CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back

(2017) Eugene V. Koonin et al.   Genome Biology and Evolution

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit

(2017) Karthik Murugan et al.   MOLECULAR CELL

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

(2017) Aaron A. Smargon et al.   MOLECULAR CELL

RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes

(2017) Alexandra East-Seletsky et al.   MOLECULAR CELL

Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers

(2017) Ole Niewoehner et al.   NATURE

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

Information theory, evolutionary innovations and evolvability

(2017) Andreas Wagner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNA editing with CRISPR-Cas13

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

CRISPR-Cas: Adapting to change

(2017) Simon A. Jackson et al.   SCIENCE

A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems

(2017) Migle Kazlauskiene et al.   SCIENCE

Nucleic acid detection with CRISPR-Cas13a/C2c2

(2017) Jonathan S. Gootenberg et al.   SCIENCE

Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance

(2017) Sarah E. Allen et al.   TRENDS IN GENETICS

Hypothesis: RNA and DNA Viral Sequence Integration into the Mammalian Host Genome Supports Long-Term B Cell and T Cell Adaptive Immunity

(2017) Julia L. Hurwitz et al.   VIRAL IMMUNOLOGY

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

A decade of discovery: CRISPR functions and applications

(2017) Rodolphe Barrangou et al.   Nature Microbiology

Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices

(2016) Eugene V. Koonin et al.   BIOESSAYS

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms

(2016) Eugene V. Koonin et al.   Biology Direct

Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity

(2016) Wenyan Jiang et al.   CELL

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

(2016) Addison V. Wright et al.   CELL

Dual nuclease activity of a Cas2 protein in CRISPR-Cas subtype I-B ofLeptospira interrogans

(2016) Bhuvan Dixit et al.   FEBS LETTERS

Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR–Cas system

(2016) Joshua R. Elmore et al.   GENES & DEVELOPMENT

Inevitability of Genetic Parasites

(2016) Jaime Iranzo et al.   Genome Biology and Evolution

An Epigenetic Perspective on the Midwife Toad Experiments of Paul Kammerer (1880-1926)

(2016) Alexander O. Vargas et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Evolutionary Ecology of Prokaryotic Immune Mechanisms

(2016) Stineke van Houte et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems

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

Host diversity limits the evolution of parasite local adaptation

(2016) Daniel Morley et al.   MOLECULAR ECOLOGY

Virology: A parasite's parasite saves host's neighbours

(2016) Eugene V. Koonin et al.   NATURE

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

Host genome integration and giant virus-induced reactivation of the virophage mavirus

(2016) Matthias G. Fischer et al.   NATURE

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection

(2016) Alexandra East-Seletsky et al.   NATURE

CRISPR–Cas adaptation: insights into the mechanism of action

(2016) Gil Amitai et al.   NATURE REVIEWS MICROBIOLOGY

The meaning of biological information

(2016) Eugene V. Koonin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6

(2016) Ole Niewoehner et al.   RNA

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

(2016) Prarthana Mohanraju et al.   SCIENCE

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

(2016) Omar O. Abudayyeh et al.   SCIENCE

Dual nucleotide specificity determinants of an infection aborting anticodon nuclease

(2016) Ekaterina Krutkina et al.   VIROLOGY

PIWI-Interacting RNA: Its Biogenesis and Functions

(2015) Yuka W. Iwasaki et al.   Annual Review of Biochemistry

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

(2015) Vladimir V Kapitonov et al.   Biology Direct

Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems

(2015) Jaime Iranzo et al.   BMC EVOLUTIONARY BIOLOGY

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

RecBCD is required to complete chromosomal replication: Implications for double-strand break frequencies and repair mechanisms

(2015) Justin Courcelle et al.   DNA REPAIR

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

(2015) Yunzhou Wei et al.   GENES & DEVELOPMENT

Of germ-plasm and zymoplasm: August Weismann, Carlo Emery and the debate about the transmission of acquired characteristics

(2015) Ariane Dröscher   HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus–host coevolution

(2015) Eugene V. Koonin et al.   Molecular BioSystems

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

Cas9 specifies functional viral targets during CRISPR–Cas adaptation

(2015) Robert Heler 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

The CRISPR-associated Csx1 protein ofPyrococcus furiosusis an adenosine-specific endoribonuclease

(2015) Nolan F. Sheppard et al.   RNA

Lamarckian Illusions

(2015) Adam Weiss   TRENDS IN ECOLOGY & EVOLUTION

Origins and evolution of viruses of eukaryotes: The ultimate modularity

(2015) Eugene V. Koonin et al.   VIROLOGY

Mutation—The Engine of Evolution: Studying Mutation and Its Role in the Evolution of Bacteria: Figure 1.

(2015) Ruth Hershberg   Cold Spring Harbor Perspectives in Biology

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution

(2015) M. Senthil Kumar et al.   PLoS Computational Biology

The basic building blocks and evolution of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Structural and functional characterization of Streptococcus pyogenes Cas2 protein under different pH conditions

(2014) Donghyun Ka et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Do all creatures possess an acquired immune system of some sort?

(2014) Jacob Rimer et al.   BIOESSAYS

Nuclease Activity of Legionella pneumophila Cas2 Promotes Intracellular Infection of Amoebal Host Cells

(2014) Felizza F. Gunderson et al.   INFECTION AND IMMUNITY

First Experimental Evidence for the Presence of a CRISPR Toxin in Sulfolobus

(2014) Fei He et al.   JOURNAL OF MOLECULAR BIOLOGY

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

(2014) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Evolution of adaptive immunity from transposable elements combined with innate immune systems

(2014) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

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

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

Type II restriction endonucleases—a historical perspective and more

(2014) Alfred Pingoud et al.   NUCLEIC ACIDS RESEARCH

DNA Binding Properties of the Small Cascade Subunit Csa5

(2014) Michael Daume et al.   PLoS One

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

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

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

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems

(2014) Kira S. Makarova et al.   Frontiers in Genetics

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

(2013) Rotem Sorek et al.   Annual Review of Biochemistry

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

(2013) Vivek Anantharaman et al.   Biology Direct

Lamarck, Evolution, and the Inheritance of Acquired Characters

(2013) Richard W. Burkhardt   GENETICS

Inter-viral conflicts that exploit host CRISPR immune systems ofSulfolobus

(2013) Susanne Erdmann et al.   MOLECULAR MICROBIOLOGY

A DNA break inducer activates the anticodon nuclease RloC and the adaptive immunity in Acinetobacter baylyi ADP1

(2013) Daniel Klaiman et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas

(2013) Eugene V. Koonin et al.   RNA Biology

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

(2013) Ekaterina Savitskaya et al.   RNA Biology

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

(2013) Krzysztof Chylinski et al.   RNA Biology

A virocentric perspective on the evolution of life

(2013) Eugene V Koonin et al.   Current Opinion in Virology

The major role of viruses in cellular evolution: facts and hypotheses

(2013) Patrick Forterre et al.   Current Opinion in Virology

Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision

(2013) Nobuto Takeuchi et al.   G3-Genes Genomes 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

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

CRISPR-Cas: To Take Up DNA or Not—That Is the Question

(2012) Ariel D. Weinberger et al.   Cell Host & Microbe

Double-stranded Endonuclease Activity inBacillus haloduransClustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas2 Protein

(2012) Ki Hyun Nam et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

New-found fundamentals of bacterial persistence

(2012) Cyrielle I. Kint et al.   TRENDS IN MICROBIOLOGY

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

RNA-Mediated Epigenetic Programming of Genome Rearrangements

(2011) Mariusz Nowacki et al.   Annual Review of Genomics and Human Genetics

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

(2011) Kira S Makarova et al.   Biology Direct

Trained Immunity: A Memory for Innate Host Defense

(2011) Mihai G. Netea et al.   Cell Host & Microbe

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

(2011) N. Takeuchi et al.   JOURNAL OF BACTERIOLOGY

Evolution and classification of the CRISPR–Cas systems

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

Phage T4-induced dTTP accretion bolsters a tRNase-based host defense

(2011) Daniel Klaiman et al.   VIROLOGY

Persister Cells

(2010) Kim Lewis   Annual Review of Microbiology

Toxin–antitoxin systems: why so many, what for?

(2010) Laurence Van Melderen   CURRENT OPINION IN MICROBIOLOGY

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

(2010) Mohan Babu et al.   MOLECULAR MICROBIOLOGY

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

(2010) Luciano A. Marraffini et al.   NATURE

Self-targeting by CRISPR: gene regulation or autoimmunity?

(2010) Adi Stern et al.   TRENDS IN GENETICS

The Great Billion-year War between Ribosome- and Capsid-encoding Organisms (Cells and Viruses) as the Major Source of Evolutionary Novelties

(2009) Patrick Forterre et al.   Annals of the New York Academy of Sciences

Is evolution Darwinian or/and Lamarckian?

(2009) Eugene V Koonin et al.   Biology Direct

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

(2009)   MICROBIOLOGY-SGM

Horizontal gene transfer and the earliest stages of the evolution of life

(2009) Anthony M. Poole   RESEARCH IN MICROBIOLOGY

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

(2009) Laurence Van Melderen et al.   PLoS Genetics

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

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

(2008) Luciano A. Marraffini et al.   SCIENCE