Precision gene editing technology and applications in nephrology

Dose-Dependent Prevention of Metabolic and Neurologic Disease in Murine MPS II by ZFN-Mediated In Vivo Genome Editing

(2018) Kanut Laoharawee et al.   MOLECULAR THERAPY

A Gene Implicated in Activation of Retinoic Acid Receptor Targets Is a Novel Renal Agenesis Gene in Humans

(2017) Patrick D. Brophy et al.   GENETICS

Evolution of Transcription Activator-Like Effectors in Xanthomonas oryzae

(2017) Annett Erkes et al.   Genome Biology and Evolution

Cytidine deaminase Apobec3a induction in fallopian epithelium after exposure to follicular fluid

(2017) Pavla Brachova et al.   GYNECOLOGIC ONCOLOGY

Impact of AAV Capsid-Specific T-Cell Responses on Design and Outcome of Clinical Gene Transfer Trials with Recombinant Adeno-Associated Viral Vectors: An Evolving Controversy

(2017) Hildegund C.J. Ertl et al.   HUMAN GENE THERAPY

Uromodulin p.Cys147Trp mutation drives kidney disease by activating ER stress and apoptosis

(2017) Bryce G. Johnson et al.   JOURNAL OF CLINICAL INVESTIGATION

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL

(2017) Z Li et al.   LEUKEMIA

RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes

(2017) Alexandra East-Seletsky et al.   MOLECULAR CELL

CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons

(2017) Pierre Billon et al.   MOLECULAR CELL

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

(2017) Nicole M. Gaudelli et al.   NATURE

Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion

(2017) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9

(2017) Dong Niu et al.   SCIENCE

Gene therapy with helper-dependent adenoviral vectors: lessons from studies in large animal models

(2017) Nicola Brunetti-Pierri et al.   VIRUS GENES

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

(2017) Takahide Kouno et al.   Nature Communications

Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus

(2017) Anne Bothmer et al.   Nature Communications

microRNA-210-3p depletion by CRISPR/Cas9 promoted tumorigenesis through revival of TWIST1 in renal cell carcinoma

(2017) Hirofumi Yoshino et al.   Oncotarget

A Gene Implicated in Activation of Retinoic Acid Receptor Targets Is a Novel Renal Agenesis Gene in Humans

(2017) Patrick D. Brophy et al.   GENETICS

Establishment of expanded and streamlined pipeline of PITCh knock-in – a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO

(2017) Kazuki Nakamae et al.   Bioengineered

Heterozygous Loss-of-Function SEC61A1 Mutations Cause Autosomal-Dominant Tubulo-Interstitial and Glomerulocystic Kidney Disease with Anemia

(2016) Nikhita Ajit Bolar et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ

(2016) Tomomi Aida et al.   BMC GENOMICS

Zinc Finger Protein 618 Regulates the Function of UHRF2 (Ubiquitin-like with PHD and Ring Finger Domains 2) as a Specific 5-Hydroxymethylcytosine Reader

(2016) Yidan Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA Sequence Alignment during Homologous Recombination

(2016) Eric C. Greene   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional validation of tensin2 SH2-PTB domain by CRISPR/Cas9-mediated genome editing

(2016) Kiyoma MARUSUGI et al.   JOURNAL OF VETERINARY MEDICAL SCIENCE

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

(2016) Alexis C. Komor et al.   NATURE

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection

(2016) Alexandra East-Seletsky et al.   NATURE

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells

(2016) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases

(2016) Shengdar Q. Tsai et al.   NATURE REVIEWS GENETICS

A role for human homologous recombination factors in suppressing microhomology-mediated end joining

(2016) Sara Ahrabi et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Efficient genome editing of differentiated renal epithelial cells

(2016) Alexis Hofherr et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Ligase I and ligase III mediate the DNA double-strand break ligation in alternative end-joining

(2016) Guangqing Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Attenuating Ischemia-Reperfusion Injury in Kidney Transplantation by Perfusing Donor Organs With siRNA Cocktail Solution

(2016) Xiufen Zheng et al.   TRANSPLANTATION

Epigenome Editing: State of the Art, Concepts, and Perspectives

(2016) Goran Kungulovski et al.   TRENDS IN GENETICS

c21orf59/kurly Controls Both Cilia Motility and Polarization

(2016) Kimberly M. Jaffe et al.   Cell Reports

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

DNA Sequence Alignment by Microhomology Sampling during Homologous Recombination

(2015) Zhi Qi et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

Effect of Adenoviral Catalase Gene Transfer on Renal Ischemia/Reperfusion Injury in Rats

