Cited by 2,331

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Evolution and classification of the CRISPR–Cas systems

Makarova, Kira S., Haft, Daniel H., Barrangou, Rodolphe, Brouns, Stan J. J., Charpentier, Emmanuelle, Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Wolf, Yuri I., Yakunin, Alexander F., van der Oost, John, Koonin, Eugene V.·2011·Nature Reviews Microbiology

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nrmicro2577

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Type II CRISPR systems require only one protein, Cas9, to scan, bind and cleave the target DNA sequence.

    “Type II CRISPR systems require only one protein, Cas9, to scan, bind and cleave the target DNA sequence (Makarova et al., 2011).”

    From Delivering CRISPR: a review of the challenges and approaches (2018) · cites this paper as Makarova et al., 2011

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 48

  1. Deveau, H., Garneau, J. E. & Moineau, S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu. Rev. Microbiol. 64, 475–493 (2010). · DOI
  2. Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167–170 (2010). · DOI
  3. Karginov, F. V. & Hannon, G. J. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol. Cell 37, 7–19 (2010). · DOI
  4. Koonin, E. V. & Makarova, K. S. CRISPR-Cas: an adaptive immunity system in prokaryotes. F1000 Biol. Rep. 1, 95 (2009). · DOI
  5. Sorek, R., Kunin, V. & Hugenholtz, P. CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Rev. Microbiol. 6, 181–186 (2008). · DOI
  6. van der Oost, J., Jore, M. M., Westra, E. R., Lundgren, M. & Brouns, S. J. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. 34, 401–407 (2009). · DOI
  7. Mojica, F. J., Diez-Villasenor, C., Soria, E. & Juez, G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 36, 244–246 (2000). · DOI
  8. Jansen, R., Embden, J. D., Gaastra, W. & Schouls, L. M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565–1575 (2002). · DOI · Paper page
  9. Makarova, K. S., Aravind, L., Grishin, N. V., Rogozin, I. B. & Koonin, E. V. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30, 482–496 (2002). · DOI · Paper page
  10. Bolotin, A., Quinquis, B., Sorokin, A. & Ehrlich, S. D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551–2561 (2005). · DOI · Paper page
  11. Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. & Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174–182 (2005). · DOI · Paper page
  12. Pourcel, C., Salvignol, G. & Vergnaud, G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151, 653–663 (2005). · DOI · Paper page
  13. Haft, D. H., Selengut, J., Mongodin, E. F. & Nelson, K. E. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1, e60 (2005). · DOI
  14. Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I. & Koonin, E. V. 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. Biol. Direct 1, 7 (2006). · DOI · Paper page
  15. Carthew, R. W. & Sontheimer, E. J. Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642–655 (2009). · DOI
  16. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007). · DOI · Paper page
  17. Garrett, R. A. et al. CRISPR-based immune systems of the Sulfolobales: complexity and diversity. Biochem. Soc. Trans. 39, 51–57 (2011). · DOI
  18. Manica, A., Zebec, Z., Teichmann, D. & Schleper, C. In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon. Mol. Microbiol. 80, 481–491 (2011). · DOI
  19. Al-Attar, S., Westra, E. R., van der Oost, J. & Brouns, S. J. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol. Chem. 392, 277–289 (2011). · DOI
  20. Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010). · DOI
  21. Sontheimer, E. J. & Marraffini, L. A. Slicer for DNA. Nature 468, 45–46 (2010). · DOI
  22. Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733–740 (2009). · DOI · Paper page
  23. Deveau, H. et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190, 1390–1400 (2008). · DOI
  24. Brouns, S. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008). · DOI · Paper page
  25. Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010). · DOI
  26. Carte, J., Wang, R., Li, H., Terns, R. M. & Terns, M. P. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22, 3489–3496 (2008). · DOI
  27. Hale, C. R. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945–956 (2009). · DOI · Paper page
  28. Wang, R., Preamplume, G., Terns, M. P., Terns, R. M. & Li, H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 19, 257–264 (2011). · DOI
  29. Marraffini, L. A. & Sontheimer, E. J. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463, 568–571 (2010). · DOI
  30. Marraffini, L. A. & Sontheimer, E. J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008). · DOI · Paper page
  31. Wiedenheft, B. et al. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17, 904–912 (2009). · DOI · Paper page
  32. Beloglazova, N. et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J. Biol. Chem. 283, 20361–20371 (2008). · DOI
  33. Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003). · DOI
  34. Sinkunas, T. et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 30, 1335–1342 (2011). · DOI
  35. Soding, J., Remmert, M., Biegert, A. & Lupas, A. N. HHsenser: exhaustive transitive profile search using HMM–HMM comparison. Nucleic Acids Res. 34, W374–W378 (2006). · DOI
  36. Kleanthous, C. et al. Structural and mechanistic basis of immunity toward endonuclease colicins. Nature Struct. Biol. 6, 243–252 (1999). · DOI
  37. Jakubauskas, A., Giedriene, J., Bujnicki, J. M. & Janulaitis, A. Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. J. Mol. Biol. 370, 157–169 (2007). · DOI
  38. Kunin, V., Sorek, R. & Hugenholtz, P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, R61 (2007). · DOI
  39. Grissa, I., Vergnaud, G. & Pourcel, C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8, 172 (2007). · DOI · Paper page
  40. Altschul, S. F. & Koonin, E. V. PSI-BLAST — a tool for making discoveries in sequence databases. Trends Biochem. Sci. 23, 444–447 (1998). · DOI
  41. Marchler-Bauer, A. & Bryant, S. H. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32, W327–W331 (2004). · DOI
  42. Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol. Direct 4, 19 (2009). · DOI
  43. Babu, M. et al. A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 79, 484–502 (2011). · DOI · Paper page
  44. Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003). · DOI
  45. Han, D., Lehmann, K. & Krauss, G. SSO1450 – a CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA. FEBS Lett. 583, 1928–1932 (2009). · DOI
  46. Han, D. & Krauss, G. Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2. FEBS Lett. 583, 771–776 (2009). · DOI
  47. Guy, C. P., Majernik, A. I., Chong, J. P. & Bolt, E. L. A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system. Nucleic Acids Res. 32, 6176–6186 (2004). · DOI
  48. Selengut, J. D. et al. TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 35, D260–D264 (2007). · DOI

Cited by

Sorted by citations

Metadata

Authors
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J. M., Wolf, Y. I., Yakunin, A. F., van der Oost, J., & Koonin, E. V.
Venue
Nature Reviews Microbiology
Published
2011-05-09
Volume
9
Issue
6
Pages
467-477
ISSN
  • 1740-1526
  • 1740-1534
Cited by
2,331
References
2
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review