CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off‐Target Evaluation, and Strategies to Mitigate Off‐Target Effects

Genome-wide profiling of adenine base editor specificity by EndoV-seq

(2019) Puping Liang et al.   Nature Communications

Gene Editing in Plants– Progress and Challenges

(2019) Yanfei Mao et al.   National Science Review

Optimizing genome editing strategy by primer-extension-mediated sequencing

(2019) Jianhang Yin et al.   Cell Discovery

Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics

(2019) Clarisse G. Ricci et al.   ACS Central Science

DNA stretching induces Cas9 off-target activity

(2019) Matthew D. Newton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide target specificity of CRISPR RNA-guided adenine base editors

(2019) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG

(2019) Zhaohui Zhong et al.   Molecular Plant

Avoiding the off-target effects of CRISPR/cas9 system is still a challenging accomplishment for genetic transformation

(2019) Roberto H. Herai   GENE

In vivo ways to unveil off-targets

(2019) Guigen Zhang et al.   CELL RESEARCH

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

CRISPR Cpf1 proteins: structure, function and implications for genome editing

(2019) Fatemeh Safari et al.   Cell and Bioscience

Analysis and minimization of cellular RNA editing by DNA adenine base editors

(2019) Holly A. Rees et al.   Science Advances

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

(2019) Changyang Zhou et al.   NATURE

CRISPR DNA base editors with reduced RNA off-target and self-editing activities

(2019) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

CRISPR base editors: genome editing without double-stranded breaks

(2018) Ayman Eid et al.   BIOCHEMICAL JOURNAL

OUP accepted manuscript

(2018)   BIOINFORMATICS

Molecular Mechanisms of RNA Targeting by Cas13-containing Type VI CRISPR–Cas Systems

(2018) Mitchell R. O'Connell   JOURNAL OF MOLECULAR BIOLOGY

Base editing with a Cpf1–cytidine deaminase fusion

(2018) Xiaosa Li et al.   NATURE BIOTECHNOLOGY

A highly specific SpCas9 variant is identified by in vivo screening in yeast

(2018) Antonio Casini et al.   NATURE BIOTECHNOLOGY

CRISPR off-target analysis in genetically engineered rats and mice

(2018) Keith R. Anderson et al.   NATURE METHODS

Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis

(2018) Digvijay Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

(2018) Jean-Paul Concordet et al.   NUCLEIC ACIDS RESEARCH

Gene Editing on Center Stage

(2018) Rasmus O. Bak et al.   TRENDS IN GENETICS

In vivo base editing of post-mitotic sensory cells

(2018) Wei-Hsi Yeh et al.   Nature Communications

Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis

(2018) Digvijay Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

(2018) Yonggang Zhang et al.   BMC Medical Genomics

In vivo CRISPR editing with no detectable genome-wide off-target mutations

(2018) Pinar Akcakaya et al.   NATURE

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo

(2018) Robert M. Yarrington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

Directed evolution of CRISPR-Cas9 to increase its specificity

(2018) Jungjoon K. Lee et al.   Nature Communications

The Enhancement of Plant Disease Resistance Using CRISPR/Cas9 Technology

(2018) Virginia M. G. Borrelli et al.   Frontiers in Plant Science

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants

(2018) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR-PLANT v2: an online resource for highly specific guide RNA spacers based on improved off-target analysis

(2018) Bastian Minkenberg et al.   PLANT BIOTECHNOLOGY JOURNAL

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

(2018) Eirini M. Kallimasioti-Pazi et al.   PLOS BIOLOGY

Genome surgery using Cas9 ribonucleoproteins for the treatment of age-related macular degeneration

(2017) Kyoungmi Kim et al.   GENOME RESEARCH

APOBEC: From mutator to editor

(2017) Bei Yang et al.   Journal of Genetics and Genomics

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

(2017) Gaelen T. Hess et al.   MOLECULAR CELL

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

CRISPR-GE: A Convenient Software Toolkit for CRISPR-Based Genome Editing

(2017) Xianrong Xie et al.   Molecular Plant

Enhanced proofreading governs CRISPR–Cas9 targeting accuracy

(2017) Janice S. Chen et al.   NATURE

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

(2017) Nicole M. Gaudelli et al.   NATURE

Refining strategies to translate genome editing to the clinic

(2017) Tatjana I Cornu et al.   NATURE MEDICINE

Unexpected mutations after CRISPR–Cas9 editing in vivo

(2017) Kellie A Schaefer et al.   NATURE METHODS

Mapping the genomic landscape of CRISPR–Cas9 cleavage

(2017) Peter Cameron et al.   NATURE METHODS

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets

(2017) Shengdar Q Tsai et al.   NATURE METHODS

Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci

(2017) Samuel Lessard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

(2017) Evan A. Boyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease

(2017) Fernando Orden Rueda et al.   Nature Communications

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

(2017) Holly A. Rees et al.   Nature Communications

Plant genome editing with TALEN and CRISPR

(2017) Aimee Malzahn et al.   Cell and Bioscience

Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion

(2017) Vladimir Nekrasov et al.   Scientific Reports

Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors

(2016) Piyush K. Jain et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

(2016) Daesik Kim et al.   GENOME RESEARCH

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

Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins

(2016) Junho K Hur et al.   NATURE BIOTECHNOLOGY

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

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

(2016) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

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

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

Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes

(2016) Juan C. Oliveros et al.   NUCLEIC ACIDS RESEARCH

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease

(2016) Youngbin Lim et al.   Nature Communications

Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes

(2016) C. D. Richardson et al.   Nature Communications

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9

(2016) Digvijay Singh et al.   Nature Communications

CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

(2016) Houxiang Zhu et al.   Scientific Reports

Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants

(2016) Yuriko Osakabe et al.   Scientific Reports

The CRISPR/Cas9 system for plant genome editing and beyond

(2015) Luisa Bortesi et al.   BIOTECHNOLOGY ADVANCES

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

(2015) Bernd Zetsche et al.   CELL

Genetic screens and functional genomics using CRISPR/Cas9 technology

(2015) Ella Hartenian et al.   FEBS Journal

Minimizing off-Target Mutagenesis Risks Caused by Programmable Nucleases

(2015) Kentaro Ishida et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Standards needed for gene-editing errors

(2015) J. Keith Joung   NATURE

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

(2015) Silvana Konermann et al.   NATURE

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

(2015) Xiaoling Wang et al.   NATURE BIOTECHNOLOGY

Inducible in vivo genome editing with CRISPR-Cas9

(2015) Lukas E Dow et al.   NATURE BIOTECHNOLOGY

Small molecule–triggered Cas9 protein with improved genome-editing specificity

(2015) Kevin M Davis et al.   Nature Chemical Biology

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

(2015) Daesik Kim et al.   NATURE METHODS

Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennialPopulusreveals 4-coumarate:CoA ligase specificity and redundancy

(2015) Xiaohong Zhou et al.   NEW PHYTOLOGIST

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

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

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

Rationally engineered Cas9 nucleases with improved specificity

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

A pre-screening FISH-based method to detect CRISPR/Cas9 off-targets in mouse embryonic stem cells

(2015) Marianna Paulis et al.   Scientific Reports

Off-target Effects in CRISPR/Cas9-mediated Genome Engineering

(2015) Xiao-Hui Zhang et al.   Molecular Therapy-Nucleic Acids

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

(2015) Manuel Stemmer et al.   PLoS One

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

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

(2014) Rasika Mundade et al.   CELL CYCLE

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

(2014) Adrian Veres et al.   Cell Stem Cell

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

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

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

(2014) Cem Kuscu 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

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

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity

(2014) John P Guilinger et al.   NATURE METHODS

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences

(2014) Y. Lin et al.   NUCLEIC ACIDS RESEARCH

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Hui Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

(2014) Mark D. Szczelkun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish

(2013) A. Hruscha et al.   DEVELOPMENT

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

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

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

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

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang 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

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

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

(2013) Nicola Crosetto et al.   NATURE METHODS

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

(2013) Thomas J. Cradick 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 Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Dissecting endonuclease and exonuclease activities in endonuclease V from Thermotoga maritima

(2010) R. Mi et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY