL

High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato

(2019) Ida Elisabeth Johansen et al.   Scientific Reports

Plant gene editing through de novo induction of meristems

(2019) Michael F. Maher et al.   NATURE BIOTECHNOLOGY

Delivering CRISPR: a review of the challenges and approaches

(2018) Christopher A. Lino et al.   DRUG DELIVERY

Improved Base Editor for Efficiently Inducing Genetic Variations in Rice with CRISPR/Cas9-Guided Hyperactive hAID Mutant

(2018) Bin Ren et al.   Molecular Plant

Engineering Introns to Express RNA Guides for Cas9- and Cpf1-Mediated Multiplex Genome Editing

(2018) Dan Ding et al.   Molecular Plant

Plant Genome Editing Using FnCpf1 and LbCpf1 Nucleases at Redefined and Altered PAM Sites

(2018) Zhaohui Zhong et al.   Molecular Plant

Expanding the Scope of CRISPR/Cpf1-Mediated Genome Editing in Rice

(2018) Shaoya Li et al.   Molecular Plant

Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

Engineering altered protein–DNA recognition specificity

(2018) Adam J Bogdanove et al.   NUCLEIC ACIDS RESEARCH

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

(2018) Jean-Paul Concordet et al.   NUCLEIC ACIDS RESEARCH

High-efficiency genome editing using a dmc1 promoter-controlled CRISPR/Cas9 system in maize

(2018) Chao Feng et al.   PLANT BIOTECHNOLOGY JOURNAL

Genotyping genome-edited mutations in plants using CRISPR ribonucleoprotein complexes

(2018) Zhen Liang et al.   PLANT BIOTECHNOLOGY JOURNAL

Efficient in planta gene targeting in Arabidopsis using egg cell-specific expression of the Cas9 nuclease of Staphylococcus aureus

(2018) Felix Wolter et al.   PLANT JOURNAL

Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention

(2018) Qiang Zhang et al.   PLANT MOLECULAR BIOLOGY

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

(2018) Janice S. Chen et al.   SCIENCE

Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges

(2018) Effi Haque et al.   Frontiers in Plant Science

CRISPR for Crop Improvement: An Update Review

(2018) Deepa Jaganathan et al.   Frontiers in Plant Science

Web-based design and analysis tools for CRISPR base editing

(2018) Gue-Ho Hwang et al.   BMC BIOINFORMATICS

Efficient generation of stable, heritable gene edits in wheat using CRISPR/Cas9

(2018) Rhian M Howells et al.   BMC PLANT BIOLOGY

CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion

(2018) Viktorija Globyte et al.   EMBO JOURNAL

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

(2018) Yuan Zong et al.   NATURE BIOTECHNOLOGY

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

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing

(2018) Xu Tang et al.   PLANT BIOTECHNOLOGY JOURNAL

xC as9 expands the scope of genome editing with reduced efficiency in rice

(2018) Junjie Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Developing a highly efficient and wildly adaptive CRISPR ‐ Sa Cas9 toolset for plant genome editing

(2018) Ruying Qin et al.   PLANT BIOTECHNOLOGY JOURNAL

Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression

(2018) Lu Long et al.   Plant Methods

Repurposing CRISPR-Cas12b for mammalian genome engineering

(2018) Fei Teng et al.   Cell Discovery

Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency

(2017) Kristopher Torp Jensen et al.   FEBS LETTERS

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

(2017) Nicole M. Gaudelli et al.   NATURE

Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion

(2017) Zenpei Shimatani et al.   NATURE BIOTECHNOLOGY

Increasing the efficiency of CRISPR-Cas9-VQR precise genome editing in rice

(2017) Xixun Hu et al.   PLANT BIOTECHNOLOGY JOURNAL

A multi-purpose toolkit to enable advanced genome engineering in plants

(2017) Tomas Cermak et al.   PLANT CELL

Multiplexed Gene Editing and Protein Overexpression Using a Tobacco mosaic virus Viral Vector

(2017) Will B. Cody et al.   PLANT PHYSIOLOGY

Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy

(2017) Mikihiro Shibata et al.   Nature Communications

Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence

(2017) Ting Zheng et al.   Scientific Reports

Dramatic Improvement of CRISPR/Cas9 Editing in Candida albicans by Increased Single Guide RNA Expression

(2017) Henry Ng et al.   mSphere

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

Leveraging Rules of Nonsense-Mediated mRNA Decay for Genome Engineering and Personalized Medicine

(2016) Maximilian W. Popp et al.   CELL

Expanding the Range of CRISPR/Cas9 Genome Editing in Rice

(2016) Xixun Hu et al.   Molecular Plant

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

(2016) Alexis C. Komor et al.   NATURE

Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation

(2016) Keith Lowe et al.   PLANT CELL

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

(2016) Iman Farasat et al.   PLoS Computational Biology

Highly specific targeted mutagenesis in plants using Staphylococcus aureus Cas9

(2016) Hidetaka Kaya et al.   Scientific Reports

Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants

(2016) Yuriko Osakabe et al.   Scientific Reports

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Potential pitfalls of CRISPR/Cas9-mediated genome editing

(2015) Rongxue Peng et al.   FEBS Journal

Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System

(2015) Zahir Ali et al.   Molecular Plant

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Parameters affecting frequency of CRISPR/Cas9 mediated targeted mutagenesis in rice

(2015) Masafumi Mikami et al.   PLANT CELL REPORTS

Highly efficient heritable plant genome engineering using Cas9 orthologues fromStreptococcus thermophilusandStaphylococcus aureus

(2015) Jeannette Steinert et al.   PLANT JOURNAL

Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice

(2015) Masafumi Mikami et al.   PLANT MOLECULAR BIOLOGY

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation

(2015) Levi G. Lowder et al.   PLANT PHYSIOLOGY

Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system

(2015) Kabin Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted mutagenesis in soybean using the CRISPR-Cas9 system

(2015) Xianjun Sun et al.   Scientific Reports

Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation

(2015) Zhi-Ping Wang et al.   GENOME BIOLOGY

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

(2014) Hui-Li Xing et al.   BMC PLANT BIOLOGY

Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice

(2014) Huanbin Zhou et al.   NUCLEIC ACIDS RESEARCH

The CRISPR/Cas system can be used as nuclease forin plantagene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny

(2014) Simon Schiml et al.   PLANT JOURNAL

Comparative assessments of CRISPR-Cas nucleases’ cleavage efficiency in planta

(2014) Ross A. Johnson et al.   PLANT MOLECULAR BIOLOGY

Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice

(2014) Rongfang Xu et al.   Rice

Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9

(2013) Jian-Feng Li et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS