The CRISPR system: small RNA-guided defense in bacteria and archaea.

[1]  S. Kuramitsu,et al.  Transcription profile of Thermus thermophilus CRISPR systems after phage infection. , 2010, Journal of molecular biology.

[2]  B. Graveley,et al.  RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex , 2009, Cell.

[3]  K. Asai,et al.  A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila , 2009, Nature.

[4]  Stan J. J. Brouns,et al.  CRISPR-based adaptive and heritable immunity in prokaryotes. , 2009, Trends in biochemical sciences.

[5]  G. Krauss,et al.  SSO1450 – A CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA , 2009, FEBS letters.

[6]  K. Zhou,et al.  Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. , 2009, Structure.

[7]  Jan R. van der Ploeg,et al.  Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages. , 2009 .

[8]  F. Rohwer,et al.  Viruses manipulate the marine environment , 2009, Nature.

[9]  Julius Brennecke,et al.  Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary , 2009, Cell.

[10]  S. Yokoyama,et al.  X‐ray crystal structure of a CRISPR‐associated RAMP superfamily protein, Cmr5, from Thermus thermophilus HB8 , 2009, Proteins.

[11]  Shiraz A. Shah,et al.  CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties , 2009, Molecular microbiology.

[12]  G. Krauss,et al.  Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2 , 2009, FEBS letters.

[13]  Shiraz A. Shah,et al.  Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. , 2009, Biochemical Society transactions.

[14]  W. Nelson,et al.  Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes , 2009, PloS one.

[15]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[16]  R. Terns,et al.  Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. , 2008, Genes & development.

[17]  R. Terns,et al.  Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. , 2008, RNA.

[18]  S. Yokoyama,et al.  X‐ray crystal structure of a CRISPR‐associated protein, Cse2, from Thermus thermophilus HB8 , 2008, Proteins.

[19]  G. O’Toole,et al.  Interaction between Bacteriophage DMS3 and Host CRISPR Region Inhibits Group Behaviors of Pseudomonas aeruginosa , 2008, Journal of bacteriology.

[20]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[21]  E. Koonin,et al.  A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats* , 2008, Journal of Biological Chemistry.

[22]  Anders F. Andersson,et al.  Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities , 2008, Science.

[23]  Ibtissem Grissa,et al.  CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats , 2008, Nucleic Acids Res..

[24]  Philippe Horvath,et al.  Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus , 2007, Journal of bacteriology.

[25]  Philippe Horvath,et al.  Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus , 2007, Journal of bacteriology.

[26]  M. Fenner,et al.  CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. , 2007 .

[27]  G. Hannon,et al.  The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race , 2007, Science.

[28]  J. Banfield,et al.  Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. , 2007, Environmental microbiology.

[29]  Ibtissem Grissa,et al.  The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats , 2007, BMC Bioinformatics.

[30]  V. Kunin,et al.  Evolutionary conservation of sequence and secondary structures in CRISPR repeats , 2007, Genome Biology.

[31]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[32]  A. Garza,et al.  Regulation of dev, an Operon That Includes Genes Essential for Myxococcus xanthus Development and CRISPR-Associated Genes and Repeats , 2007, Journal of bacteriology.

[33]  R. Garrett,et al.  A putative viral defence mechanism in archaeal cells. , 2006, Archaea.

[34]  Julian Parkhill,et al.  The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome , 2006, Nature Genetics.

[35]  I. Tanaka,et al.  Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif‐like domain , 2006, Protein science : a publication of the Protein Society.

[36]  J. S. Godde,et al.  The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes , 2006, Journal of Molecular Evolution.

[37]  Karen E. Nelson,et al.  Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences , 2006, Journal of bacteriology.

[38]  N. Grishin,et al.  A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action , 2006, Biology Direct.

[39]  Daniel H. Haft,et al.  A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes , 2005, PLoS Comput. Biol..

[40]  S. Henikoff,et al.  Epigenetic inheritance in Arabidopsis: selective silence. , 2005, Current opinion in genetics & development.

[41]  E. Bidnenko,et al.  Phage abortive infection in lactococci: variations on a theme. , 2005, Current opinion in microbiology.

[42]  Forest Rohwer,et al.  Here a virus, there a virus, everywhere the same virus? , 2005, Trends in microbiology.

[43]  J. García-Martínez,et al.  Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements , 2005, Journal of Molecular Evolution.

[44]  R. Garrett,et al.  Identification of novel non‐coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus , 2004, Molecular microbiology.

