Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering

Abstract

Deployment of RNA-guided DNA endonuclease CRISPR–Cas technology has led to radical advances in biology. As the functional diversity of CRISPR–Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, we chart progress in the RNA-targeting CRISPR–Cas (RCas) field and illustrate how continuing evolution in scientific discovery translates into applications for RNA biology and insights into mysteries, obstacles, and alternative technologies that lie ahead.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: RNA-targeting CRISPR–Cas (RCas) and parallel systems.
Fig. 2: Applications of RCas in basic biology.
Fig. 3: Opportunities for RCas in biotechnology.

References

  1. 1.

    Bertrand, E. et al. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437–445 (1998).

    CAS  PubMed  Google Scholar 

  2. 2.

    Coller, J. M., Gray, N. K. & Wickens, M. P. mRNA stabilization by poly(A) binding protein is independent of poly(A) and requires translation. Genes Dev. 12, 3226–3235 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).

    CAS  PubMed  Google Scholar 

  5. 5.

    Marraffini, L. A. CRISPR-Cas immunity in prokaryotes. Nature 526, 55–61 (2015).

    CAS  PubMed  Google Scholar 

  6. 6.

    Koonin, E. V., Makarova, K. S. & Zhang, F. Diversity, classification and evolution of CRISPR-Cas systems. Curr. Opin. Microbiol. 37, 67–78 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Classification and nomenclature of CRISPR-Cas systems: where from here? CRISPR J. 1, 325–336 (2018).

    PubMed  PubMed Central  Google Scholar 

  8. 8.

    Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262–1278 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    O’Connell, M. R. et al. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516, 263–266 (2014).

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Shmakov, S. et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat. Rev. Microbiol. 15, 169–182 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Crawley, A. B., Henriksen, J. R. & Barrangou, R. CRISPRdisco: an automated pipeline for the discovery and analysis of CRISPR-Cas systems. CRISPR J. 1, 171–181 (2018).

    PubMed  PubMed Central  Google Scholar 

  13. 13.

    Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60, 385–397 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Smargon, A. A. et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol. Cell 65, 618–630.e7 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233–239 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Yan, W. X. et al. Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol. Cell 70, 327–339.e5 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Hale, C. R. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945–956 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Staals, R. H. et al. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Mol. Cell 56, 518–530 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Tamulaitis, G. et al. Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus. Mol. Cell 56, 506–517 (2014).

    CAS  PubMed  Google Scholar 

  20. 20.

    Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Strutt, S. C., Torrez, R. M., Kaya, E., Negrete, O. A. & Doudna, J. A. RNA-dependent RNA targeting by CRISPR-Cas9. eLife 7, e32724 (2018).

    PubMed  PubMed Central  Google Scholar 

  22. 22.

    Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016).

    PubMed  PubMed Central  Google Scholar 

  23. 23.

    East-Seletsky, A. et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270–273 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Konermann, S. et al. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173, 665–676.e14 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Liu, L. et al. The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170, 714–726.e10 (2017).

    CAS  PubMed  Google Scholar 

  26. 26.

    Zhang, B. et al. Structural insights into Cas13b-guided CRISPR RNA maturation and recognition. Cell Res. 28, 1198–1201 (2018).

    PubMed  PubMed Central  Google Scholar 

  27. 27.

    Zhang, C. et al. Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cell 175, 212–223.e17 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Makarova, K. S., Wolf, Y. I., van der Oost, J. & Koonin, E. V. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol. Direct 4, 29 (2009).

    PubMed  PubMed Central  Google Scholar 

  29. 29.

    Lapinaite, A., Doudna, J. A. & Cate, J. H. D. Programmable RNA recognition using a CRISPR-associated Argonaute. Proc. Natl Acad. Sci. USA 115, 3368–3373 (2018).

    CAS  PubMed  Google Scholar 

  30. 30.

    Peters, L. & Meister, G. Argonaute proteins: mediators of RNA silencing. Mol. Cell 26, 611–623 (2007).

    CAS  PubMed  Google Scholar 

  31. 31.

    Dias, N. & Stein, C. A. Antisense oligonucleotides: basic concepts and mechanisms. Mol. Cancer Ther. 1, 347–355 (2002).

    CAS  PubMed  Google Scholar 

  32. 32.

