Priming in a permissive type I-C CRISPR–Cas system reveals distinct dynamics of spacer acquisition and loss

The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer

(2017) Ming Li et al.   NUCLEIC ACIDS RESEARCH

Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity

(2017) MaryClare F. Rollins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spacer capture and integration by a type I-F Cas1–Cas2-3 CRISPR adaptation complex

(2017) Robert D. Fagerlund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas: Adapting to change

(2017) Simon A. Jackson et al.   SCIENCE

Cas3 is a limiting factor for CRISPR-Cas immunity in Escherichia coli cells lacking H-NS

(2016) Kristina Majsec et al.   BMC MICROBIOLOGY

Active and adaptiveLegionellaCRISPR-Cas reveals a recurrent challenge to the pathogen

(2016) Chitong Rao et al.   CELLULAR MICROBIOLOGY

Conformational Control of Cascade Interference and Priming Activities in CRISPR Immunity

(2016) Chaoyou Xue et al.   MOLECULAR CELL

Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems

(2016) Adrian G. Patterson et al.   MOLECULAR CELL

Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems

(2016) Ryan T. Leenay et al.   MOLECULAR CELL

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

(2016) Tim Künne et al.   MOLECULAR CELL

Highly efficient primed spacer acquisition from targets destroyed by theEscherichia colitype I-E CRISPR-Cas interfering complex

(2016) Ekaterina Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quorum sensing controls thePseudomonas aeruginosaCRISPR-Cas adaptive immune system

(2016) Nina M. Høyland-Kroghsbo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system

(2016) Raymond H. J. Staals et al.   Nature Communications

An Active Type I-E CRISPR-Cas System Identified in Streptomyces avermitilis

(2016) Yi Qiu et al.   PLoS One

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

(2015) Sy Redding et al.   CELL

Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems

(2015) Jiuyu Wang 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

Two Distinct DNA Binding Modes Guide Dual Roles of a CRISPR-Cas Protein Complex

(2015) Timothy R. Blosser et al.   MOLECULAR CELL

Foreign DNA capture 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

An updated evolutionary classification of CRISPR–Cas systems

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

CRISPR interference and priming varies with individual spacer sequences

(2015) Chaoyou Xue et al.   NUCLEIC ACIDS RESEARCH

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Robert Heler et al.   MOLECULAR MICROBIOLOGY

Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation

(2014) Yanwu Huo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation

(2014) M. Li 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

Pervasive generation of oppositely oriented spacers during CRISPR adaptation

(2014) Sergey Shmakov et al.   NUCLEIC ACIDS RESEARCH

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference

(2014) M. L. Hochstrasser 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

Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages

(2014) Alexander P. Hynes et al.   Nature Communications

In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus

(2013) Tomas Sinkunas et al.   EMBO JOURNAL

In VitroReconstitution of anEscherichia coliRNA-guided Immune System Reveals Unidirectional, ATP-dependent Degradation of DNA Target

(2013) Sabin Mulepati et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Phylogenetic Reconstruction of the Legionella pneumophila Philadelphia-1 Laboratory Strains through Comparative Genomics

(2013) Chitong Rao et al.   PLoS One

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

(2013) I. Yosef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput analysis of type I-E CRISPR/Cas spacer acquisition inE. coli

(2013) Ekaterina Savitskaya et al.   RNA Biology

CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants ofEscherichia coli

(2013) César Díez-Villaseñor et al.   RNA Biology

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

(2013) Wenyan Jiang et al.   PLoS Genetics

The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity

(2012) Edze R. Westra et al.   Annual Review of Genetics

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

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

The CRISPR/Cas Adaptive Immune System of Pseudomonas aeruginosa Mediates Resistance to Naturally Occurring and Engineered Phages

(2012) K. C. Cady et al.   JOURNAL OF BACTERIOLOGY

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

Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms

(2012) Susanne Erdmann et al.   MOLECULAR MICROBIOLOGY

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

In Vivo Protein Interactions and Complex Formation in the Pectobacterium atrosepticum Subtype I-F CRISPR/Cas System

(2012) Corinna Richter et al.   PLoS One

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

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

Experimental Evolution of Legionella pneumophila in Mouse Macrophages Leads to Strains with Altered Determinants of Environmental Survival

(2012) Alexander W. Ensminger et al.   PLoS Pathogens

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

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

RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

(2011) B. Wiedenheft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009)   MICROBIOLOGY-SGM

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