CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects

Engineering Herbicide-Resistant Rice Plants through CRISPR/Cas9-Mediated Homologous Recombination of Acetolactate Synthase

(2016) Yongwei Sun et al.   Molecular Plant

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Precision Targeted Mutagenesis via Cas9 Paired Nickases in Rice

(2016) Masafumi Mikami et al.   PLANT AND CELL PHYSIOLOGY

Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes

(2016) Holger Puchta   PLANT JOURNAL

Oligonucleotide-Mediated Genome Editing Provides Precision and Function to Engineered Nucleases and Antibiotics in Plants

(2016) Noel J. Sauer et al.   PLANT PHYSIOLOGY

RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency

(2016) Jun Song et al.   Nature Communications

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Small Molecules Enhance CRISPR Genome Editing in Pluripotent Stem Cells

(2015) Chen Yu et al.   Cell Stem Cell

Single-step generation of rabbits carrying a targeted allele of the tyrosinase gene using CRISPR/Cas9

(2015) Arata HONDA et al.   EXPERIMENTAL ANIMALS

A Simple CRISPR/Cas9 System for Multiplex Genome Editing in Rice

(2015) Chun Wang et al.   Journal of Genetics and Genomics

DNase H Activity of Neisseria meningitidis Cas9

(2015) Yan Zhang et al.   MOLECULAR CELL

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

(2015) Xingliang Ma et al.   Molecular Plant

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann 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

DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins

(2015) Je Wook Woo et al.   NATURE BIOTECHNOLOGY

A split-Cas9 architecture for inducible genome editing and transcription modulation

(2015) Bernd Zetsche 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

Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications inArabidopsis

(2015) Yanfei Mao et al.   PLANT BIOTECHNOLOGY JOURNAL

A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis

(2015) Zhengjing Zhang et al.   PLANT CELL REPORTS

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

(2015) Jeannette Steinert et al.   PLANT JOURNAL

Cas9-Guide RNA Directed Genome Editing in Soybean

(2015) Zhongsen Li et al.   PLANT PHYSIOLOGY

A Defect in DNA Ligase4 Enhances the Frequency of TALEN-Mediated Targeted Mutagenesis in Rice

(2015) Ayako Nishizawa-Yokoi et al.   PLANT PHYSIOLOGY

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

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

Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA

(2015) Sergei Svitashev et al.   PLANT PHYSIOLOGY

Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering

(2015) Mustapha Aouida et al.   PLoS One

Multicolor CRISPR labeling of chromosomal loci in human cells

(2015) Hanhui Ma 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

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing

(2015) Kangquan Yin et al.   Scientific Reports

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system

(2015) Nicholas J. Baltes et al.   Nature Plants

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

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

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells

(2014) Lior Nissim et al.   MOLECULAR CELL

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

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

(2014) John P Guilinger et al.   NATURE BIOTECHNOLOGY

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

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

DNA Replicons for Plant Genome Engineering

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

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

Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering inArabidopsis thaliana

(2014) Friedrich Fauser et al.   PLANT JOURNAL

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

Generation of Marker-free Transgenic Plants Concurrently Resistant to a DNA Geminivirus and a RNA Tospovirus

(2014) Ching-Fu Yang et al.   Scientific Reports

Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR

(2013) Toshitsugu Fujita et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

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

(2013) Y. Qi et al.   GENOME RESEARCH

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

Self-processing of ribozyme-flanked RNAs into guide RNAsin vitroandin vivofor CRISPR-mediated genome editing

(2013) Yangbin Gao et al.   Journal of Integrative Plant Biology

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

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

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Activation domains for controlling plant gene expression using designed transcription factors

(2013) Jianquan Li et al.   PLANT BIOTECHNOLOGY JOURNAL

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-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors

(2012) Shiv B. Tiwari et al.   PLANT JOURNAL

Designed transcriptional regulators for trait development

(2012) Joseph F. Petolino et al.   PLANT SCIENCE

In planta gene targeting

(2012) F. Fauser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) M. Jinek et al.   SCIENCE

Genome Engineering With Zinc-Finger Nucleases

(2011) Dana Carroll   GENETICS

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

A TALE nuclease architecture for efficient genome editing

(2010) Jeffrey C Miller et al.   NATURE BIOTECHNOLOGY

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

First transgenic geminivirus-resistant plant in the field

(2009) Francisco J L Aragão et al.   NATURE BIOTECHNOLOGY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

A chemical compound that stimulates the human homologous recombination protein RAD51

(2008) K. Jayathilaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA