1932

Abstract

CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a -activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances.

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2021-11-23
2024-12-05
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Literature Cited

  1. 1. 
    Acharya S, Mishra A, Paul D, Ansari AH, Azhar M et al. 2019. Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. PNAS 116:4220959–68
    [Google Scholar]
  2. 2. 
    Anders C, Niewoehner O, Duerst A, Jinek M. 2014. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513:7519569–73
    [Google Scholar]
  3. 3. 
    Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:58191709–12
    [Google Scholar]
  4. 4. 
    Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ et al. 2017. Elimination of toxic microsatellite repeat expansion RNA by RNA-targeting Cas9. Cell 170:5899–912.e10
    [Google Scholar]
  5. 5. 
    Briner AE, Donohoue PD, Gomaa AA, Selle K, Slorach EM et al. 2014. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol. Cell 56:2333–39
    [Google Scholar]
  6. 6. 
    Briner AE, Henriksen ED, Barrangou R. 2016. Prediction and validation of native and engineered Cas9 guide sequences. Cold Spring Harb. Protoc. 2016:7628–634
    [Google Scholar]
  7. 7. 
    Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH et al. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:5891960–64
    [Google Scholar]
  8. 8. 
    Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K et al. 2017. New CRISPR-Cas systems from uncultivated microbes. Nature 542:7640237–41
    [Google Scholar]
  9. 9. 
    Carte J, Pfister NT, Compton MM, Terns RM, Terns MP. 2010. Binding and cleavage of CRISPR RNA by Cas6. RNA 16:112181–88
    [Google Scholar]
  10. 10. 
    Carte J, Wang R, Li H, Terns RM, Terns MP. 2008. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 22:243489–96
    [Google Scholar]
  11. 11. 
    Chang N, Sun C, Gao L, Zhu D, Xu X et al. 2013. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23:4465–72
    [Google Scholar]
  12. 12. 
    Chen F, Ding X, Feng Y, Seebeck T, Jiang Y, Davis GD. 2017. Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting. Nat. Commun. 8:14958
    [Google Scholar]
  13. 13. 
    Chen JS, Ma E, Harrington LB, Da Costa M, Tian X et al. 2018. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360:6387436–39
    [Google Scholar]
  14. 14. 
    Cho SW, Kim S, Kim JM, Kim J-S. 2013. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 31:3230–32
    [Google Scholar]
  15. 15. 
    Chylinski K, Le Rhun A, Charpentier E 2013. The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol 10:5726–37
    [Google Scholar]
  16. 16. 
    Chyou T-Y, Brown CM. 2019. Prediction and diversity of tracrRNAs from type II CRISPR-Cas systems. RNA Biol 16:4423–34
    [Google Scholar]
  17. 17. 
    Cong L, Ran FA, Cox D, Lin S, Barretto R et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:6121819–23
    [Google Scholar]
  18. 18. 
    Cress BF, Toparlak ÖD, Guleria S, Lebovich M, Stieglitz JT et al. 2015. CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli. ACS Synth. Biol. 4:9987–1000
    [Google Scholar]
  19. 19. 
    Creutzburg SCA, Wu WY, Mohanraju P, Swartjes T, Alkan F et al. 2020. Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a. Nucleic Acids Res 48:63228–43
    [Google Scholar]
  20. 20. 
    Dahlman JE, Abudayyeh OO, Joung J, Gootenberg JS, Zhang F, Konermann S. 2015. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat. Biotechnol. 33:111159–61
    [Google Scholar]
  21. 21. 
    Dang Y, Jia G, Choi J, Ma H, Anaya E et al. 2015. Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency. Genome Biol 16:1280
    [Google Scholar]
  22. 22. 
    Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y et al. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:7340602–7
    [Google Scholar]
  23. 23. 
    DeWeirdt PC, Sanson KR, Sangree AK, Hegde M, Hanna RE et al. 2021. Optimization of AsCas12a for combinatorial genetic screens in human cells. Nat. Biotechnol. 39:194–104
    [Google Scholar]
  24. 24. 
    Dong C, Fontana J, Patel A, Carothers JM, Zalatan JG. 2018. Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. Nat. Commun. 9:12489
    [Google Scholar]
  25. 25. 
    Dooley SK, Baken EK, Moss WN, Howe A, Young JK. 2020. Identification and evolution of Cas9 tracrRNAs. CRISPR J 4:3438–47
    [Google Scholar]
  26. 26. 
    Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R et al. 2013. High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLOS Genet 9:5e1003495
    [Google Scholar]
  27. 27. 
    Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU et al. 2018. CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9. Mol. Cell 69:5893–905.e7
    [Google Scholar]
  28. 28. 
    Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. 2013. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10:111116–21
    [Google Scholar]
  29. 29. 
    Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lécrivain A-L et al. 2014. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res 42:42577–90
    [Google Scholar]
  30. 30. 
    Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E 2016. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532:7600517–21
    [Google Scholar]
  31. 31. 
    Galizi R, Duncan JN, Rostain W, Quinn CM, Storch M et al. 2020. Engineered RNA-interacting CRISPR guide RNAs for genetic sensing and diagnostics. CRISPR J 3:5398–408
    [Google Scholar]
  32. 32. 
    Gao Y, Zhao Y. 2014. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J. Integr. Plant Biol. 56:4343–49
    [Google Scholar]
  33. 33. 
    Gasiunas G, Young JK, Karvelis T, Kazlauskas D, Urbaitis T et al. 2020. A catalogue of biochemically diverse CRISPR-Cas9 orthologs. Nat. Commun. 11:15512
    [Google Scholar]
  34. 34. 
    Gratz SJ, Cummings AM, Nguyen JN, Hamm DC, Donohue LK et al. 2013. Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194:41029–35
    [Google Scholar]
  35. 35. 
    Hanewich-Hollatz MH, Chen Z, Hochrein LM, Huang J, Pierce NA. 2019. Conditional guide RNAs: programmable conditional regulation of CRISPR/Cas function in bacterial and mammalian cells via dynamic RNA nanotechnology. ACS Cent. Sci. 5:71241–49
    [Google Scholar]
  36. 36. 
    Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E et al. 2018. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:6416839–42
    [Google Scholar]
  37. 37. 
    Harrington LB, Ma E, Chen JS, Witte IP, Gertz D et al. 2020. A scoutRNA is required for some type V CRISPR-Cas systems. Mol. Cell 79:3416–24.e5
    [Google Scholar]
  38. 38. 
    Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. 2010. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329:59971355–58
    [Google Scholar]
  39. 39. 
    Heler R, Samai P, Modell JW, Weiner C, Goldberg GW et al. 2015. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 519:7542199–202
    [Google Scholar]
  40. 40. 
    Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M et al. 2016. Structure and engineering of Francisella novicida Cas9. Cell 164:5950–61
    [Google Scholar]
  41. 41. 
    Hoikkala V, Ravantti J, Díez-Villaseñor C, Tiirola M, Conrad RA et al. 2021. Cooperation between different CRISPR-Cas types enables adaptation in an RNA-targeting system. mBio 12:2e03338-20
    [Google Scholar]
  42. 42. 
    Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31:9827–32
    [Google Scholar]
  43. 43. 
    Huai C, Li G, Yao R, Zhang Y, Cao M et al. 2017. Structural insights into DNA cleavage activation of CRISPR-Cas9 system. Nat. Commun. 8:11375
    [Google Scholar]
  44. 44. 
    Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ et al. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31:3227–29
    [Google Scholar]
  45. 45. 
    Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K et al. 2016. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351:6275867–71
    [Google Scholar]
  46. 46. 
    Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. 2015. A Cas9-guide RNA complex preorganized for target DNA recognition. Science 348:62421477–81
    [Google Scholar]
  47. 47. 
    Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. 2013. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31:3233–39
    [Google Scholar]
  48. 48. 
    Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T et al. 2021. Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science 372:6545941–48
    [Google Scholar]
  49. 49. 
    Jin M, Garreau de Loubresse N, Kim Y, Kim J, Yin P. 2019. Programmable CRISPR-Cas repression, activation, and computation with sequence-independent targets and triggers. ACS Synth. Biol. 8:71583–89
    [Google Scholar]
  50. 50. 
    Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:6096816–21
    [Google Scholar]
  51. 51. 
    Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J 2013. RNA-programmed genome editing in human cells. eLife 2:e00471
    [Google Scholar]
  52. 52. 
    Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E et al. 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343:61761247997
    [Google Scholar]
  53. 53. 
    Kabadi AM, Ousterout DG, Hilton IB, Gersbach CA. 2014. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res 42:19e147
    [Google Scholar]
  54. 54. 
    Karvelis T, Bigelyte G, Young JK, Hou Z, Zedaveinyte R et al. 2020. PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res 48:95016–23
    [Google Scholar]
  55. 55. 
    Karvelis T, Gasiunas G, Miksys A, Barrangou R, Horvath P, Siksnys V. 2013. crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol 10:5841–51
    [Google Scholar]
  56. 56. 
    Karvelis T, Young JK, Siksnys V. 2019. A pipeline for characterization of novel Cas9 orthologs. Methods Enzymol 616:219–40
    [Google Scholar]
  57. 57. 
    Kiani S, Chavez A, Tuttle M, Hall RN, Chari R et al. 2015. Cas9 gRNA engineering for genome editing, activation and repression. Nat. Methods 12:111051–54
    [Google Scholar]
  58. 58. 
    Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH 2019. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature 571:219–25
    [Google Scholar]
  59. 59. 
    Koonin EV, Makarova KS. 2013. CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol 10:5679–86
    [Google Scholar]
  60. 60. 
    Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH et al. 2019. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat. Commun. 10:12127
    [Google Scholar]
  61. 61. 
    Leenay RT, Beisel CL. 2017. Deciphering, communicating, and engineering the CRISPR PAM. J. Mol. Biol. 429:2177–91
    [Google Scholar]
  62. 62. 
    Leenay RT, Vento JM, Shah M, Martino ME, Leulier F, Beisel CL. 2019. Genome editing with CRISPR-Cas9 in Lactobacillus plantarum revealed that editing outcomes can vary across strains and between methods. Biotechnol. J. 14:3e1700583
    [Google Scholar]
  63. 63. 
    Li Z, Zhang H, Xiao R, Han R, Chang L 2021. Cryo-EM structure of the RNA-guided ribonuclease Cas12g. Nat. Chem. Biol. 17:387–93
    [Google Scholar]
  64. 64. 
    Lian J, HamediRad M, Hu S, Zhao H. 2017. Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system. Nat. Commun. 8:11688
    [Google Scholar]
  65. 65. 
    Liao C, Ttofali F, Slotkowski RA, Denny SR, Cecil TD et al. 2019. Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis. Nat. Commun. 10:12948
    [Google Scholar]
  66. 66. 
    Liu G, Yin K, Zhang Q, Gao C, Qiu J-L. 2019. Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo. Genome Biol 20:1145
    [Google Scholar]
  67. 67. 
    Liu J-J, Orlova N, Oakes BL, Ma E, Spinner HB et al. 2019. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566:7743218–23
    [Google Scholar]
  68. 68. 
    Liu L, Chen P, Wang M, Li X, Wang J et al. 2017. C2c1-sgRNA complex structure reveals RNA-guided DNA cleavage mechanism. Mol. Cell 65:2310–22
    [Google Scholar]
  69. 69. 
    Ma H, Tu L-C, Naseri A, Chung Y-C, Grunwald D et al. 2018. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat. Methods 15:11928–31
    [Google Scholar]
  70. 70. 
    Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS et al. 2020. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18:267–83
    [Google Scholar]
  71. 71. 
    Mali P, Yang L, Esvelt KM, Aach J, Guell M et al. 2013. RNA-guided human genome engineering via Cas9. Science 339:6121823–26
    [Google Scholar]
  72. 72. 
    McCarty NS, Graham AE, Studená L, Ledesma-Amaro R. 2020. Multiplexed CRISPR technologies for gene editing and transcriptional regulation. Nat. Commun. 11:11281
    [Google Scholar]
  73. 73. 
    Meeske AJ, Marraffini LA. 2018. RNA guide complementarity prevents self-targeting in type VI CRISPR systems. Mol. Cell 71:5791–801.e3
    [Google Scholar]
  74. 74. 
    Mullally G, van Aelst K, Naqvi MM, Diffin FM, Karvelis T et al. 2020. 5′ modifications to CRISPR-Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage. Nucleic Acids Res 48:126811–23
    [Google Scholar]
  75. 75. 
    Mullard A. 2020. CRISPR pioneers win Nobel prize. Nat. Rev. Drug Discov. 19:12827
    [Google Scholar]
  76. 76. 
    Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR et al. 2018. Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat. Biotechnol. 36:2179–89
    [Google Scholar]
  77. 77. 
    Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165:2488–96
    [Google Scholar]
  78. 78. 
    Nicholson AW. 2014. Ribonuclease III mechanisms of double-stranded RNA cleavage. WIREs RNA 5:131–48
    [Google Scholar]
  79. 79. 
    Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B et al. 2015. Crystal structure of Staphylococcus aureus Cas9. Cell 162:51113–26
    [Google Scholar]
  80. 80. 
    Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI et al. 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156:5935–49
    [Google Scholar]
  81. 81. 
    O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. 2014. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516:7530263–66
    [Google Scholar]
  82. 82. 
    Peters JE, Makarova KS, Shmakov S, Koonin EV. 2017. Recruitment of CRISPR-Cas systems by Tn7-like transposons. PNAS 114:E735866
    [Google Scholar]
  83. 83. 
    Pickar-Oliver A, Gersbach CA 2019. The next generation of CRISPR-Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 20:8490–507
    [Google Scholar]
  84. 84. 
    Port F, Bullock SL. 2016. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat. Methods 13:10852–54
    [Google Scholar]
  85. 85. 
    Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. 2015. Cas9-mediated targeting of viral RNA in eukaryotic cells. PNAS 112:196164–69
    [Google Scholar]
  86. 86. 
    Ratner HK, Escalera-Maurer A, Le Rhun A, Jaggavarapu S, Wozniak JE et al. 2019. Catalytically active Cas9 mediates transcriptional interference to facilitate bacterial virulence. Mol. Cell 75:3498–510.e5
    [Google Scholar]
  87. 87. 
    Reimann V, Alkhnbashi OS, Saunders SJ, Scholz I, Hein S et al. 2017. Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs. Nucleic Acids Res 45:2915–25
    [Google Scholar]
  88. 88. 
    Reis AC, Halper SM, Vezeau GE, Cetnar DP, Hossain A et al. 2019. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nat. Biotechnol. 37:111294–301
    [Google Scholar]
  89. 89. 
    Rousseau BA, Hou Z, Gramelspacher MJ, Zhang Y. 2018. Programmable RNA cleavage and recognition by a natural CRISPR-Cas9 system from Neisseria meningitidis. Mol. Cell 69:5906–14.e4
    [Google Scholar]
  90. 90. 
    Saito M, Ladha A, Strecker J, Faure G, Neumann E et al. 2021. Dual modes of CRISPR-associated transposon homing. Cell 184:2441–53.e18
    [Google Scholar]
  91. 91. 
    Sakuma T, Nishikawa A, Kume S, Chayama K, Yamamoto T. 2014. Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system. Sci. Rep. 4:5400
    [Google Scholar]
  92. 92. 
    Sampson TR, Saroj SD, Llewellyn AC, Tzeng Y-L, Weiss DS. 2013. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497:7448254–57
    [Google Scholar]
  93. 93. 
    Scott T, Urak R, Soemardy C, Morris KV. 2019. Improved Cas9 activity by specific modifications of the tracrRNA. Sci. Rep. 9:116104
    [Google Scholar]
  94. 94. 
    Sharma CM, Vogel J. 2014. Differential RNA-seq: the approach behind and the biological insight gained. Curr. Opin. Microbiol. 19:97–105
    [Google Scholar]
  95. 95. 
    Shen B, Zhang J, Wu H, Wang J, Ma K et al. 2013. Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res 23:5720–23
    [Google Scholar]
  96. 96. 
    Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS et al. 2015. Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems. Mol. Cell 60:3385–97
    [Google Scholar]
  97. 97. 
