Nuclease-mediated genome editing: At the front-line of functional genomics technology

Screening Methods to Identify TALEN-Mediated Knockout Mice

(2014) Yoshiko Nakagawa et al.   EXPERIMENTAL ANIMALS

Plant Genome Engineering with Sequence-Specific Nucleases

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

Mojo Hand, a TALEN design tool for genome editing applications

(2013) Kevin L Neff et al.   BMC BIOINFORMATICS

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

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

(2013) Lei S. Qi et al.   CELL

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

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

(2013) F. Ann Ran et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Versatile strategy for isolating transcription activator-like effector nuclease-mediated knockout mutants inCaenorhabditis elegans

(2013) Takuma Sugi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Targeted mutagenesis in sea urchin embryos using TALENs

(2013) Sayaka Hosoi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Targeted mutagenesis of multiple and paralogous genes inXenopus laevisusing two pairs of transcription activator-like effector nucleases

(2013) Yuto Sakane et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Transcription activator-like effector nucleases efficiently disrupt the target gene in Iberian ribbed newts (Pleurodeles waltl), an experimental model animal for regeneration

(2013) Toshinori Hayashi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Use of zinc-finger nucleases to knock out the WAS gene in K562 cells: a human cellular model for Wiskott-Aldrich syndrome

(2013) M. G. Toscano et al.   Disease Models & Mechanisms

Efficient TALEN construction and evaluation methods for human cell and animal applications

(2013) Tetsushi Sakuma et al.   GENES TO CELLS

Efficient identification of TALEN-mediated genome modifications using heteroduplex mobility assays

(2013) Satoshi Ota et al.   GENES TO CELLS

Modeling human epilepsy by TALEN targeting of mouse sodium channelScn8a

(2013) Julie M. Jones et al.   GENESIS

Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease

(2013) Scott J. Gratz et al.   GENETICS

Precise and Heritable Genome Editing in Evolutionarily Diverse Nematodes Using TALENs and CRISPR/Cas9 to Engineer Insertions and Deletions

(2013) T.-W. Lo et al.   GENETICS

Efficient Targeted Mutagenesis in Medaka Using Custom-Designed Transcription Activator-Like Effector Nucleases

(2013) S. Ansai et al.   GENETICS

Targeted chromosomal deletions and inversions in zebrafish

(2013) A. Gupta et al.   GENOME RESEARCH

Cancer translocations in human cells induced by zinc finger and TALE nucleases

(2013) M. Piganeau et al.   GENOME RESEARCH

Cut-and-Paste of DNA Using an Artificial Restriction DNA Cutter

(2013) Makoto Komiyama   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Reading Frame Correction by Targeted Genome Editing Restores Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients

(2013) David G Ousterout et al.   MOLECULAR THERAPY

Targeted Gene Addition in Human Epithelial Stem Cells by Zinc-finger Nuclease-mediated Homologous Recombination

(2013) Andrea Coluccio et al.   MOLECULAR THERAPY

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

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

Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems

(2013) Wei Li et al.   NATURE BIOTECHNOLOGY

Knockout mice created by TALEN-mediated gene targeting

(2013) Young Hoon Sung 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

Whole-rat conditional gene knockout via genome editing

(2013) Andrew J Brown et al.   NATURE METHODS

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

(2013) Daniel J Dickinson et al.   NATURE METHODS

Robust, synergistic regulation of human gene expression using TALE activators

(2013) Morgan L Maeder et al.   NATURE METHODS

TALE-mediated modulation of transcriptional enhancers in vivo

(2013) Justin Crocker et al.   NATURE METHODS

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

TALEN-mediated precise genome modification by homologous recombination in zebrafish

(2013) Yao Zu et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Engineering nucleases for gene targeting: safety and regulatory considerations

(2013) Katia Pauwels et al.   New Biotechnology

A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells

(2013) Thomas Gaj et al.   NUCLEIC ACIDS RESEARCH

Transcription activator like effector (TALE)-directed piggyBac transposition in human cells

(2013) Jesse B. Owens et al.   NUCLEIC ACIDS RESEARCH

Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease

(2013) Wataru Fujii et al.   NUCLEIC ACIDS RESEARCH

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

(2013) An Xiao et al.   NUCLEIC ACIDS RESEARCH

E-TALEN: a web tool to design TALENs for genome engineering

(2013) Florian Heigwer et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity

(2013) Thomas J. Cradick et al.   NUCLEIC ACIDS RESEARCH

Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination

(2013) Changchun Chen et al.   NUCLEIC ACIDS RESEARCH

TALEN-Based Gene Disruption in the Dengue Vector Aedes aegypti

(2013) Azadeh Aryan et al.   PLoS One

Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System

(2013) Woong Y. Hwang et al.   PLoS One

Targeted Mutagenesis in the Malaria Mosquito Using TALE Nucleases

(2013) Andrea L. Smidler et al.   PLoS One

Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides

(2013) B. Wefers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

(2013) Li-En Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis

(2013) Z. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

piggyBac transposase tools for genome engineering

(2013) X. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient nonmeiotic allele introgression in livestock using custom endonucleases

(2013) W. Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding

(2013) Nancy Podevin et al.   TRENDS IN BIOTECHNOLOGY

Evaluating the Mutagenic Activity of Targeted Endonucleases Containing a Sharkey FokI Cleavage Domain Variant in Zebrafish

(2013) Laura M. Pillay et al.   Zebrafish

Compact designer TALENs for efficient genome engineering

(2013) Marine Beurdeley et al.   Nature Communications

Efficient gene targeting by TAL effector nucleases coinjected with exonucleases in zygotes

(2013) Tomoji Mashimo et al.   Scientific Reports

Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus

(2013) Hirotaka Ebina et al.   Scientific Reports

Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity

(2013) Tetsushi Sakuma et al.   Scientific Reports

High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos

(2013) K.-i. T. Suzuki et al.   Biology Open

Quantitative assay for TALEN activity at endogenous genomic loci

(2013) Y. Hisano et al.   Biology Open

TALE nucleases: tailored genome engineering made easy

(2012) Claudio Mussolino et al.   CURRENT OPINION IN BIOTECHNOLOGY

Targeted disruption of exogenous EGFP gene in medaka using zinc-finger nucleases

(2012) Satoshi Ansai et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Efficient targeted mutagenesis of the chordate Ciona intestinalis genome with zinc-finger nucleases

(2012) Narudo Kawai et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Generation of Rag1-knockout immunodeficient rats and mice using engineered meganucleases

(2012) Séverine Ménoret et al.   FASEB JOURNAL

Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme

(2012) J. Wang et al.   GENOME RESEARCH

Precision genome engineering with programmable DNA-nicking enzymes

(2012) E. Kim et al.   GENOME RESEARCH

Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases

(2012) C. Merlin et al.   GENOME RESEARCH

Transcription Activator-Like Effector Proteins Induce the Expression of the Frataxin Gene

(2012) Jacques P. Tremblay et al.   HUMAN GENE THERAPY

Efficient and Specific Modifications of the Drosophila Genome by Means of an Easy TALEN Strategy

(2012) Jiyong Liu et al.   Journal of Genetics and Genomics

In vivo genome editing using a high-efficiency TALEN system

(2012) Victoria M. Bedell et al.   NATURE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

Targeted gene knockout by direct delivery of zinc-finger nuclease proteins

(2012) Thomas Gaj et al.   NATURE METHODS

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects

(2012) Cherie L. Ramirez et al.   NUCLEIC ACIDS RESEARCH

Chimeric TALE recombinases with programmable DNA sequence specificity

(2012) Andrew C. Mercer et al.   NUCLEIC ACIDS RESEARCH

EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering

(2012) An Xiao et al.   NUCLEIC ACIDS RESEARCH

Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs

(2012) Lindsay Cade et al.   NUCLEIC ACIDS RESEARCH

TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction

(2012) Erin L. Doyle et al.   NUCLEIC ACIDS RESEARCH

Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification

(2012) Lixin Li et al.   PLANT MOLECULAR BIOLOGY

Highly Efficient and Specific Genome Editing in Silkworm Using Custom TALENs

(2012) Sanyuan Ma et al.   PLoS One

Modeling disease mutations by gene targeting in one-cell mouse embryos

(2012) M. Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Monomeric site-specific nucleases for genome editing

(2012) B. P. Kleinstiver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos

(2012) H. Ochiai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient TALEN-mediated gene knockout in livestock

(2012) D. F. Carlson 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

Non-transgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases

(2012) Takahito Watanabe et al.   Nature Communications

Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome

(2012) Timothy J. Dahlem et al.   PLoS Genetics

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

(2011) Thomas J Cradick et al.   BMC BIOINFORMATICS

Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases

(2011) H. J. Lee et al.   GENOME RESEARCH

Genetic engineering of human pluripotent cells using TALE nucleases

(2011) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Knockout rats generated by embryo microinjection of TALENs

(2011) Laurent Tesson et al.   NATURE BIOTECHNOLOGY

Diseases in a dish: modeling human genetic disorders using induced pluripotent cells

(2011) Gustavo Tiscornia et al.   NATURE MEDICINE

Surrogate reporters for enrichment of cells with nuclease-induced mutations

(2011) Hyojin Kim et al.   NATURE METHODS

High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases

(2011) Fuqiang Chen et al.   NATURE METHODS

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

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase

(2011) C. A. Gersbach et al.   NUCLEIC ACIDS RESEARCH

Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases

(2011) J. J. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases

(2011) J. Hauschild et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Genome Editing Across Species Using ZFNs and TALENs

(2011) Andrew J. Wood et al.   SCIENCE

TAL effectors: finding plant genes for disease and defense

(2010) Adam J Bogdanove et al.   CURRENT OPINION IN PLANT BIOLOGY

Targeted Genome Modification in Mice Using Zinc-Finger Nucleases

(2010) I. D. Carbery et al.   GENETICS

Directed Evolution of an Enhanced and Highly Efficient FokI Cleavage Domain for Zinc Finger Nucleases

(2010) Jing Guo et al.   JOURNAL OF MOLECULAR BIOLOGY

Creating Designed Zinc-Finger Nucleases with Minimal Cytotoxicity

(2010) Sivaprakash Ramalingam et al.   JOURNAL OF MOLECULAR BIOLOGY

Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo

(2010) Nathalia Holt et al.   NATURE BIOTECHNOLOGY

Targeted integration in rat and mouse embryos with zinc-finger nucleases

(2010) Xiaoxia Cui et al.   NATURE BIOTECHNOLOGY

A protocol describing the genetic correction of somatic human cells and subsequent generation of iPS cells

(2010) Ángel Raya et al.   Nature Protocols

Genome editing with engineered zinc finger nucleases

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

ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool

(2010) J. D. Sander et al.   NUCLEIC ACIDS RESEARCH

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus

(2010) Inés G. Muñoz et al.   NUCLEIC ACIDS RESEARCH

Generation of Knockout Rats with X-Linked Severe Combined Immunodeficiency (X-SCID) Using Zinc-Finger Nucleases

(2010) Tomoji Mashimo et al.   PLoS One

Gene targeting by homologous recombination in mouse zygotes mediated by zinc-finger nucleases

(2010) M. Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sandwiched zinc-finger nucleases harboring a single-chain FokI dimer as a DNA-cleavage domain

(2009) Tomoaki Mori et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Targeted chromosomal deletions in human cells using zinc finger nucleases

(2009) H. J. Lee et al.   GENOME RESEARCH

Efficient double-stranded DNA cleavage by artificial zinc-finger nucleases composed of one zinc-finger protein and a single-chain FokI dimer

(2009) Takashi Mino et al.   JOURNAL OF BIOTECHNOLOGY

Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases

(2009) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon

(2009) Kosuke Yusa et al.   NATURE METHODS

Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays

(2009) Morgan L Maeder et al.   Nature Protocols

Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease

(2009) Sylvestre Grizot et al.   NUCLEIC ACIDS RESEARCH

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

ENU Mutagenesis, a Way Forward to Understand Gene Function

(2008) Abraham Acevedo-Arozena et al.   Annual Review of Genomics and Human Genetics

Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases

(2008) Elena E Perez et al.   NATURE BIOTECHNOLOGY

Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases

(2008) Yannick Doyon et al.   NATURE BIOTECHNOLOGY

Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases

(2008) Xiangdong Meng et al.   NATURE BIOTECHNOLOGY

Unexpected failure rates for modular assembly of engineered zinc fingers

(2008) Cherie L Ramirez et al.   NATURE METHODS

Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA

(2008) Michal Minczuk et al.   NUCLEIC ACIDS RESEARCH

Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases

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