Current and future prospects for CRISPR-based tools in bacteria

One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces

(2015) He Huang et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase

(2015) Tao Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Coupling the CRISPR/Cas9 System with Lambda Red Recombineering Enables Simplified Chromosomal Gene Replacement in Escherichia coli

(2015) Michael E. Pyne et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System

(2015) Yu Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity

(2015) Poulami Samai et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

The structural biology of CRISPR-Cas systems

(2015) Fuguo Jiang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system

(2015) Yi Wang et al.   JOURNAL OF BIOTECHNOLOGY

Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing

(2015) Yifan Li et al.   METABOLIC ENGINEERING

Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog

(2015) Takuo Osawa et al.   MOLECULAR CELL

CRISPR adaptation biases explain preference for acquisition of foreign DNA

(2015) Asaf Levy et al.   NATURE

Cas9 specifies functional viral targets during CRISPR–Cas adaptation

(2015) Robert Heler et al.   NATURE

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

(2015) Silvana Konermann et al.   NATURE

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

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

Cas9-mediated targeting of viral RNA in eukaryotic cells

(2015) Aryn A. Price et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria

(2015) Ido Yosef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system

(2015) Kabin Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Cas9-guide RNA complex preorganized for target DNA recognition

(2015) F. Jiang et al.   SCIENCE

Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

(2015) D. W. Taylor et al.   SCIENCE

Structural Principles of CRISPR RNA Processing

(2015) Hong Li   STRUCTURE

Harnessing CRISPR–Cas systems for bacterial genome editing

(2015) Kurt Selle et al.   TRENDS IN MICROBIOLOGY

Gene silencing by CRISPR interference in mycobacteria

(2015) Eira Choudhary et al.   Nature Communications

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

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

(2014) Hiroshi Nishimasu et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

Gene regulation by engineered CRISPR-Cas systems

(2014) Peter C Fineran et al.   CURRENT OPINION IN MICROBIOLOGY

Fitting CRISPR-associated Cas3 into the Helicase Family Tree

(2014) Ryan N. Jackson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) inHaloferax volcanii

(2014) Jutta Brendel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

(2014) Raymond H.J. Staals et al.   MOLECULAR CELL

Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus thermophilus

(2014) Gintautas Tamulaitis et al.   MOLECULAR 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-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity

(2014) Rodolphe Barrangou et al.   MOLECULAR CELL

Adapting to new threats: the generation of memory by CRISPR-Cas immune systems

(2014) Robert Heler et al.   MOLECULAR MICROBIOLOGY

Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks

(2014) A. A. Nielsen et al.   Molecular Systems Biology

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

(2014) Yuexin Zhou et al.   NATURE

Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli

(2014) Hongtu Zhao et al.   NATURE

Programmable RNA recognition and cleavage by CRISPR/Cas9

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

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

(2014) Robert J Citorik et al.   NATURE BIOTECHNOLOGY

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard 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

CRISPR transcriptional repression devices and layered circuits in mammalian cells

(2014) Samira Kiani et al.   NATURE METHODS

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity

(2014) James K Nuñez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Efficient programmable gene silencing by Cascade

(2014) Devashish Rath et al.   NUCLEIC ACIDS RESEARCH

CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus

(2014) Ziga Zebec et al.   NUCLEIC ACIDS RESEARCH

An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference

(2014) Wenfang Peng et al.   NUCLEIC ACIDS RESEARCH

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

(2014) Michelle L. Luo et al.   NUCLEIC ACIDS RESEARCH

Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer

(2014) Corinna Richter et al.   NUCLEIC ACIDS RESEARCH

CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri

(2014) Jee-Hwan Oh et al.   NUCLEIC ACIDS RESEARCH

Classification and evolution of type II CRISPR-Cas systems

(2014) Krzysztof Chylinski et al.   NUCLEIC ACIDS RESEARCH

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

Degenerate target sites mediate rapid primed CRISPR adaptation

(2014) P. C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli

(2014) R. N. Jackson et al.   SCIENCE

To acquire or resist: the complex biological effects of CRISPR–Cas systems

(2014) Joseph Bondy-Denomy et al.   TRENDS IN MICROBIOLOGY

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

(2014) A. A. Gomaa et al.   mBio

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system

(2014) Tobias Anton et al.   Nucleus

Exploiting CRISPR/Cas systems for biotechnology

(2013) Timothy R. Sampson et al.   BIOESSAYS

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

(2013) Lei S. Qi et al.   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

Genetic Characterization of Antiplasmid Immunity through a Type III-A CRISPR-Cas System

(2013) A. Hatoum-Aslan et al.   JOURNAL OF BACTERIOLOGY

Structure of an RNA Silencing Complex of the CRISPR-Cas Immune System

(2013) Michael Spilman et al.   MOLECULAR CELL

Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus

(2013) Raymond H.J. Staals et al.   MOLECULAR CELL

Structure of the CRISPR Interference Complex CSM Reveals Key Similarities with Cascade

(2013) Christophe Rouillon et al.   MOLECULAR CELL

A CRISPR/Cas system mediates bacterial innate immune evasion and virulence

(2013) Timothy R. Sampson et al.   NATURE

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

(2013) Hiroko Koike-Yusa et al.   NATURE BIOTECHNOLOGY

Synthetic circuits integrating logic and memory in living cells

(2013) Piro Siuti 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

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

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9

(2013) Jian-Feng Li et al.   NATURE BIOTECHNOLOGY

Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease

(2013) Vladimir Nekrasov et al.   NATURE BIOTECHNOLOGY

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

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

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

(2013) Daniel J Dickinson et al.   NATURE METHODS

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

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

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Heritable genome editing in C. elegans via a CRISPR-Cas9 system

(2013) Ari E Friedland et al.   NATURE METHODS

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

(2013) Matthew H Larson et al.   Nature Protocols

Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases

(2013) O. Niewoehner et al.   NUCLEIC ACIDS RESEARCH

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

(2013) James E. DiCarlo et al.   NUCLEIC ACIDS RESEARCH

Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing inSulfolobus islandicus

(2013) Wenfang Peng et al.   RNA Biology

The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems

(2013) Krzysztof Chylinski et al.   RNA Biology

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Strong bias in the bacterial CRISPR elements that confer immunity to phage

(2013) David Paez-Espino et al.   Nature Communications

Highly Efficient Targeted Mutagenesis of Drosophila with the CRISPR/Cas9 System

(2013) Andrew R. Bassett et al.   Cell Reports

Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands

(2013) Reuben B. Vercoe et al.   PLoS Genetics

Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids

(2013) Wenyan Jiang et al.   PLoS Genetics

Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition

(2013) Edze R. Westra et al.   PLoS Genetics

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs

(2012) Caryn R. Hale et al.   MOLECULAR CELL

CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3

(2012) Edze R. Westra et al.   MOLECULAR CELL

Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System

(2012) Dipali G. Sashital et al.   MOLECULAR CELL

RNA processing enables predictable programming of gene expression

(2012) Lei Qi et al.   NATURE BIOTECHNOLOGY

Membrane protein expression triggers chromosomal locus repositioning in bacteria

(2012) E. A. Libby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Rewritable digital data storage in live cells via engineered control of recombination directionality

(2012) J. Bonnet 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

Microbiota-Targeted Therapies: An Ecological Perspective

(2012) K. P. Lemon et al.   Science Translational Medicine

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

(2012) Ki Hyun Nam et al.   STRUCTURE

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Structures of the RNA-guided surveillance complex from a bacterial immune system

(2011) Blake Wiedenheft et al.   NATURE

Evolution and classification of the CRISPR–Cas systems

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

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

(2011) Matthijs M Jore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus

(2010) Muktak Aklujkar et al.   BMC EVOLUTIONARY BIOLOGY

The Escherichia coli CRISPR System Protects from   Lysogenization, Lysogens, and Prophage Induction

(2010) R. Edgar et al.   JOURNAL OF BACTERIOLOGY

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Self versus non-self discrimination during CRISPR RNA-directed immunity

(2010) Luciano A. Marraffini et al.   NATURE

Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease

(2010) Rachel E. Haurwitz et al.   SCIENCE

Self-targeting by CRISPR: gene regulation or autoimmunity?

(2010) Adi Stern et al.   TRENDS IN GENETICS

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

(2009) Caryn R. Hale et al.   CELL

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

(2009)   MICROBIOLOGY-SGM

Synthetic Gene Networks That Count

(2009) A. E. Friedland et al.   SCIENCE

Microbes in Gastrointestinal Health and Disease

(2008) Andrew S. Neish   GASTROENTEROLOGY

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

(2008) J. Carte et al.   GENES & DEVELOPMENT

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

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

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

(2008) Luciano A. Marraffini et al.   SCIENCE