[45]  P. Le Flèche,et al.  High Genetic Diversity Revealed by Variable-Number Tandem Repeat Genotyping and Analysis of hsp65 Gene Polymorphism in a Large Collection of “Mycobacterium canettii” Strains Indicates that the M. tuberculosis Complex Is a Recently Emerged Clone of “M. canettii” , 2004, Journal of Clinical Microbiology.

[46]  H. Brüssow,et al.  Phage-Host Interaction: an Ecological Perspective , 2004, Journal of bacteriology.

[47]  M. Gorovsky,et al.  Small RNAs in genome rearrangement in Tetrahymena. , 2004, Current opinion in genetics & development.

[48]  Ronald H. A. Plasterk,et al.  Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi , 2003, Nature.

[49]  A. Sonenshein,et al.  Efficient sporulation in Clostridium difficile requires disruption of the σK gene , 2003, Molecular microbiology.

[50]  R. Garrett,et al.  Genus-Specific Protein Binding to the Large Clusters of DNA Repeats (Short Regularly Spaced Repeats) Present in Sulfolobus Genomes , 2003, Journal of bacteriology.

[51]  A. Hüttenhofer,et al.  Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Nick V Grishin,et al.  A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. , 2002, Nucleic acids research.

[53]  Mark A. Ragan,et al.  The complete genome of the crenarchaeon Sulfolobus solfataricus P2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Michael Y. Galperin,et al.  Who's your neighbor? New computational approaches for functional genomics , 2000, Nature Biotechnology.

[55]  F. J. Mojica,et al.  Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria , 2000, Molecular microbiology.

[56]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[57]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[58]  J. Musser,et al.  Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. , 1999, Emerging infectious diseases.

[59]  R. Garrett,et al.  Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon , 1998, Extremophiles.

[60]  N. Morrison,et al.  IS6110 Transposition and Evolutionary Scenario of the Direct Repeat Locus in a Group of Closely Related Mycobacterium tuberculosis Strains , 1998, Journal of bacteriology.

[61]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[62]  G. Church,et al.  Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics , 1997, Journal of bacteriology.

[63]  D van Soolingen,et al.  Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology , 1997, Journal of clinical microbiology.

[64]  R. Fleischmann,et al.  Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii , 1996, Science.

[65]  B. Masepohl,et al.  Long tandemly repeated repetitive (LTRR) sequences in the filamentous cyanobacterium Anabaena sp. PCC 7120. , 1996, Biochimica et biophysica acta.

[66]  F. Rodríguez-Valera,et al.  Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning , 1995, Molecular microbiology.

[67]  P. Groenen,et al.  Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method , 1993, Molecular microbiology.

[68]  T. Bickle,et al.  Biology of DNA restriction. , 1993, Microbiological reviews.

[69]  Eugene V. Koonin,et al.  Helicases: amino acid sequence comparisons and structure-function relationships , 1993 .

[70]  D van Soolingen,et al.  Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains , 1991, Infection and immunity.

[71]  J. Mandel,et al.  Instability of a 550-base pair DNA segment and abnormal methylation in fragile X syndrome , 1991, Science.

[72]  K. Makino,et al.  Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome , 1989, Journal of bacteriology.

[73]  K. Makino,et al.  Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product , 1987, Journal of bacteriology.

[74]  J. García-Martínez,et al.  Short motif sequences determine the targets of the prokaryotic CRISPR defence system. , 2009, Microbiology.

[75]  Graham F Hatfull,et al.  Bacteriophage genomics. , 2008, Current opinion in microbiology.

[76]  S. Yokoyama,et al.  associated protein, Cse2, from Thermus thermophilus HB8 , 2008 .

[77]  S. Ehrlich,et al.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. , 2005, Microbiology.

[78]  G Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[79]  R. Edwards,et al.  Viral metagenomics , 2005, Nature Reviews Microbiology.

[80]  G. Fitzgerald,et al.  Bacteriophage defence systems in lactic acid bacteria , 2004, Antonie van Leeuwenhoek.

[81]  L. Schouls,et al.  Identification of a novel family of sequence repeats among prokaryotes. , 2002, Omics : a journal of integrative biology.

[82]  Y. Kawarabayasi,et al.  Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.

[83]  C. Sensen,et al.  Completing the sequence of the Sulfolobus solfataricus P2 genome , 1998, Extremophiles.

[84]  F. Robb,et al.  Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.