    Siu K-H, Chen W 2019. Riboregulated toehold-gated gRNA for programmable CRISPR-Cas9 function. Nat. Chem. Biol. 15:3217–20
    [Google Scholar]
  98. 98. 
    Storz G, Vogel J, Wassarman KM. 2011. Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell 43:6880–91
    [Google Scholar]
  99. 99. 
    Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B et al. 2019. Engineering of CRISPR-Cas12b for human genome editing. Nat. Commun. 10:1212
    [Google Scholar]
  100. 100. 
    Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS et al. 2019. RNA-guided DNA insertion with CRISPR-associated transposases. Science 365:644848–53
    [Google Scholar]
  101. 101. 
    Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA. 2018. RNA-dependent RNA targeting by CRISPR-Cas9. eLife 7:e32724
    [Google Scholar]
  102. 102. 
    Sun W, Yang J, Cheng Z, Amrani N, Liu C et al. 2019. Structures of Neisseria meningitidis Cas9 complexes in catalytically poised and anti-CRISPR-inhibited states. Mol. Cell 76:6938–52.e5
    [Google Scholar]
  103. 103. 
    Takeda SN, Nakagawa R, Okazaki S, Hirano H, Kobayashi K et al. 2021. Structure of the miniature type V-F CRISPR-Cas effector enzyme. Mol. Cell 81:3558–70.e3
    [Google Scholar]
  104. 104. 
    Tang W, Hu JH, Liu DR. 2017. Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation. Nat. Commun. 8:15939
    [Google Scholar]
  105. 105. 
    Teng F, Cui T, Feng G, Guo L, Xu K et al. 2018. Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discov 4:63
    [Google Scholar]
  106. 106. 
    Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V et al. 2014. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol. 32:6569–76
    [Google Scholar]
  107. 107. 
    Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW et al. 2013. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:4910–18
    [Google Scholar]
  108. 108. 
    Wei Y, Terns RM, Terns MP. 2015. Cas9 function and host genome sampling in Type II-A CRISPR–Cas adaptation. Genes Dev 29:4356–61
    [Google Scholar]
  109. 109. 
    Wimmer F, Beisel CL. 2019. CRISPR-Cas systems and the paradox of self-targeting spacers. Front. Microbiol. 10:3078
    [Google Scholar]
  110. 110. 
    Workman RE, Pammi T, Nguyen BTK, Graeff LW, Smith E et al. 2021. A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR-Cas expression. Cell 184:3675–88.e19
    [Google Scholar]
  111. 111. 
    Xiao R, Li Z, Wang S, Han R, Chang L 2021. Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR–Cas12f nuclease. Nucleic Acids Res. 49:4120–28
    [Google Scholar]
  112. 112. 
    Xie K, Minkenberg B, Yang Y. 2015. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. PNAS 112:113570–75
    [Google Scholar]
  113. 113. 
    Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran FA et al. 2017. Crystal structure of the minimal Cas9 from Campylobacter jejuni reveals the molecular diversity in the CRISPR-Cas9 systems. Mol. Cell 65:61109–21.e3
    [Google Scholar]
  114. 114. 
    Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E et al. 2019. Functionally diverse type V CRISPR-Cas systems. Science 363:642288–91
    [Google Scholar]
  115. 115. 
    Yang H, Gao P, Rajashankar KR, Patel DJ. 2016. PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease. Cell 167:71814–28.e12
    [Google Scholar]
  116. 116. 
    Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH et al. 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160:1–2339–50
    [Google Scholar]
  117. 117. 
    Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS et al. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:3759–71
    [Google Scholar]
  118. 118. 
    Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS et al. 2013. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol. Cell 50:4488–503
    [Google Scholar]
  119. 119. 
    Zhang Y, Zhang H, Xu X, Wang Y, Chen W et al. 2020. Catalytic-state structure and engineering of Streptococcus thermophilus Cas9. Nat. Catal. 3:10813–23
    [Google Scholar]
  120. 120. 
    Zuo Z, Zolekar A, Babu K, Lin VJ, Hayatshahi HS et al. 2019. Structural and functional insights into the catalytic state of Cas9 HNH nuclease domain. eLife 8:e46500
    [Google Scholar]
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