Recent advances in developing molecular tools for targeted genome engineering of mammalian cells

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

Principles and applications of TAL effectors for plant physiology and metabolism

(2014) Adam J Bogdanove   CURRENT OPINION IN PLANT BIOLOGY

Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus

(2014) Yupeng Wang et al.   NUCLEIC ACIDS RESEARCH

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

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

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

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

A library of TAL effector nucleases spanning the human genome

(2013) Yongsub Kim et al.   NATURE BIOTECHNOLOGY

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

(2013) Seung Woo Cho 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

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

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

(2013) Thomas Gaj 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

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering

(2013) Sandrine Boissel et al.   NUCLEIC ACIDS RESEARCH

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

A CRISPR way to engineer the human genome

(2013) Sivaprakash Ramalingam et al.   GENOME BIOLOGY

Retroviral integration profiles: their determinants and implications for gene therapy

(2012) Kwang-Il Lim   BMB Reports

Precision genome engineering with programmable DNA-nicking enzymes

(2012) E. Kim et al.   GENOME RESEARCH

Overcoming Transcription Activator-like Effector (TALE) DNA Binding Domain Sensitivity to Cytosine Methylation

(2012) Julien Valton et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays

(2012) Fengli Fu et al.   NUCLEIC ACIDS RESEARCH

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription

(2011) Feng Zhang et al.   NATURE BIOTECHNOLOGY

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection

(2011) Vikram Pattanayak et al.   NATURE METHODS

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

(2011) Kathy N. Lam et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity

(2011) Claudio Mussolino et al.   NUCLEIC ACIDS RESEARCH

Assembly of Designer TAL Effectors by Golden Gate Cloning

(2011) Ernst Weber et al.   PLoS One

Frequent Endonuclease Cleavage at Off-target Locations In Vivo

(2010) Lisa M Petek et al.   MOLECULAR THERAPY

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

(2010) Xiaoxia Cui et al.   NATURE BIOTECHNOLOGY

Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)

(2010) Jeffry D Sander et al.   NATURE METHODS

Directed evolution of recombinase specificity by split gene reassembly

(2010) Charles A. Gersbach et al.   NUCLEIC ACIDS RESEARCH

Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties

(2010) Kwang-il Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

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 redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds

(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

Attenuation of Zinc Finger Nuclease Toxicity by Small-Molecule Regulation of Protein Levels

(2009) Shondra M. Pruett-Miller et al.   PLoS Genetics

Comparison of nonhomologous end joining and homologous recombination in human cells

(2008) Z MAO et al.   DNA REPAIR

Comparison of Zinc Finger Nucleases for Use in Gene Targeting in Mammalian Cells

(2008) Shondra M Pruett-Miller et al.   MOLECULAR THERAPY

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

(2008) Elena E Perez et al.   NATURE BIOTECHNOLOGY

DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases

(2007) Tatjana I Cornu et al.   MOLECULAR THERAPY