    Rauch, S. et al. Programmable RNA-guided RNA effector proteins built from human parts. Cell 178, 122–134.e12 (2019).

    CAS  PubMed  Google Scholar 

  33. 33.

    Katrekar, D. et al. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat. Methods 16, 239–242 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Vandevenne, M. et al. Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA. Angew. Chem. Int. Edn Engl. 53, 7848–7852 (2014).

    CAS  Google Scholar 

  35. 35.

    Filipovska, A., Razif, M. F., Nygård, K. K. & Rackham, O. A universal code for RNA recognition by PUF proteins. Nat. Chem. Biol. 7, 425–427 (2011).

    CAS  PubMed  Google Scholar 

  36. 36.

    Adamala, K. P., Martin-Alarcon, D. A. & Boyden, E. S. Programmable RNA-binding protein composed of repeats of a single modular unit. Proc. Natl Acad. Sci. USA 113, E2579–E2588 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Barkan, A. & Small, I. Pentatricopeptide repeat proteins in plants. Annu. Rev. Plant Biol. 65, 415–442 (2014).

    CAS  PubMed  Google Scholar 

  38. 38.

    Abudayyeh, O. O. et al. RNA targeting with CRISPR-Cas13. Nature 550, 280–284 (2017).

    PubMed  PubMed Central  Google Scholar 

  39. 39.

    Glass, Z., Lee, M., Li, Y. & Xu, Q. Engineering the delivery system for CRISPR-based genome editing. Trends Biotechnol. 36, 173–185 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Nelles, D. A. et al. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165, 488–496 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019–1027 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Vogel, P. et al. Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs. Nat. Methods 15, 535–538 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Vogel, P. & Stafforst, T. Critical review on engineering deaminases for site-directed RNA editing. Curr. Opin. Biotechnol. 55, 74–80 (2019).

    CAS  PubMed  Google Scholar 

  44. 44.

    Merkle, T. et al. Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat. Biotechnol. 37, 133–138 (2019).

    CAS  PubMed  Google Scholar 

  45. 45.

    Qu, L. et al. Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs. Nat. Biotechnol. 37, 1059–1069 (2019).

    CAS  PubMed  Google Scholar 

  46. 46.

    Meeske, A. J., Nakandakari-Higa, S. & Marraffini, L. A. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 570, 241–245 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Batra, R. et al. Elimination of toxic microsatellite repeat expansion RNA by RNA-targeting Cas9. Cell 170, 899–912.e10 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Zhang, X. H., Tee, L. Y., Wang, X. G., Huang, Q. S. & Yang, S. H. Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol. Ther. Nucleic Acids 4, e264 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Nelson, C. E. et al. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351, 403–407 (2016).

    CAS  PubMed  Google Scholar 

  51. 51.

    Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Liu, X. M., Zhou, J., Mao, Y., Ji, Q. & Qian, S. B. Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates. Nat. Chem. Biol. 15, 865–871 (2019).

    CAS  PubMed  Google Scholar 

  53. 53.

    Wang, H. et al. CRISPR-mediated programmable 3D genome positioning and nuclear organization. Cell 175, 1405–1417.e14 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Gerstberger, S., Hafner, M. & Tuschl, T. A census of human RNA-binding proteins. Nat. Rev. Genet. 15, 829–845 (2014).

    CAS  PubMed  Google Scholar 

  55. 55.

    Van Nostrand, E.L. et al. A large-scale binding and functional map of human RNA binding proteins. Preprint at bioRxiv https://doi.org/10.1101/179648 (2018).

  56. 56.

    Myers, S. A. et al. Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling. Nat. Methods 15, 437–439 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84–87 (2014).

    CAS  PubMed  Google Scholar 

  58. 58.

    Jusiak, B., Cleto, S., Perez-Piñera, P. & Lu, T. K. Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol. 34, 535–547 (2016).

    CAS  PubMed  Google Scholar 

  59. 59.

    Wroblewska, L. et al. Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery. Nat. Biotechnol. 33, 839–841 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Gootenberg, J. S. et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356, 438–442 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    East-Seletsky, A., O’Connell, M. R., Burstein, D., Knott, G. J. & Doudna, J. A. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell 66, 373–383.e3 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Gootenberg, J. S. et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360, 439–444 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Myhrvold, C. et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science 360, 444–448 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Chen, J. S. et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436–439 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Jain, A. & Vale, R. D. RNA phase transitions in repeat expansion disorders. Nature 546, 243–247 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66.

    Lagier-Tourenne, C. et al. Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration. Proc. Natl Acad. Sci. USA 110, E4530–E4539 (2013).

    CAS  PubMed  Google Scholar 

  67. 67.

    Geary, R. S., Norris, D., Yu, R. & Bennett, C. F. Pharmacokinetics, biodistribution and cell uptake of antisense oligonucleotides. Adv. Drug Deliv. Rev. 87, 46–51 (2015).

    CAS  PubMed  Google Scholar 

  68. 68.

    Batra, R. et al. Reversal of molecular pathology by RNA-targeting Cas9 in a myotonic dystrophy mouse model. Preprint at bioRxiv https://doi.org/10.1101/184408 (2017).

  69. 69.

    Freije, C. A. et al. Programmable inhibition and detection of RNA viruses using Cas13. Mol. Cell 76, 826–837.e11 (2019).

    CAS  PubMed  Google Scholar 

  70. 70.

    Aman, R. et al. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 19, 1 (2018).

    PubMed  PubMed Central  Google Scholar 

  71. 71.

    Gantz, V. M. et al. Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proc. Natl Acad. Sci. USA 112, E6736–E6743 (2015).

    CAS  PubMed  Google Scholar 

  72. 72.

    Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2015).

    CAS  PubMed  Google Scholar 

  73. 73.

    Chen, X., Zaro, J. L. & Shen, W. C. Fusion protein linkers: property, design and functionality. Adv. Drug Deliv. Rev. 65, 1357–1369 (2013).

    CAS  PubMed  Google Scholar 

  74. 74.

    Khvorova, A. & Watts, J. K. The chemical evolution of oligonucleotide therapies of clinical utility. Nat. Biotechnol. 35, 238–248 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75.

    Staahl, B. T. et al. Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes. Nat. Biotechnol. 35, 431–434 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. 76.

    Hu, J. H., Davis, K. M. & Liu, D. R. Chemical biology approaches to genome editing: understanding, controlling, and delivering programmable nucleases. Cell Chem. Biol. 23, 57–73 (2016).

    CAS  PubMed  Google Scholar 

  77. 77.

    Oakes, B. L. et al. CRISPR-Cas9 circular permutants as programmable scaffolds for genome modification. Cell 176, 254–267.e16 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78.

    Richter, F. et al. Switchable Cas9. Curr. Opin. Biotechnol. 48, 119–126 (2017).

    CAS  PubMed  Google Scholar 

  79. 79.

    Sakamoto, K. M. et al. Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl Acad. Sci. USA 98, 8554–8559 (2001).

    CAS  PubMed  Google Scholar 

  80. 80.

    Pawluk, A., Davidson, A. R. & Maxwell, K. L. Anti-CRISPR: discovery, mechanism and function. Nat. Rev. Microbiol. 16, 12–17 (2018).

    CAS  PubMed  Google Scholar 

  81. 81.

    Larsson, E., Sander, C. & Marks, D. mRNA turnover rate limits siRNA and microRNA efficacy. Mol. Syst. Biol. 6, 433 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    Iwakawa, H. O. & Tomari, Y. The functions of MicroRNAs: mRNA decay and translational repression. Trends Cell Biol. 25, 651–665 (2015).

    CAS  PubMed  Google Scholar 

  83. 83.

    Tambe, A., East-Seletsky, A., Knott, G. J., Doudna, J. A. & O’Connell, M. R. RNA Binding and HEPN-nuclease activation are decoupled in CRISPR-Cas13a. Cell Rep. 24, 1025–1036 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84.

    Grünewald, J. et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569, 433–437 (2019).

    PubMed  PubMed Central  Google Scholar 

  85. 85.

    Chen, J. S. et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 550, 407–410 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86.

    Jung, C. et al. Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips. Cell 170, 35–47.e13 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87.

    Hu, J. H. et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556, 57–63 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88.

    Kim, H. K. et al. Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity. Nat. Biotechnol. 36, 239–241 (2018).

    CAS  PubMed  Google Scholar 

  89. 89.

    Srivastava, A. In vivo tissue-tropism of adeno-associated viral vectors. Curr. Opin. Virol. 21, 75–80 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90.

    Zincarelli, C., Soltys, S., Rengo, G. & Rabinowitz, J. E. Analysis of AAV serotypes 1-9 mediated gene expression and tropism in mice after systemic injection. Mol. Ther. 16, 1073–1080 (2008).

    CAS  PubMed  Google Scholar 

  91. 91.

    Choudhury, S. R. et al. In vivo selection yields AAV-B1 capsid for central nervous system and muscle gene therapy. Mol. Ther. 24, 1247–1257 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92.

    Song, E. et al. Surface chemistry governs cellular tropism of nanoparticles in the brain. Nat. Commun. 8, 15322 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. 93.

    Zhai, J. et al. Epidermal growth factor receptor-targeted lipid nanoparticles retain self-assembled nanostructures and provide high specificity. Nanoscale 7, 2905–2913 (2015).

    CAS  PubMed  Google Scholar 

  94. 94.

    Shah, R., Patel, T. & Freedman, J. E. Circulating extracellular vesicles in human disease. N. Engl. J. Med. 379, 958–966 (2018).

    CAS  PubMed  Google Scholar 

  95. 95.

    Kim, S. et al. CRISPR RNAs trigger innate immune responses in human cells. Genome Res. 28, 367–373 (2018).

    CAS  PubMed Central  Google Scholar 

  96. 96.

    Charlesworth, C. T. et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat. Med. 25, 249–254 (2019).

    CAS  PubMed  Google Scholar 

  97. 97.

    Wagner, D. L. et al. High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population. Nat. Med. 25, 242–248 (2019).

    CAS  PubMed  Google Scholar 

  98. 98.

    Chew, W. L. Immunity to CRISPR Cas9 and Cas12a therapeutics. Wiley Interdiscip. Rev. Syst. Biol. Med. 10, e1408 (2018).

    Google Scholar 

  99. 99.

    Ferdosi, S. R. et al. Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes. Nat. Commun. 10, 1842 (2019).

    PubMed  PubMed Central  Google Scholar 

  100. 100.

    Moreno, A. M. et al. Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy. Nat. Biomed. Eng. 3, 806–816 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. 101.

    Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V. & Koonin, E. V. Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proc. Natl Acad. Sci. USA 115, E5307–E5316 (2018).

    CAS  PubMed  Google Scholar 

  102. 102.

    Yan, W. X. et al. Functionally diverse type V CRISPR-Cas systems. Science 363, 88–91 (2019).

    CAS  PubMed  Google Scholar 

  103. 103.

    Dugar, G. et al. CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9. Mol. Cell 69, 893–905.e7 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. 104.

    Hudson, W. H. & Ortlund, E. A. The structure, function and evolution of proteins that bind DNA and RNA. Nat. Rev. Mol. Cell Biol. 15, 749–760 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. 105.

    Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    CAS  PubMed  Google Scholar 

  106. 106.

    Huang, P. S., Boyken, S. E. & Baker, D. The coming of age of de novo protein design. Nature 537, 320–327 (2016).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors wish to acknowledge J. Schwartz and J. Schmok for their helpful comments in preparing this manuscript. G.W.Y. is supported by grants from the NIH (NS103172, MH107367, EY029166, HG009889, HG004659), from TargetALS, the ALS Association and a Chan-Zuckerberg Initiative Neurodegeneration Challenge Network grant.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Gene W. Yeo.

Ethics declarations

Competing interests

A.A.S. declares inventorship on the following published patents, applied for by the Broad Institute of MIT and Harvard and the Massachusetts Institute of Technology: WO2018035250A1 on methods for bioinformatic discovery of class 2 CRISPR–Cas systems; WO2017070605 on systems, methods, and compositions for targeting nucleic acids with type VI-B CRISPR–Cas systems. G.W.Y is co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Locana and Eclipse BioInnovations. G.W.Y. is a Distinguished Visiting Professor at the National University of Singapore. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Smargon, A.A., Shi, Y.J. & Yeo, G.W. RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering. Nat Cell Biol 22, 143–150 (2020). https://doi.org/10.1038/s41556-019-0454-7

Download citation

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing