Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies

GuideScan software for improved single and paired CRISPR guide RNA design

(2017) Alexendar R Perez et al.   NATURE BIOTECHNOLOGY

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

RPA binds histone H3-H4 and functions in DNA replication–coupled nucleosome assembly

(2017) Shaofeng Liu et al.   SCIENCE

Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9

(2017) Peiwu Qin et al.   Nature Communications

Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting

(2017) Fuqiang Chen et al.   Nature Communications

Imaging Specific Genomic DNA in Living Cells

(2016) Baohui Chen et al.   Annual Review of Biophysics

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

(2016) Jigar N. Bandaria et al.   CELL

Live Cell Imaging Reveals the Dynamics of Telomerase Recruitment to Telomeres

(2016) Jens C. Schmidt et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering

(2016) Addison V. Wright et al.   CELL

CRISPR-Cas9 nuclear dynamics and target recognition in living cells

(2016) Hanhui Ma et al.   JOURNAL OF CELL BIOLOGY

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

(2016) Josh Tycko et al.   MOLECULAR CELL

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow

(2016) Hanhui Ma et al.   NATURE BIOTECHNOLOGY

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

(2016) Christopher D Richardson 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

Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system

(2016) Shipeng Shao et al.   NUCLEIC ACIDS RESEARCH

Expanding the CRISPR imaging toolset withStaphylococcus aureusCas9 for simultaneous imaging of multiple genomic loci

(2016) Baohui Chen et al.   NUCLEIC ACIDS RESEARCH

CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci

(2016) Yi Fu 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

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

(2016) Iman Farasat et al.   PLoS Computational Biology

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

(2016) R Stefan Isaac et al.   eLife

Cas9 Functionally Opens Chromatin

(2016) Amira A. Barkal et al.   PLoS One

An RNA-aptamer-based two-color CRISPR labeling system

(2016) Siyuan Wang et al.   Scientific Reports

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

(2015) Lauren R. Polstein et al.   GENOME RESEARCH

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Conformational control of DNA target cleavage by CRISPR–Cas9

(2015) Samuel H. Sternberg et al.   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

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

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

(2015) Daesik Kim et al.   NATURE METHODS

Landscape and mechanisms of transcription factor cooperativity

(2015) Joana Osório   NATURE REVIEWS GENETICS

A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture

(2015) Henriette O'Geen et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

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

CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

(2015) Wulan Deng 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

Dynamics of CRISPR-Cas9 genome interrogation in living cells

(2015) Spencer C. Knight et al.   SCIENCE

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

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

(2014) Luke A. Gilbert et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech 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

CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants

(2014) Yang Lei et al.   Molecular Plant

Programmable RNA recognition and cleavage by CRISPR/Cas9

(2014) Mitchell R. O’Connell et al.   NATURE

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu 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

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench 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

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

CRISPR-based technologies: prokaryotic defense weapons repurposed

(2014) Rebecca M. Terns et al.   TRENDS IN GENETICS

Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system

(2014) Tetsushi Sakuma et al.   Scientific Reports

Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing

(2013) Ning Sun et al.   BIOTECHNOLOGY AND BIOENGINEERING

The Cell Biology of Genomes: Bringing the Double Helix to Life

(2013) Tom Misteli   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

DNA repair mechanisms in dividing and non-dividing cells

(2013) Teruaki Iyama et al.   DNA REPAIR

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

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

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Live visualization of chromatin dynamics with fluorescent TALEs

(2013) Yusuke Miyanari et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Targeting and tracing of specific DNA sequences with dTALEs in living cells

(2013) Katharina Thanisch et al.   NUCLEIC ACIDS RESEARCH

Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors

(2013) H. Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial Dynamics of Chromosome Translocations in Living Cells

(2013) V. Roukos et al.   SCIENCE

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

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

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

(2012) M. Jinek et al.   SCIENCE

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

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

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

(2011) Vikram Pattanayak et al.   NATURE METHODS

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

(2011) W. Wang et al.   SCIENCE

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

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

HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis

(2008) Georgyi V. Los et al.   ACS Chemical Biology

Histone Modifications and Nuclear Architecture: A Review

(2008) Eva Bártová et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY