CRISPR-Cas: biology, mechanisms and relevance

The diversity-generating benefits of a prokaryotic adaptive immune system

(2016) Stineke van Houte et al.   NATURE

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

(2016) Ines Fonfara et al.   NATURE

A bacterial Argonaute with noncanonical guide RNA specificity

(2016) Emine Kaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in therapeutic CRISPR/Cas9 genome editing

(2016) Nataša Savić et al.   Translational Research

Next Generation Prokaryotic Engineering: The CRISPR-Cas Toolkit

(2016) Ioannis Mougiakos et al.   TRENDS IN BIOTECHNOLOGY

CRISPR/Cas9-Derived Mutations Both Inhibit HIV-1 Replication and Accelerate Viral Escape

(2016) Zhen Wang et al.   Cell Reports

The CRISPR-Cas immune system: Biology, mechanisms and applications

(2015) Devashish Rath et al.   BIOCHIMIE

Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System

(2015) Sy Redding et al.   CELL

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

(2015) Poulami Samai et al.   CELL

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

(2015) Sidi Chen et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense

(2015) Edze R. Westra et al.   CURRENT BIOLOGY

Cas9 function and host genome sampling in Type II-A CRISPR–Cas adaptation

(2015) Yunzhou Wei et al.   GENES & DEVELOPMENT

Delivery and Specificity of CRISPR/Cas9 Genome Editing Technologies for Human Gene Therapy

(2015) Jennifer L. Gori et al.   HUMAN GENE THERAPY

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales

(2015) Uri Gophna et al.   ISME Journal

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity

(2015) James K. Nuñez et al.   NATURE

CRISPR adaptation biases explain preference for acquisition of foreign DNA

(2015) Asaf Levy et al.   NATURE

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins

(2015) Joseph Bondy-Denomy et al.   NATURE

Cas9 specifies functional viral targets during CRISPR–Cas adaptation

(2015) Robert Heler et al.   NATURE

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

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

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

(2015) Pratiksha I Thakore et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

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

Foreign DNA acquisition by the I-F CRISPR–Cas system requires all components of the interference machinery

(2015) Daria Vorontsova et al.   NUCLEIC ACIDS RESEARCH

Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus

(2015) Yunzhou Wei et al.   NUCLEIC ACIDS RESEARCH

Different genome stability proteins underpin primed and naïve adaptation inE. coliCRISPR-Cas immunity

(2015) Ivana Ivančić-Baće et al.   NUCLEIC ACIDS RESEARCH

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

Costs of CRISPR-Cas-mediated resistance inStreptococcus thermophilus

(2015) Pedro F. Vale et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition

(2015) Clare Rollie et al.   eLife

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens

(2014) Asma Hatoum-Aslan et al.   CURRENT OPINION IN MICROBIOLOGY

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA

(2014) S. Ramakrishna et al.   GENOME RESEARCH

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

(2014) S. Kim et al.   GENOME RESEARCH

A CRISPR with Roles in Myxococcus xanthus Development and Exopolysaccharide Production

(2014) R. A. Wallace et al.   JOURNAL OF BACTERIOLOGY

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

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

(2014) Gregory W. Goldberg et al.   NATURE

DNA-guided DNA interference by a prokaryotic Argonaute

(2014) Daan C. Swarts et al.   NATURE

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

(2014) Robert J Citorik et al.   NATURE BIOTECHNOLOGY

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype

(2014) Hao Yin et al.   NATURE BIOTECHNOLOGY

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

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

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

Detection and characterization of spacer integration intermediates in type I-E CRISPR–Cas system

(2014) Zihni Arslan 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

Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection

(2014) Lin Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection

(2014) W. Hu 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

A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa

(2014) A. Pawluk et al.   mBio

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

(2014) A. A. Gomaa et al.   mBio

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

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

(2013) Luke A. Gilbert et al.   CELL

Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients

(2013) Gerald Schwank et al.   Cell Stem Cell

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

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

Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

(2013) Yan Zhang et al.   MOLECULAR CELL

Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA

(2013) Ivan Olovnikov et al.   MOLECULAR CELL

A novel interference mechanism by a type IIIB CRISPR-Cmr module inSulfolobus

(2013) Ling Deng et al.   MOLECULAR MICROBIOLOGY

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity

(2013) Kimberley D. Seed et al.   NATURE

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

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

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

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

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

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

(2013) Matthew H Larson et al.   Nature Protocols

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process

(2013) Ming Li et al.   NUCLEIC ACIDS RESEARCH

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

The CRISPR-Associated Gene cas2 of Legionella pneumophila Is Required for Intracellular Infection of Amoebae

(2013) F. F. Gunderson et al.   mBio

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

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

CRISPR Interference Can Prevent Natural Transformation and Virulence Acquisition during In Vivo Bacterial Infection

(2012) David Bikard et al.   Cell Host & Microbe

A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain–Barré syndrome

(2012) R. Louwen et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

How RecBCD Enzyme and Chi Promote DNA Break Repair and Recombination: a Molecular Biologist's View

(2012) G. R. Smith   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity

(2012) Jing Zhang 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

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

TALENs: a widely applicable technology for targeted genome editing

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

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

(2012) Hagen Richter et al.   NUCLEIC ACIDS RESEARCH

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

CRISPR Interference Directs Strand Specific Spacer Acquisition

(2012) Daan C. Swarts et al.   PLoS One

Cascade-mediated binding and bending of negatively supercoiled DNA

(2012) Edze R. Westra et al.   RNA Biology

Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

(2012) E. L. Garside et al.   RNA

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

(2012) M. Jinek et al.   SCIENCE

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

Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information

(2012) Peter C. Fineran et al.   VIROLOGY

Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

(2012) A. D. Weinberger et al.   mBio

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

(2012) Kirill A. Datsenko et al.   Nature Communications

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars ofSalmonella entericasubsp.enterica

(2011) Fenyun Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

(2011) Fenyun Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2011) Elitza Deltcheva et al.   NATURE

Evolution and classification of the CRISPR–Cas systems

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

An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3

(2011) Dipali G Sashital et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2011) Rimantas Sapranauskas et al.   NUCLEIC ACIDS RESEARCH

Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site

(2011) A. Hatoum-Aslan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage

(2011) Ruiying Wang et al.   STRUCTURE

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair

(2010) Mohan Babu et al.   MOLECULAR MICROBIOLOGY

Identification and characterization ofE. coliCRISPR-caspromoters and their silencing by H-NS

(2010) Ümit Pul et al.   MOLECULAR MICROBIOLOGY

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

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

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

Multidrug-Resistant Enterococci Lack CRISPR-cas

(2010) K. L. Palmer et al.   mBio

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

The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair

(2009) Peter C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense

(2009) Blake Wiedenheft et al.   STRUCTURE

Novel macroarray-based method of Corynebacterium diphtheriae genotyping: evaluation in a field study in Belarus

(2008) I. Mokrousov et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

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

A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats

(2008) Natalia Beloglazova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats

(2008) Yujun Cui et al.   PLoS One

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