Cited by 176

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

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

Koonin, Eugene V., Makarova, Kira S.·2017·Genome Biology and Evolution

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 · 10.1093/gbe/evx192

Cites

8 of 8 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?

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

Show all 8 references

Research works printed but not linked: 125

  1. 2016, C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science, 353, aaf5573., 10.1126/science.aaf5573 · DOI · Paper page
  2. 2017, Necessity is the mother of invention: ciliates, transposons, and transgenerational inheritance, Trends Genet., 33, 197, 10.1016/j.tig.2017.01.005 · DOI
  3. 2016, CRISPR-Cas adaptation: insights into the mechanism of action, Nat Rev Microbiol., 14, 67, 10.1038/nrmicro.2015.14 · DOI
  4. 2013, Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing, Biol Direct, 8, 15., 10.1186/1745-6150-8-15 · DOI
  5. 2013, Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements, Mob DNA, 4, 12., 10.1186/1759-8753-4-12 · DOI
  6. 2017, A decade of discovery: CRISPR functions and applications, Nat Microbiol, 2, 17092., 10.1038/nmicrobiol.2017.92 · DOI
  7. 2014, CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity, Mol Cell, 54, 234, 10.1016/j.molcel.2014.03.011 · DOI · Paper page
  8. 2016, Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems, Nucleic Acids Res, 44, 10367
  9. 2015, Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions, Front Microbiol, 6, 656.
  10. 2008, A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats, J Biol Chem., 283, 20361, 10.1074/jbc.M803225200 · DOI
  11. 2011, Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference, Embo J., 30, 4616, 10.1038/emboj.2011.377 · DOI
  12. 2014, Programmed rearrangement in ciliates: paramecium, Microbiol Spectr, 2
  13. 2015, Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins, Nature, 526, 136, 10.1038/nature15254 · DOI
  14. 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689 · DOI · Paper page
  15. 2015, Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity, FEMS Microbiol Rev., 39, 428, 10.1093/femsre/fuv023 · DOI
  16. 2014, Classification and evolution of type II CRISPR-Cas systems, Nucleic Acids Res., 42, 6091, 10.1093/nar/gku241 · DOI · Paper page
  17. 2016, Dual nuclease activity of a Cas2 protein in CRISPR-Cas subtype I-B of Leptospira interrogans, FEBS Lett., 590, 1002, 10.1002/1873-3468.12124 · DOI
  18. 2016, The crystal structure of Cpf1 in complex with CRISPR RNA, Nature, 532, 522, 10.1038/nature17944 · DOI · Paper page
  19. 2012, Transposon invasion of the paramecium germline genome countered by a domesticated PiggyBac transposase and the NHEJ pathway, Int J Evol Biol, 2012, 436196.
  20. 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 538, 270, 10.1038/nature19802 · DOI · Paper page
  21. 2008, The diversity of retrotransposons and the properties of their reverse transcriptases, Virus Res., 134, 221
  22. 2016, Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR-Cas system, Genes Dev., 30, 447, 10.1101/gad.272153.115 · DOI
  23. 2017, Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex, Proc Natl Acad Sci U S A, 114, E5122
  24. 2016, The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA, Nature, 532, 517, 10.1038/nature17945 · DOI · Paper page
  25. 2011, Bacterial integrative mobile genetic elements
  26. 2012, Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses, PLoS One, 7, e33802., 10.1371/journal.pone.0033802 · DOI
  27. 2012, Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proc Natl Acad Sci U S A., 109, E2579, 10.1073/pnas.1208507109 · DOI · Paper page
  28. 2005, Prokaryotic toxin-antitoxin stress response loci, Nat Rev Microbiol., 3, 371, 10.1038/nrmicro1147 · DOI
  29. 2014, Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3, Proc Natl Acad Sci U S A., 111, 16359, 10.1073/pnas.1410806111 · DOI
  30. 2015, Cas9 specifies functional viral targets during CRISPR-Cas adaptation, Nature, 519, 199, 10.1038/nature14245 · DOI
  31. 2017, Mutations in Cas9 enhance the rate of acquisition of viral spacer sequences during the CRISPR-Cas immune response, Mol Cell, 65, 168, 10.1016/j.molcel.2016.11.031 · DOI
  32. 2015, The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications, Nucleic Acids Res, 43, 10576, 10.1093/nar/gkv1180 · DOI
  33. 2016, Structure and engineering of Francisella novicida Cas9, Cell, 164, 950, 10.1016/j.cell.2016.01.039 · DOI
  34. 2015, Cutting it close: CRISPR-associated endoribonuclease structure and function, Trends Biochem Sci., 40, 58, 10.1016/j.tibs.2014.10.007 · DOI
  35. 2016, The bacteriophage carrier state of Campylobacter jejuni features changes in host non-coding RNAs and the acquisition of new host-derived CRISPR spacer sequences, Front Microbiol, 7, 355.
  36. 2015, Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein, Front Microbiol, 5, 744.
  37. 2014, Development and applications of CRISPR-Cas9 for genome engineering, Cell, 157, 1262, 10.1016/j.cell.2014.05.010 · DOI · Paper page
  38. 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
  39. 2014, Prokaryotic Argonautes defend genomes against invasive DNA, Trends Biochem Sci., 39, 257, 10.1016/j.tibs.2014.04.006 · DOI
  40. 2008, Argonaute proteins: key players in RNA silencing, Nat Rev Mol Cell Biol., 9, 22, 10.1038/nrm2321 · DOI
  41. 2017, CRISPR-Cas: adapting to change, Science, 356, eaal5056., 10.1126/science.aal5056 · DOI
  42. 2017, CRISPR-Cas9 structures and mechanisms, Annu Rev Biophys, 46, 505, 10.1146/annurev-biophys-062215-010822 · DOI · Paper page
  43. 2016, Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage, Science, 351, 867, 10.1126/science.aad8282 · DOI
  44. 2016, Degradation of phage transcripts by CRISPR-associated RNases enables type III CRISPR-Cas immunity, Cell, 164, 710, 10.1016/j.cell.2015.12.053 · DOI
  45. 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 · DOI · Paper page
  46. 2014, Structural and functional characterization of Streptococcus pyogenes Cas2 protein under different pH conditions, Biochem Biophys Res Commun., 451, 152, 10.1016/j.bbrc.2014.07.087 · DOI
  47. 2005, RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons, PLoS Biol., 3, e181., 10.1371/journal.pbio.0030181 · DOI · Paper page
  48. 2006, Self-synthesizing DNA transposons in eukaryotes, Proc Natl Acad Sci U S A., 103, 4540, 10.1073/pnas.0600833103 · DOI
  49. 2015, Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon, Biol Direct, 10, 20., 10.1186/s13062-015-0055-8 · DOI
  50. 2015, ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs, J Bacteriol., 198, 797
  51. 2017, A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems, Science, 357, 605, 10.1126/science.aao0100 · DOI · Paper page
  52. 2001, Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution, Nucleic Acids Res., 29, 3742, 10.1093/nar/29.18.3742 · DOI · Paper page
  53. 2017, CRISPR-based technologies for the manipulation of eukaryotic genomes, Cell, 168, 20
  54. 2017, Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence, Biol Direct, 12, 5., 10.1186/s13062-017-0177-2 · DOI
  55. 2015, Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nat Rev Genet., 16, 184, 10.1038/nrg3859 · DOI
  56. 2009, CRISPR-Cas: an adaptive immunity system in prokaryotes, F1000 Biol Rep, 1, 95.
  57. 2009, Is evolution Darwinian or/and Lamarckian?, Biol Direct, 4, 42., 10.1186/1745-6150-4-42 · DOI
  58. 2016, Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms, Biol Direct, 11, 9., 10.1186/s13062-016-0111-z · DOI
  59. 2017, Coupling immunity and programmed cell suicide in prokaryotes: life-or-death choices, Bioessays, 39, 1, 10.1002/bies.201600186 · DOI
  60. 2017, Casposons: the mobile elements that gave rise to the adaptation module of CRISPR-Cas systems, Curr Opin Microbiol, 38, 36, 10.1016/j.mib.2017.04.004 · DOI
  61. 2015, Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease, Biol Direct, 10, 65., 10.1186/s13062-015-0093-2 · DOI
  62. 2015, Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nat Rev Microbiol., 13, 105, 10.1038/nrmicro3389 · DOI
  63. 2016, Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Curr Opin Microbiol, 31, 25, 10.1016/j.mib.2016.01.006 · DOI
  64. 2014, Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biol, 12, 36., 10.1186/1741-7007-12-36 · DOI
  65. 2016, Recent mobility of casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity, Genome Biol Evol., 8, 375, 10.1093/gbe/evw006 · DOI
  66. 2016, Cas3-derived target DNA degradation fragments fuel primed CRISPR adaptation, Mol Cell, 63, 852, 10.1016/j.molcel.2016.07.011 · DOI
  67. 2017, Building the class 2 CRISPR-Cas Arsenal, Mol Cell, 65, 377, 10.1016/j.molcel.2017.01.024 · DOI
  68. 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
  69. 2017, C2c1-sgRNA complex structure reveals RNA-guided DNA cleavage mechanism, Mol Cell, 65, 310, 10.1016/j.molcel.2016.11.040 · DOI
  70. 2017, Two distant catalytic sites are responsible for C2c2 RNase activities, Cell, 168, 121
  71. 2012, Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes, Biol Direct, 7, 40., 10.1186/1745-6150-7-40 · DOI
  72. 2014, CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems, Front Genet, 5, 102.
  73. 2006, 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., 10.1186/1745-6150-1-7 · DOI · Paper page
  74. 2011, Evolution and classification of the CRISPR-Cas systems, Nat Rev Microbiol, 9, 467, 10.1038/nrmicro2577 · DOI · Paper page
  75. 2015, An updated evolutionary classification of CRISPR-Cas systems, Nat Rev Microbiol., 13, 722, 10.1038/nrmicro3569 · DOI · Paper page
  76. 2009, Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes, Biol Direct, 4, 19., 10.1186/1745-6150-4-19 · DOI
  77. 2013, The basic building blocks and evolution of CRISPR-cas systems, Biochem Soc Trans., 41, 1392, 10.1042/BST20130038 · DOI · Paper page
  78. 2013, Comparative genomics of defense systems in archaea and bacteria, Nucleic Acids Res., 41, 4360, 10.1093/nar/gkt157 · DOI
  79. 2010, CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea, Nat Rev Genet., 11, 181, 10.1038/nrg2749 · DOI · Paper page
  80. 2016, Group II introns: versatile ribozymes and retroelements, Wiley Interdiscip Rev RNA, 7, 341, 10.1002/wrna.1339 · DOI
  81. 2016, Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems, Science, 353, aad5147., 10.1126/science.aad5147 · DOI
  82. 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
  83. 2017, Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers, Nature
  84. 2016, Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6, RNA, 22, 318, 10.1261/rna.054098.115 · DOI
  85. 2015, Crystal structure of Staphylococcus aureus Cas9, Cell, 162, 1113, 10.1016/j.cell.2015.08.007 · DOI
  86. 2017, Structures and mechanisms of CRISPR RNA-guided effector nucleases, Curr Opin Struct Biol, 43, 68, 10.1016/j.sbi.2016.11.013 · DOI
  87. 2011, RNA-mediated epigenetic programming of genome rearrangements, Annu Rev Genomics Hum Genet, 12, 367, 10.1146/annurev-genom-082410-101420 · DOI
  88. 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. 2015, Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity, Nature
  90. 2013, ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB, Mol Microbiol., 88, 443, 10.1111/mmi.12194 · DOI
  91. 2016, Naturally occurring Off-switches for CRISPR-Cas9, Cell, 167, 1829, 10.1016/j.cell.2016.11.017 · DOI
  92. 2016, Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species, Nat Microbiol., 1, 16085., 10.1038/nmicrobiol.2016.85 · DOI
  93. 2017, Recruitment of CRISPR-Cas systems by Tn7-like transposons, Proc Natl Acad Sci U S A.