(2015) Chih-Ching Yang   CHINESE JOURNAL OF PHYSIOLOGY

Potential pitfalls of CRISPR/Cas9-mediated genome editing

(2015) Rongxue Peng et al.   FEBS Journal

Mineralocorticoid Excess or Glucocorticoid InsufficiencyNovelty and Significance

(2015) Linda J. Mullins et al.   HYPERTENSION

PKD1 Mono-Allelic Knockout Is Sufficient to Trigger Renal Cystogenesis in a Mini-Pig Model

(2015) Jin He et al.   International Journal of Biological Sciences

Modulation of Polycystic Kidney Disease Severity by Phosphodiesterase 1 and 3 Subfamilies

(2015) H. Ye et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

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

(2015) Takeshi Maruyama 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

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems

(2015) Tetsushi Sakuma et al.   Nature Protocols

Genetic dissection of kidney disorders

(2015) Friedhelm Hildebrandt   Nature Reviews Nephrology

Intermedin is upregulated and attenuates renal fibrosis by inhibition of oxidative stress in rats with unilateral ureteral obstruction

(2015) Xi Qiao et al.   NEPHROLOGY

Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms

(2015) Kaja Kostyrko et al.   NUCLEIC ACIDS RESEARCH

Rationally engineered Cas9 nucleases with improved specificity

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

Genome-wide inactivation of porcine endogenous retroviruses (PERVs)

(2015) L. Yang et al.   SCIENCE

Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy

(2015) C. Long et al.   SCIENCE

In vivo gene editing in dystrophic mouse muscle and muscle stem cells

(2015) M. Tabebordbar et al.   SCIENCE

In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy

(2015) C. E. Nelson et al.   SCIENCE

Molecular scissors and their application in genetically modified farm animals

(2015) Bjoern Petersen et al.   TRANSGENIC RESEARCH

Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids

(2015) Benjamin S. Freedman et al.   Nature Communications

CTGF siRNA ameliorates tubular cell apoptosis and tubulointerstitial fibrosis in obstructed mouse kidneys in a Sirt1-independent manner

(2015) Yunzhuo Ren et al.   Drug Design Development and Therapy

Genome-wide identification of CRISPR/Cas9 off-targets in human genome

(2014) Jinzhi Duan et al.   CELL RESEARCH

Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs

(2014) Cory Smith et al.   Cell Stem Cell

Making designer mutants in model organisms

(2014) Y. Peng et al.   DEVELOPMENT

HV1 Acts as a Sodium Sensor and Promotes Superoxide Production in Medullary Thick Ascending Limb of Dahl Salt-Sensitive Rats

(2014) Chunhua Jin et al.   HYPERTENSION

CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity

(2014) Rodolphe Barrangou et al.   MOLECULAR CELL

Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

(2014) Carolin Anders et al.   NATURE

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

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

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

(2014) Cem Kuscu 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

Protospacer Adjacent Motif (PAM)-Distal Sequences Engage CRISPR Cas9 DNA Target Cleavage

(2014) Regina Cencic et al.   PLoS One

Mutation of Plekha7 attenuates salt-sensitive hypertension in the rat

(2014) B. T. Endres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Erasers of Histone Acetylation: The Histone Deacetylase Enzymes

(2014) E. Seto et al.   Cold Spring Harbor Perspectives in Biology

Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9

(2014) Shota Nakade et al.   Nature Communications

AAV-Mediated Gene Therapy for Research and Therapeutic Purposes

(2014) R. Jude Samulski et al.   Annual Review of Virology

Genetic mutation of recombination activating gene 1 in Dahl salt-sensitive rats attenuates hypertension and renal damage

(2013) David L. Mattson et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

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

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

(2013) Scott J. Gratz et al.   GENETICS

Heritable Gene Knockout in Caenorhabditis elegans by Direct Injection of Cas9–sgRNA Ribonucleoproteins

(2013) Seung Woo Cho et al.   GENETICS

Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair

(2013) T. O. Auer 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

Heterozygous Disruption of Renal Outer Medullary Potassium Channel in Rats Is Associated With Reduced Blood Pressure

(2013) Xiaoyan Zhou et al.   HYPERTENSION

Structural basis for the modular recognition of single-stranded RNA by PPR proteins

