Cited by 989

The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

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

Wright, Addison V., Nuñez, James K., Doudna, Jennifer A.·2016·Cell

Abstract

Bacteria and archaea possess a range of defense mechanisms to combat plasmids and viral infections. Unique among these are the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems, which provide adaptive immunity against foreign nucleic acids. CRISPR systems function by acquiring genetic records of invaders to facilitate robust interference upon reinfection. In this Review, we discuss recent advances in understanding the diverse mechanisms by which Cas proteins respond to foreign nucleic acids and how these systems have been harnessed for precision genome manipulation in a wide array of organisms.

Overview

Integrity signals

Registry

Crossref · 10.1016/j.cell.2015.12.035

Cites

8 of 8 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 155

  1. Anders, 2014, Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease, Nature, 513, 569, 10.1038/nature13579 · DOI · Paper page
  2. Arslan, 2013, Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2, Nucleic Acids Res., 41, 6347, 10.1093/nar/gkt315 · DOI
  3. Arslan, 2014, Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system, Nucleic Acids Res., 42, 7884, 10.1093/nar/gku510 · DOI
  4. Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
  5. Blackwood, 2013, End-resection at DNA double-strand breaks in the three domains of life, Biochem. Soc. Trans., 41, 314, 10.1042/BST20120307 · DOI
  6. Blosser, 2015, Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex, Mol. Cell, 58, 60, 10.1016/j.molcel.2015.01.028 · DOI
  7. Blundell, 2014, Beyond genome sequencing: Lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer, Genomics, 104, 417, 10.1016/j.ygeno.2014.09.005 · DOI
  8. Bolotin, 2005, Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, 151, 2551, 10.1099/mic.0.28048-0 · DOI · Paper page
  9. Bondy-Denomy, 2014, To acquire or resist: the complex biological effects of CRISPR-Cas systems, Trends Microbiol., 22, 218, 10.1016/j.tim.2014.01.007 · DOI
  10. Bondy-Denomy, 2013, Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system, Nature, 493, 429, 10.1038/nature11723 · DOI
  11. Bondy-Denomy, 2015, Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins, Nature, 526, 136, 10.1038/nature15254 · DOI
  12. Borchardt, 2015, Controlling mRNA stability and translation with the CRISPR endoribonuclease Csy4, RNA, 21, 1921, 10.1261/rna.051227.115 · DOI
  13. Brendel, 2014, A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii, J. Biol. Chem., 289, 7164, 10.1074/jbc.M113.508184 · DOI
  14. Briner, 2014, Guide RNA functional modules direct Cas9 activity and orthogonality, Mol. Cell, 56, 333, 10.1016/j.molcel.2014.09.019 · DOI
  15. Brouns, 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689 · DOI · Paper page
  16. Bryson, 2015, Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9, MBio, 6, e00648, 10.1128/mBio.00648-15 · DOI
  17. Carte, 2008, Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes, Genes Dev., 22, 3489, 10.1101/gad.1742908 · DOI
  18. Charpentier, 2015, Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity, FEMS Microbiol. Rev., 39, 428, 10.1093/femsre/fuv023 · DOI
  19. Chow, 1992, Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus, Science, 255, 723, 10.1126/science.1738845 · DOI
  20. Chu, 2015, Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells, Nat. Biotechnol., 33, 543, 10.1038/nbt.3198 · DOI · Paper page
  21. Chylinski, 2014, Classification and evolution of type II CRISPR-Cas systems, Nucleic Acids Res., 42, 6091, 10.1093/nar/gku241 · DOI · Paper page
  22. D’Astolfo, 2015, Efficient intracellular delivery of native proteins, Cell, 161, 674, 10.1016/j.cell.2015.03.028 · DOI · Paper page
  23. Datsenko, 2012, Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system, Nat. Commun., 3, 945, 10.1038/ncomms1937 · DOI · Paper page
  24. Davis, 2015, Small molecule-triggered Cas9 protein with improved genome-editing specificity, Nat. Chem. Biol., 11, 316, 10.1038/nchembio.1793 · DOI
  25. Deng, 2013, A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus, Mol. Microbiol., 87, 1088, 10.1111/mmi.12152 · DOI
  26. Deveau, 2008, Phage response to CRISPR-encoded resistance in Streptococcus thermophilus, J. Bacteriol., 190, 1390, 10.1128/JB.01412-07 · DOI
  27. Díez-Villaseñor, 2013, CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli, RNA Biol., 10, 792, 10.4161/rna.24023 · DOI
  28. Dillingham, 2008, RecBCD enzyme and the repair of double-stranded DNA breaks, Microbiol. Mol. Biol. Rev., 72, 642, 10.1128/MMBR.00020-08 · DOI
  29. Du, 2015, Engineering translational activators with CRISPR-Cas system, ACS Synth. Biol.
  30. Dugar, 2013, High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates, PLoS Genet., 9, e1003495, 10.1371/journal.pgen.1003495 · DOI
  31. Ellinger, 2012, The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae, J. Struct. Biol., 178, 350, 10.1016/j.jsb.2012.04.006 · DOI
  32. Engelman, 1991, HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer, Cell, 67, 1211, 10.1016/0092-8674(91)90297-C · DOI · Paper page
  33. Garrett, 2015, CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity, Life (Basel), 5, 783
  34. Garside, 2012, Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases, RNA, 18, 2020, 10.1261/rna.033100.112 · DOI
  35. Gasiunas, 2012, Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proc. Natl. Acad. Sci. USA, 109, E2579, 10.1073/pnas.1208507109 · DOI · Paper page
  36. Gesner, 2011, Recognition and maturation of effector RNAs in a CRISPR interference pathway, Nat. Struct. Mol. Biol., 18, 688, 10.1038/nsmb.2042 · DOI · Paper page
  37. Goldberg, 2014, Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature, 514, 633, 10.1038/nature13637 · DOI
  38. Gong, 2014, Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3, Proc. Natl. Acad. Sci. USA, 111, 16359, 10.1073/pnas.1410806111 · DOI
  39. Gori, 2015, Delivery and Specificity of CRISPR-Cas9 Genome Editing Technologies for Human Gene Therapy, Hum. Gene Ther., 26, 443, 10.1089/hum.2015.074 · DOI
  40. Hale, 2008, Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus, RNA, 14, 2572, 10.1261/rna.1246808 · DOI
  41. Hale, 2009, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040 · DOI · Paper page
  42. Haurwitz, 2010, Sequence- and structure-specific RNA processing by a CRISPR endonuclease, Science, 329, 1355, 10.1126/science.1192272 · DOI
  43. Heler, 2015, Cas9 specifies functional viral targets during CRISPR-Cas adaptation, Nature, 519, 199, 10.1038/nature14245 · DOI
  44. Hochstrasser, 2015, Cutting it close: CRISPR-associated endoribonuclease structure and function, Trends Biochem. Sci., 40, 58, 10.1016/j.tibs.2014.10.007 · DOI
  45. Hochstrasser, 2014, CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference, Proc. Natl. Acad. Sci. USA, 111, 6618, 10.1073/pnas.1405079111 · DOI
  46. Hooton, 2014, Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein, Front Microbiol, 5, 744
  47. Howes, 2015, Genome engineering using Adeno-Associated Virus (AAV), Methods Mol. Biol., 1239, 75, 10.1007/978-1-4939-1862-1_5 · DOI
  48. Huo, 2014, Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation, Nat. Struct. Mol. Biol., 21, 771, 10.1038/nsmb.2875 · DOI
  49. Hynes, 2014, Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages, Nat. Commun., 5, 4399, 10.1038/ncomms5399 · DOI
  50. Ishino, 1987, Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, J. Bacteriol., 169, 5429, 10.1128/jb.169.12.5429-5433.1987 · DOI · Paper page
  51. Jackson, 2015, A Conserved Structural Chassis for Mounting Versatile CRISPR RNA-Guided Immune Responses, Mol. Cell, 58, 722, 10.1016/j.molcel.2015.05.023 · DOI
  52. Jackson, 2014, Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli, Science, 345, 1473, 10.1126/science.1256328 · DOI
  53. Jansen, 2002, Identification of genes that are associated with DNA repeats in prokaryotes, Mol. Microbiol., 43, 1565, 10.1046/j.1365-2958.2002.02839.x · DOI · Paper page
  54. Jiang, 2015, CRISPR-Cas: New Tools for Genetic Manipulations from Bacterial Immunity Systems, Annu. Rev. Microbiol., 69, 209, 10.1146/annurev-micro-091014-104441 · DOI
  55. Jiang, 2015, STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition, Science, 348, 1477, 10.1126/science.aab1452 · DOI
  56. Jore, 2011, Structural basis for CRISPR RNA-guided DNA recognition by Cascade, Nat. Struct. Mol. Biol., 18, 529, 10.1038/nsmb.2019 · DOI
  57. Juranek, 2012, A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs, RNA, 18, 783, 10.1261/rna.031468.111 · DOI
  58. Kenchappa, 2013, Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2, Nucleic Acids Res., 41, 3424, 10.1093/nar/gks1465 · DOI
  59. Koo, 2012, Crystal structure of Streptococcus pyogenes Csn2 reveals calcium-dependent conformational changes in its tertiary and quaternary structure, PLoS ONE, 7, e33401, 10.1371/journal.pone.0033401 · DOI
  60. Kuhn, 2013, Eukaryotic Argonautes come into focus, Trends Biochem. Sci., 38, 263, 10.1016/j.tibs.2013.02.008 · DOI
  61. Kunin, 2007, Evolutionary conservation of sequence and secondary structures in CRISPR repeats, Genome Biol., 8, R61, 10.1186/gb-2007-8-4-r61 · DOI
  62. Labrie, 2010, Bacteriophage resistance mechanisms, Nat. Rev. Microbiol., 8, 317, 10.1038/nrmicro2315 · DOI
  63. Lee, 2012, Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR-mediated bacterial immunity, Proteins, 80, 2573, 10.1002/prot.24138 · DOI
  64. Lee, 2013, RNA-protein analysis using a conditional CRISPR nuclease, Proc. Natl. Acad. Sci. USA, 110, 5416, 10.1073/pnas.1302807110 · DOI
  65. Lemak, 2013, Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus, J. Am. Chem. Soc., 135, 17476, 10.1021/ja408729b · DOI
  66. Levy, 2015, CRISPR adaptation biases explain preference for acquisition of foreign DNA, Nature, 520, 505, 10.1038/nature14302 · DOI
  67. Li, 2014, Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process, Nucleic Acids Res., 42, 2483, 10.1093/nar/gkt1154 · DOI
  68. Lin, 2014, Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery, eLife, 3, e04766, 10.7554/eLife.04766 · DOI · Paper page
  69. Lintner, 2011, Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE), J. Biol. Chem., 286, 21643, 10.1074/jbc.M111.238485 · DOI
  70. Ma, 2015, Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes, Mol. Cell, 60, 398, 10.1016/j.molcel.2015.10.030 · DOI
  71. Makarova, 2015, Annotation and Classification of CRISPR-Cas Systems, Methods Mol. Biol., 1311, 47, 10.1007/978-1-4939-2687-9_4 · DOI
  72. Makarova, 2011, Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems, Biol. Direct, 6, 38, 10.1186/1745-6150-6-38 · DOI
  73. Makarova, 2011, Evolution and classification of the CRISPR-Cas systems, Nat. Rev. Microbiol., 9, 467, 10.1038/nrmicro2577 · DOI · Paper page
  74. Makarova, 2013, The basic building blocks and evolution of CRISPR-CAS systems, Biochem. Soc. Trans., 41, 1392, 10.1042/BST20130038 · DOI · Paper page
  75. Makarova, 2015, An updated evolutionary classification of CRISPR-Cas systems, Nat. Rev. Microbiol., 13, 722, 10.1038/nrmicro3569 · DOI · Paper page
  76. Marraffini, 2008, CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science, 322, 1843, 10.1126/science.1165771 · DOI · Paper page
  77. Marraffini, 2010, Self versus non-self discrimination during CRISPR RNA-directed immunity, Nature, 463, 568, 10.1038/nature08703 · DOI
  78. Mizuuchi, 1991, Inversion of the phosphate chirality at the target site of Mu DNA strand transfer: evidence for a one-step transesterification mechanism, Cell, 66, 129, 10.1016/0092-8674(91)90145-O · DOI
  79. Mojica, 2005, Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, J. Mol. Evol., 60, 174, 10.1007/s00239-004-0046-3 · DOI · Paper page
  80. Mojica, 2009, Short motif sequences determine the targets of the prokaryotic CRISPR defence system, Microbiology, 155, 733, 10.1099/mic.0.023960-0 · DOI · Paper page
  81. Mulepati, 2011, Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3), J. Biol. Chem., 286, 31896, 10.1074/jbc.M111.270017 · DOI
  82. Mulepati, 2013, In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target, J. Biol. Chem., 288, 22184, 10.1074/jbc.M113.472233 · DOI · Paper page
  83. Mulepati, 2014, Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target, Science, 345, 1479, 10.1126/science.1256996 · DOI
  84. Nam, 2012, Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system, Structure, 20, 1574, 10.1016/j.str.2012.06.016 · DOI
  85. Nihongaki, 2015, Photoactivatable CRISPR-Cas9 for optogenetic genome editing, Nat. Biotechnol., 33, 755, 10.1038/nbt.3245 · DOI
  86. Nishimasu, 2015, Crystal Structure of Staphylococcus aureus Cas9, Cell, 162, 1113, 10.1016/j.cell.2015.08.007 · DOI
  87. Nissim, 2014, Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells, Mol. Cell, 54, 698, 10.1016/j.molcel.2014.04.022 · DOI
  88. Nuñez, 2014, Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity, Nat. Struct. Mol. Biol., 21, 528, 10.1038/nsmb.2820 · DOI · Paper page
  89. Nuñez, 2015, Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity, Nature, 519, 193, 10.1038/nature14237 · DOI · Paper page
  90. Nuñez, 2015, Foreign DNA capture during CRISPR-Cas adaptive immunity, Nature, 527, 535, 10.1038/nature15760 · DOI · Paper page
  91. Osawa, 2015, Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog, Mol. Cell, 58, 418, 10.1016/j.molcel.2015.03.018 · DOI · Paper page
  92. Paez-Espino, 2013, Strong bias in the bacterial CRISPR elements that confer immunity to phage, Nat. Commun., 4, 1430, 10.1038/ncomms2440 · DOI
  93. Paez-Espino, 2015, CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus, MBio, 6, 10.1128/mBio.00262-15 · DOI
  94. Patterson, 2015, Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference, Nucleic Acids Res., 43, 6038, 10.1093/nar/gkv517 · DOI
  95. Pawluk, 2014, A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa, mBio., 5, 10.1128/mBio.00896-14 · DOI
  96. Plagens, 2012, Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax, J. Bacteriol., 194, 2491, 10.1128/JB.00206-12 · DOI
  97. Plagens, 2014, In vitro assembly and activity of an archaeal CRISPR-Cas type I-A Cascade interference complex, Nucleic Acids Res., 42, 5125, 10.1093/nar/gku120 · DOI
  98. Plagens, 2015, DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes, FEMS Microbiol. Rev., 39, 442, 10.1093/femsre/fuv019 · DOI
  99. Polstein, 2015, A light-inducible CRISPR-Cas9 system for control of endogenous gene activation, Nat. Chem. Biol., 11, 198, 10.1038/nchembio.1753 · DOI
  100. Pourcel, 2005, CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology, 151, 653, 10.1099/mic.0.27437-0 · DOI · Paper page
  101. Pul, 2010, Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS, Mol. Microbiol., 75, 1495, 10.1111/j.1365-2958.2010.07073.x · DOI · Paper page
  102. Rath, 2015, Efficient programmable gene silencing by Cascade, Nucleic Acids Res., 43, 237, 10.1093/nar/gku1257 · DOI
  103. Ratner, 2015, I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope, Curr. Opin. Infect. Dis., 28, 267, 10.1097/QCO.0000000000000154 · DOI
  104. Redding, 2015, Surveillance and processing of foreign DNA by the Escherichia coli CRISPR-Cas system, Cell, 163, 854, 10.1016/j.cell.2015.10.003 · DOI · Paper page
