Use of designer nucleases for targeted gene and genome editing in plants

The CRISPR/Cas9 system for plant genome editing and beyond

(2015) Luisa Bortesi et al.   BIOTECHNOLOGY ADVANCES

Targeted genome modifications in soybean with CRISPR/Cas9

(2015) Thomas B Jacobs et al.   BMC BIOTECHNOLOGY

Editing plant genomes with CRISPR/Cas9

(2015) Khaoula Belhaj et al.   CURRENT OPINION IN BIOTECHNOLOGY

The structural biology of CRISPR-Cas systems

(2015) Fuguo Jiang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design

(2015) Behnom Farboud et al.   GENETICS

Genome editing in plants via designed zinc finger nucleases

(2015) Joseph F. Petolino   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

Genomic Engineering and the Future of Medicine

(2015) Jennifer A. Doudna   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Targeted gene mutation in tetraploid potato through transient TALEN expression in protoplasts

(2015) Alessandro Nicolia et al.   JOURNAL OF BIOTECHNOLOGY

CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system

(2015) Meng Yan et al.   Journal of Integrative Plant Biology

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

(2015) Xingliang Ma et al.   Molecular Plant

CRISPR, the disruptor

(2015) Heidi Ledford   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

(2015) Takeshi Maruyama et al.   NATURE BIOTECHNOLOGY

Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors

(2015) Xiaoling Wang et al.   NATURE BIOTECHNOLOGY

Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells

(2015) Van Trung Chu et al.   NATURE BIOTECHNOLOGY

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Photoactivatable CRISPR-Cas9 for optogenetic genome editing

(2015) Yuta Nihongaki et al.   NATURE BIOTECHNOLOGY

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells

(2015) Daesik Kim et al.   NATURE METHODS

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14

(2015) Yong-Qiang Ning et al.   NUCLEIC ACIDS RESEARCH

Perspectives on transgenic, herbicide-resistant crops in the United States almost 20 years after introduction

(2015) Stephen O Duke   PEST MANAGEMENT SCIENCE

Creation of fragrant rice by targeted knockout of theOsBADH2gene using TALEN technology

(2015) Qiwei Shan et al.   PLANT BIOTECHNOLOGY JOURNAL

Heritable site-specific mutagenesis using TALENs in maize

(2015) Si Nian Char et al.   PLANT BIOTECHNOLOGY JOURNAL

Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system

(2015) Shaohui Wang et al.   PLANT CELL REPORTS

Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice

(2015) Junhui Zhou et al.   PLANT JOURNAL

Expression activation and functional analysis of HLA3, a putative inorganic carbon transporter in Chlamydomonas reinhardtii

(2015) Han Gao et al.   PLANT JOURNAL

Auxin binding protein 1 (ABP1) is not required for either auxin signaling orArabidopsisdevelopment

(2015) Yangbin Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Rational design of a split-Cas9 enzyme complex

(2015) Addison V. Wright et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TALE nickase-mediatedSP110knockin endows cattle with increased resistance to tuberculosis

(2015) Haibo Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mutagenic chain reaction: A method for converting heterozygous to homozygous mutations

(2015) V. M. Gantz et al.   SCIENCE

Molecular scissors and their application in genetically modified farm animals

(2015) Bjoern Petersen et al.   TRANSGENIC RESEARCH

Enabling plant synthetic biology through genome engineering

(2015) Nicholas J. Baltes et al.   TRENDS IN BIOTECHNOLOGY

Looking forward to genetically edited fruit crops

(2015) Chidananda Nagamangala Kanchiswamy et al.   TRENDS IN BIOTECHNOLOGY

Positive–negative-selection-mediated gene targeting in rice

(2015) Zenpei Shimatani et al.   Frontiers in Plant Science

Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design

(2015) Behnom Farboud et al.   GENETICS

Precise Correction of the Dystrophin Gene in Duchenne Muscular Dystrophy Patient Induced Pluripotent Stem Cells by TALEN and CRISPR-Cas9

(2015) Hongmei Lisa Li et al.   Stem Cell Reports

Recommendations from the workshop on Comparative Approaches to Safety Assessment of GM Plant Materials: A road toward harmonized criteria?

(2015) Andrew Bartholomaeus et al.   GM Crops & Food-Biotechnology in Agriculture and the Food Chain

Genome Engineering with Targetable Nucleases

(2014) Dana Carroll   Annual Review of Biochemistry

TALEN-mediated genome editing: prospects and perspectives

(2014) David A. Wright et al.   BIOCHEMICAL JOURNAL

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

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

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii

(2014) Wenzhi Jiang et al.   EUKARYOTIC CELL

Genome-Wide Prediction of Highly Specific Guide RNA Spacers for CRISPR–Cas9-Mediated Genome Editing in Model Plants and Major Crops

(2014) Kabin Xie et al.   Molecular Plant

CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants

(2014) Yang Lei et al.   Molecular Plant

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

(2014) Yanpeng Wang et al.   NATURE BIOTECHNOLOGY

Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification

(2014) John P Guilinger et al.   NATURE BIOTECHNOLOGY

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

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

(2014) Huanbin Zhou et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9-Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L.

(2014) Shigeo S. Sugano et al.   PLANT AND CELL PHYSIOLOGY

Multigene Knockout Utilizing Off-Target Mutations of the CRISPR/Cas9 System in Rice

(2014) Masaki Endo et al.   PLANT AND CELL PHYSIOLOGY

Genome Editing with Engineered Nucleases in Plants

(2014) Y. Osakabe et al.   PLANT AND CELL PHYSIOLOGY

RNA-guided transcriptional regulationin plantavia synthetic dCas9-based transcription factors

(2014) Agnieszka Piatek et al.   PLANT BIOTECHNOLOGY JOURNAL

The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation

(2014) Hui Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family

(2014) William Haun et al.   PLANT BIOTECHNOLOGY JOURNAL

DNA Replicons for Plant Genome Engineering

(2014) N. J. Baltes et al.   PLANT CELL

Emerging tools for synthetic biology in plants

(2014) Ian Small et al.   PLANT JOURNAL

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

CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum

(2014) Junping Gao et al.   PLANT MOLECULAR BIOLOGY

Hairy Root Transformation Using Agrobacterium rhizogenes as a Tool for Exploring Cell Type-Specific Gene Expression and Function Using Tomato as a Model

(2014) M. Ron et al.   PLANT PHYSIOLOGY

Targeted Mutagenesis of the Tomato PROCERA Gene Using Transcription Activator-Like Effector Nucleases

(2014) V. S. Lor et al.   PLANT PHYSIOLOGY

Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System

(2014) C. Brooks et al.   PLANT PHYSIOLOGY

Targeted mutagenesis using zinc-finger nucleases in perennial fruit trees

(2014) Reut Peer et al.   PLANTA

True-Breeding Targeted Gene Knock-Out in Barley Using Designer TALE-Nuclease in Haploid Cells

(2014) Maia Gurushidze et al.   PLoS One

Efficient CRISPR/Cas9-Mediated Gene Editing in Arabidopsis thaliana and Inheritance of Modified Genes in the T2 and T3 Generations

(2014) WenZhi Jiang et al.   PLoS One

Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis

(2014) Z. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulating gene drives

(2014) K. A. Oye et al.   SCIENCE

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

Genome edited sheep and cattle

(2014) Chris Proudfoot et al.   TRANSGENIC RESEARCH

Inhibiting replication of begomoviruses using artificial zinc finger nucleases that target viral-conserved nucleotide motif

(2014) Wei Chen et al.   VIRUS GENES

Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology

(2014) Fayza Daboussi et al.   Nature Communications

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

(2014) Luhan Yang et al.   Nature Communications

TALE activation of endogenous genes in Chlamydomonas reinhardtii

(2014) Han Gao et al.   Algal Research-Biomass Biofuels and Bioproducts

Plant Genome Engineering with Sequence-Specific Nucleases

(2013) Daniel F. Voytas   Annual Review of Plant Biology

Efficient genome editing in plants using a CRISPR/Cas system

(2013) Zhengyan Feng et al.   CELL RESEARCH

Targeted mutagenesis in rice using CRISPR-Cas system

(2013) Jin Miao et al.   CELL RESEARCH

Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways

(2013) Y. Qi et al.   GENOME RESEARCH

From Agrobacterium to viral vectors: genome modification of plant cells by rare cutting restriction enzymes

(2013) Ira Marton et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System

(2013) Zhen Liang et al.   Journal of Genetics and Genomics

Application of the CRISPR–Cas System for Efficient Genome Engineering in Plants

(2013) Yanfei Mao et al.   Molecular Plant

Rapid and Efficient Gene Modification in Rice and Brachypodium Using TALENs

(2013) Qiwei Shan et al.   Molecular Plant

RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System

(2013) Kabin Xie et al.   Molecular Plant

US regulation misses some GM crops

(2013) Heidi Ledford   NATURE

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

Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease

(2013) Vladimir Nekrasov et al.   NATURE BIOTECHNOLOGY

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

Trait stacking via targeted genome editing

(2013) William M. Ainley et al.   PLANT BIOTECHNOLOGY JOURNAL

Targeted molecular trait stacking in cotton through targeted double-strand break induction

(2013) Kathleen D'Halluin et al.   PLANT BIOTECHNOLOGY JOURNAL

Male-sterile maize plants produced by targeted mutagenesis of the cytochrome P450-like gene (MS26) using a re-designed I-CreI homing endonuclease

(2013) Vesna Djukanovic et al.   PLANT JOURNAL

TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants

(2013) Toni Wendt et al.   PLANT MOLECULAR BIOLOGY

Mesoporous Silica Nanoparticle-Mediated Intracellular Cre Protein Delivery for Maize Genome Editing via loxP Site Excision,

(2013) S. Martin-Ortigosa et al.   PLANT PHYSIOLOGY

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

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins

(2013) Erin L. Doyle et al.   TRENDS IN CELL BIOLOGY

Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases

(2013) Yiping Qi et al.   G3-Genes Genomes Genetics

Targeted Mutagenesis of Arabidopsis thaliana Using Engineered TAL Effector Nucleases

(2013) Michelle Christian et al.   G3-Genes Genomes Genetics

RNA-Guided Genome Editing for Target Gene Mutations in Wheat

(2013) Santosh Kumar Upadhyay et al.   G3-Genes Genomes Genetics

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

High-efficiency TALEN-based gene editing produces disease-resistant rice

(2012) Ting Li et al.   NATURE BIOTECHNOLOGY

Transcriptional activation ofBrassica napusβ-ketoacyl-ACP synthase II with an engineered zinc finger protein transcription factor

(2012) Manju Gupta et al.   PLANT BIOTECHNOLOGY JOURNAL

ZFN-mediated gene targeting of the Arabidopsisprotoporphyrinogen oxidasegene throughAgrobacterium-mediated floral dip transformation

(2012) Sylvia de Pater et al.   PLANT BIOTECHNOLOGY JOURNAL

The requirement for recombination factors differs considerably between different pathways of homologous double-strand break repair in somatic plant cells

(2012) Nadine Roth et al.   PLANT JOURNAL

Nuclear gene targeting inChlamydomonasusing engineered zinc-finger nucleases

(2012) Irina Sizova et al.   PLANT JOURNAL

Transcription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering

(2012) Y. Zhang et al.   PLANT PHYSIOLOGY

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

(2012) M. Jinek et al.   SCIENCE

Synthetic Zinc Finger Nuclease Design and Rapid Assembly

(2011) Mark J. Osborn et al.   HUMAN GENE THERAPY

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes

(2011) Ting Li et al.   NUCLEIC ACIDS RESEARCH

Localized egg-cell expression of effector proteins for targeted modification of the Arabidopsis genome

(2011) Liron Even-Faitelson et al.   PLANT JOURNAL

Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein

(2011) Magdy M. Mahfouz et al.   PLANT MOLECULAR BIOLOGY

Targeted Mutagenesis of Duplicated Genes in Soybean with Zinc-Finger Nucleases

(2011) S. J. Curtin et al.   PLANT PHYSIOLOGY

De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks

(2011) M. M. Mahfouz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

Tuber-Specific Silencing of the Acid Invertase Gene Substantially Lowers the Acrylamide-Forming Potential of Potato

(2010) Jingsong Ye et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain

(2010) Ting Li et al.   NUCLEIC ACIDS RESEARCH

Zinc finger nuclease-mediated transgene deletion

(2010) Joseph F. Petolino et al.   PLANT MOLECULAR BIOLOGY

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases

(2010) F. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases

(2010) K. Osakabe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-frequency modification of plant genes using engineered zinc-finger nucleases

(2009) Jeffrey A. Townsend et al.   NATURE

Precise genome modification in the crop species Zea mays using zinc-finger nucleases

(2009) Vipula K. Shukla et al.   NATURE

Heritable targeted mutagenesis in maize using a designed endonuclease

(2009) Huirong Gao et al.   PLANT JOURNAL

Targeted transgene integration in plant cells using designed zinc finger nucleases

(2009) Charles Q. Cai et al.   PLANT MOLECULAR BIOLOGY

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Rapid “Open-Source” Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification

(2008) Morgan L. Maeder et al.   MOLECULAR CELL