(2013) Ping Yin et al.   NATURE

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

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

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

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

TALENs and ZFNs are associated with different mutation signatures

(2013) Yongsub Kim et al.   NATURE METHODS

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

(2013) Daniel J Dickinson et al.   NATURE METHODS

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

TALEN-mediated precise genome modification by homologous recombination in zebrafish

(2013) Yao Zu et al.   NATURE METHODS

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

(2013) Florian Heigwer et al.   NUCLEIC ACIDS RESEARCH

Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals

(2013) Shan Xiao 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

Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases

(2013) Brian M. Lamb et al.   NUCLEIC ACIDS RESEARCH

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

(2013) Khaoula Belhaj et al.   Plant Methods

Solution Structure of an Archaeal DNA Binding Protein with an Eukaryotic Zinc Finger Fold

(2013) Florence Guillière et al.   PLoS One

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Recognition of methylated DNA by TAL effectors

(2012) Dong Deng et al.   CELL RESEARCH

Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs

(2012) B L Ellis et al.   GENE THERAPY

Highly active zinc-finger nucleases by extended modular assembly

(2012) M. S. Bhakta et al.   GENOME RESEARCH

A Vector–Host System to Fingerprint Virus Tropism

(2012) Matthew L. Hillestad et al.   HUMAN GENE THERAPY

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

An optimized two-finger archive for ZFN-mediated gene targeting

(2012) Ankit Gupta et al.   NATURE METHODS

TALENs: a widely applicable technology for targeted genome editing

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

Heterozygous knockout of transforming growth factor-β1 protects Dahl S rats against high salt-induced renal injury

(2012) Chun Cheng Andy Chen et al.   PHYSIOLOGICAL GENOMICS

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

(2012) D. Deng et al.   SCIENCE

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

(2012) M. Jinek et al.   SCIENCE

Targeted mutation of the talpid3 gene in zebrafish reveals its conserved requirement for ciliogenesis and Hedgehog signalling across the vertebrates

(2011) J. Ben et al.   DEVELOPMENT

Genome Engineering With Zinc-Finger Nucleases

(2011) Dana Carroll   GENETICS

Therapeutic implications of mesenchymal stem cells transfected with hepatocyte growth factor transplanted in rat kidney with unilateral ureteral obstruction

(2011) Xin Liu et al.   JOURNAL OF PEDIATRIC SURGERY

Exon skipping and dystrophin restoration in patients with Duchenne muscular dystrophy after systemic phosphorodiamidate morpholino oligomer treatment: an open-label, phase 2, dose-escalation study

(2011) Sebahattin Cirak et al.   LANCET

Genetic engineering of human pluripotent cells using TALE nucleases

(2011) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

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

(2011) Feng Zhang et al.   NATURE BIOTECHNOLOGY

An unbiased genome-wide analysis of zinc-finger nuclease specificity

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

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

(2011) Fuqiang Chen et al.   NATURE METHODS

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

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

(2011) T. Cermak et al.   NUCLEIC ACIDS RESEARCH

The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli

(2011) Rimantas Sapranauskas 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

TAL Effectors: Customizable Proteins for DNA Targeting

(2011) A. J. Bogdanove et al.   SCIENCE

Adenovirus-mediated anti-sense ERK2 gene therapy inhibits tubular epithelial–mesenchymal transition and ameliorates renal allograft fibrosis

(2011) Zhao Ding et al.   TRANSPLANT IMMUNOLOGY

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

Zinc-finger Nuclease-induced Gene Repair With Oligodeoxynucleotides: Wanted and Unwanted Target Locus Modifications

(2010) Sarah Radecke et al.   MOLECULAR THERAPY

Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures

(2010) Yannick Doyon et al.   NATURE METHODS

Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly

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

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM

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

Analysis of AAV Serotypes 1–9 Mediated Gene Expression and Tropism in Mice After Systemic Injection

(2008) Carmela Zincarelli et al.   MOLECULAR THERAPY

Expanding or Restricting the Target Site Repertoire of Zinc-finger Nucleases: The Inter-domain Linker as a Major Determinant of Target Site Selectivity

(2008) Eva-Maria Händel et al.   MOLECULAR THERAPY

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

(2008) Yannick Doyon et al.   NATURE BIOTECHNOLOGY

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE

MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings

(2008) Mitch McVey et al.   TRENDS IN GENETICS

Alternative-NHEJ Is a Mechanistically Distinct Pathway of Mammalian Chromosome Break Repair

(2008) Nicole Bennardo et al.   PLoS Genetics

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

(2007) Tatjana I Cornu et al.   MOLECULAR THERAPY