  105. Richter, 2013, The subtype I-F CRISPR-Cas system influences pathogenicity island retention in Pectobacterium atrosepticum via crRNA generation and Csy complex formation, Biochem. Soc. Trans., 41, 1468, 10.1042/BST20130151 · DOI
  106. Richter, 2012, In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas System, PLoS ONE, 7, e49549, 10.1371/journal.pone.0049549 · DOI
  107. Richter, 2014, Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer, Nucleic Acids Res., 42, 8516, 10.1093/nar/gku527 · DOI
  108. Rollie, 2015, Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition, eLife, 4, 4, 10.7554/eLife.08716 · DOI
  109. Rollins, 2015, Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa, Nucleic Acids Res., 43, 2216, 10.1093/nar/gkv094 · DOI
  110. Rutkauskas, 2015, Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection, Cell Rep., 10, 1534, 10.1016/j.celrep.2015.01.067 · DOI
  111. Salvail-Lacoste, 2013, Affinity purification of T7 RNA transcripts with homogeneous ends using ARiBo and CRISPR tags, RNA, 19, 1003, 10.1261/rna.037432.112 · DOI
  112. Samai, 2015, Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity, Cell, 161, 1164, 10.1016/j.cell.2015.04.027 · DOI · Paper page
  113. Sashital, 2011, An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3, Nat. Struct. Mol. Biol., 18, 680, 10.1038/nsmb.2043 · DOI
  114. Sashital, 2012, Mechanism of foreign DNA selection in a bacterial adaptive immune system, Mol. Cell, 46, 606, 10.1016/j.molcel.2012.03.020 · DOI
  115. Savitskaya, 2013, High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli, RNA Biol., 10, 716, 10.4161/rna.24325 · DOI
  116. Schunder, 2013, First indication for a functional CRISPR/Cas system in Francisella tularensis, Int. J. Med. Microbiol., 303, 51, 10.1016/j.ijmm.2012.11.004 · DOI
  117. Semenova, 2011, Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence, Proc. Natl. Acad. Sci. USA, 108, 10098, 10.1073/pnas.1104144108 · DOI · Paper page
  118. Servick, 2015, SCIENCE POLICY. U.S. to review agricultural biotech regulations, Science, 349, 131, 10.1126/science.349.6244.131 · DOI
  119. Shao, 2013, Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6, Structure, 21, 385, 10.1016/j.str.2013.01.010 · DOI
  120. Shmakov, 2014, Pervasive generation of oppositely oriented spacers during CRISPR adaptation, Nucleic Acids Res., 42, 5907, 10.1093/nar/gku226 · DOI · Paper page
  121. Shmakov, 2015, Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems, Mol. Cell, 60, 385, 10.1016/j.molcel.2015.10.008 · DOI · Paper page
  122. Sinkunas, 2011, Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system, EMBO J., 30, 1335, 10.1038/emboj.2011.41 · DOI
  123. Sinkunas, 2013, In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus, EMBO J., 32, 385, 10.1038/emboj.2012.352 · DOI · Paper page
  124. Sokolowski, 2014, Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system, Nucleic Acids Res., 42, 6532, 10.1093/nar/gku308 · DOI
  125. Staals, 2014, RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus, Mol. Cell, 56, 518, 10.1016/j.molcel.2014.10.005 · DOI
  126. Sternberg, 2015, Expanding the Biologist’s Toolkit with CRISPR-Cas9, Mol. Cell, 58, 568, 10.1016/j.molcel.2015.02.032 · DOI
  127. Sternberg, 2012, Mechanism of substrate selection by a highly specific CRISPR endoribonuclease, RNA, 18, 661, 10.1261/rna.030882.111 · DOI
  128. Sternberg, 2014, DNA interrogation by the CRISPR RNA-guided endonuclease Cas9, Nature, 507, 62, 10.1038/nature13011 · DOI · Paper page
  129. Sternberg, 2015, Conformational control of DNA target cleavage by CRISPR-Cas9, Nature, 527, 110, 10.1038/nature15544 · DOI · Paper page
  130. Swarts, 2012, CRISPR interference directs strand specific spacer acquisition, PLoS ONE, 7, e35888, 10.1371/journal.pone.0035888 · DOI
  131. Szczelkun, 2014, Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes, Proc. Natl. Acad. Sci. USA, 111, 9798, 10.1073/pnas.1402597111 · DOI
  132. Tamulaitis, 2014, Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus, Mol. Cell, 56, 506, 10.1016/j.molcel.2014.09.027 · DOI
  133. Taylor, 2015, Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning, Science, 348, 581, 10.1126/science.aaa4535 · DOI
  134. Tsai, 2014, Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing, Nat. Biotechnol., 32, 569, 10.1038/nbt.2908 · DOI · Paper page
  135. Tsui, 2015, Structure Principles of CRISPR-Cas Surveillance and Effector Complexes, Annu. Rev. Biophys., 44, 229, 10.1146/annurev-biophys-060414-033939 · DOI
  136. van der Oost, 2009, CRISPR-based adaptive and heritable immunity in prokaryotes, Trends Biochem. Sci., 34, 401, 10.1016/j.tibs.2009.05.002 · DOI
  137. van der Oost, 2014, Unravelling the structural and mechanistic basis of CRISPR-Cas systems, Nat. Rev. Microbiol., 12, 479, 10.1038/nrmicro3279 · DOI
  138. van Erp, 2015, Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli, Nucleic Acids Res., 43, 8381, 10.1093/nar/gkv793 · DOI
  139. Vestergaard, 2014, CRISPR adaptive immune systems of Archaea, RNA Biol., 11, 156, 10.4161/rna.27990 · DOI
  140. Wang, 2015, Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems, Cell, 163, 840, 10.1016/j.cell.2015.10.008 · DOI · Paper page
  141. Wei, 2015, Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus, Nucleic Acids Res., 43, 1749, 10.1093/nar/gku1407 · DOI
  142. Wei, 2015, Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation, Genes Dev., 29, 356, 10.1101/gad.257550.114 · DOI
  143. Westra, 2012, CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3, Mol. Cell, 46, 595, 10.1016/j.molcel.2012.03.018 · DOI
  144. Westra, 2014, CRISPR-Cas systems: beyond adaptive immunity, Nat. Rev. Microbiol., 12, 317, 10.1038/nrmicro3241 · DOI
  145. Wiedenheft, 2011, Structures of the RNA-guided surveillance complex from a bacterial immune system, Nature, 477, 486, 10.1038/nature10402 · DOI
  146. Wiedenheft, 2011, RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions, Proc. Natl. Acad. Sci. USA, 108, 10092, 10.1073/pnas.1102716108 · DOI
  147. Wright, 2015, Rational design of a split-Cas9 enzyme complex, Proc. Natl. Acad. Sci. USA, 112, 2984, 10.1073/pnas.1501698112 · DOI
  148. Yosef, 2012, Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli, Nucleic Acids Res., 40, 5569, 10.1093/nar/gks216 · DOI · Paper page
  149. Yosef, 2013, DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array, Proc. Natl. Acad. Sci. USA, 110, 14396, 10.1073/pnas.1300108110 · DOI
  150. Zetsche, 2015, Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System, Cell, 163, 759, 10.1016/j.cell.2015.09.038 · DOI · Paper page
  151. Zetsche, 2015, A split-Cas9 architecture for inducible genome editing and transcription modulation, Nat. Biotechnol., 33, 139, 10.1038/nbt.3149 · DOI
  152. Zhang, 2013, Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis, Mol. Cell, 50, 488, 10.1016/j.molcel.2013.05.001 · DOI
  153. Zhang, 2015, DNase H Activity of Neisseria meningitidis Cas9, Mol. Cell, 60, 242, 10.1016/j.molcel.2015.09.020 · DOI
  154. Zhao, 2014, Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli, Nature, 515, 147, 10.1038/nature13733 · DOI
  155. Zuris, 2015, Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo, Nat. Biotechnol., 33, 73, 10.1038/nbt.3081 · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Wright, A. V., Nuñez, J. K., & Doudna, J. A.
Venue
Cell
Publisher
Elsevier BV
Published
2016-01
Volume
164
Issue
1-2
Pages
29-44
ISSN
0092-8674
Cited by
989
References
8
Language
en
Funders
US National Science Foundation (1244557)

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