  94. 2016, Type II restriction endonucleases – a historical perspective and more, Nucleic Acids Res
  95. 2015, DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes, FEMS Microbiol Rev., 39, 442, 10.1093/femsre/fuv019 · DOI
  96. 2007, Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses, Gene, 390, 3
  97. 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
  98. 2013, Structure of the CRISPR interference complex CSM reveals key similarities with cascade, Mol Cell, 52, 124, 10.1016/j.molcel.2013.08.020 · DOI · Paper page
  99. 2013, A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity, Nature, 494, 489, 10.1038/nature11927 · DOI
  100. 2008, Origins and evolution of eukaryotic RNA interference, Trends Ecol Evol., 23, 578, 10.1016/j.tree.2008.06.005 · DOI
  101. 2016, The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease, RNA, 22, 216, 10.1261/rna.039842.113 · DOI
  102. 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
  103. 2017, Diversity and evolution of class 2 CRISPR-Cas systems, Nat Rev Microbiol
  104. 2016, Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein, Science, 351, aad4234., 10.1126/science.aad4234 · DOI · Paper page
  105. 2017, On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyper-diverse, enigmatic spacer repertoires, MBio, 8, e00897-17., 10.1128/mBio.00897-17 · DOI · Paper page
  106. 2011, Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system, EMBO J
  107. 2017, Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28, Mol Cell
  108. 2013, Structure of an RNA silencing complex of the CRISPR-Cas immune system, Mol Cell, 52, 146, 10.1016/j.molcel.2013.09.008 · DOI
  109. 2013, Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus, Mol Cell, 52, 135, 10.1016/j.molcel.2013.09.013 · DOI
  110. 2014, The evolutionary journey of Argonaute proteins, Nat Struct Mol Biol., 21, 743, 10.1038/nsmb.2879 · DOI
  111. 2017, Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a, Mol Cell, 66, 221, 10.1016/j.molcel.2017.03.016 · DOI
  112. 2012, Nature and intensity of selection pressure on CRISPR-associated genes, J Bacteriol., 194, 1216, 10.1128/JB.06521-11 · DOI
  113. 2014, Comprehensive phylogenetic analysis of bacterial reverse transcriptases, PLoS One, 9, e114083., 10.1371/journal.pone.0114083 · DOI
  114. 2009, CRISPR-based adaptive and heritable immunity in prokaryotes, Trends Biochem Sci., 34, 401, 10.1016/j.tibs.2009.05.002 · DOI
  115. 2010, Toxin-antitoxin systems: why so many, what for?, Curr Opin Microbiol., 13, 781, 10.1016/j.mib.2010.10.006 · DOI
  116. 2009, Bacterial toxin-antitoxin systems: more than selfish entities?, PLoS Genet., 5, e1000437., 10.1371/journal.pgen.1000437 · DOI
  117. 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
  118. 2011, Structures of the RNA-guided surveillance complex from a bacterial immune system, Nature, 477, 486, 10.1038/nature10402 · DOI
  119. 2016, Biology and applications of CRISPR systems: harnessing nature’s toolbox for genome engineering, Cell, 164, 29
  120. 2016, Crystal structure of Cpf1 in complex with guide RNA and target DNA, Cell, 165, 949, 10.1016/j.cell.2016.04.003 · DOI
  121. 2016, PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease, Cell, 167, 1814, 10.1016/j.cell.2016.11.053 · DOI
  122. 2015, Identification and characterization of a HEPN-MNT family type II toxin-antitoxin in Shewanella oneidensis, Microb Biotechnol., 8, 961, 10.1111/1751-7915.12294 · DOI
  123. 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
  124. 2017, Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array, Nat Biotechnol., 35, 31
  125. 2015, An unexplored diversity of reverse transcriptases in bacteria, Microbiol Spectr., 3, MDNA3

Cited by

Sorted by citations

Metadata

Authors
Koonin, E. V., & Makarova, K. S.
Venue
Genome Biology and Evolution
Published
2017-09-18
Volume
9
Issue
10
Pages
2812-2825
ISSN
1759-6653
Cited by
176
References
8
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