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Cellular and Molecular Life Sciences

, Volume 76, Issue 24, pp 4861–4867 | Cite as

Programmable RNA manipulation in living cells

  • Yu Pei
  • Mingxing LuEmail author
Review

Abstract

RNAs are responsible for mediating genetic information flow within the cell. RNA splicing, modification, trafficking, translation, and stability are all controlled at the transcript level. However, biological tools to study and manipulate them in a programmable fashion are currently limited. In this review, we summarize recent advances regarding available RNA-targeting systems discovered so far, including CRISPR-based technologies—Cas9 and Cas13, and programmable RNA-binding proteins—PUF and PPR. These tools allow transcript-specific manipulation in gene expression.

Keywords

CRISPR RNA-binding proteins Cas9 Cas13 PUF PPR APEX2 bioID 

Notes

Acknowledgements

Dr. Jianling Xie for comments.

Author contributions

MXL conceived the ideas and wrote the manuscript together with YP.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

References

  1. 1.
    Knott GJ, Doudna JA (2018) CRISPR–Cas guides the future of genetic engineering. Science 361:866–869PubMedPubMedCentralGoogle Scholar
  2. 2.
    Wang H, La Russa M, Qi LS (2016) CRISPR/Cas9 in genome editing and beyond. Annu Rev Biochem 85:227–264PubMedGoogle Scholar
  3. 3.
    Komor AC, Badran AH, Liu DR (2017) Leading edge CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 168:20–36PubMedGoogle Scholar
  4. 4.
    Schwanhüusser B et al (2011) Global quantification of mammalian gene expression control. Nature 473:337–342Google Scholar
  5. 5.
    Liu Y, Beyer A, Aebersold R (2016) On the dependency of cellular protein levels on mRNA abundance. Cell 165:535–550PubMedGoogle Scholar
  6. 6.
    Levin AA (2019) Treating disease at the RNA level with oligonucleotides. N Engl J Med 380:57–70PubMedGoogle Scholar
  7. 7.
    Lieberman J (2018) Tapping the RNA world for therapeutics. Nat Struct Mol Biol 25:357–364PubMedPubMedCentralGoogle Scholar
  8. 8.
    Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA–chromatin interactions. Mol Cell 44:667–678PubMedPubMedCentralGoogle Scholar
  9. 9.
    Simon MD et al (2011) The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci 108:20497–20502PubMedGoogle Scholar
  10. 10.
    Engreitz JM et al (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341:1237973PubMedPubMedCentralGoogle Scholar
  11. 11.
    Chu C, Spitale RC, Chang HY (2015) Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol 22:29–35PubMedGoogle Scholar
  12. 12.
    McHugh CA et al (2015) The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521:232–236PubMedPubMedCentralGoogle Scholar
  13. 13.
    Munschauer M et al (2018) The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature 561:132–136PubMedGoogle Scholar
  14. 14.
    Shmakov S et al (2015) Discovery and functional characterization of diverse class 2 CRISPR–Cas systems. Mol Cell 60:385–397PubMedPubMedCentralGoogle Scholar
  15. 15.
    Hille F et al (2018) The biology of CRISPR–Cas: backward and forward. Cell 172:1239–1259PubMedGoogle Scholar
  16. 16.
    Terns MP (2018) CRISPR-based technologies: impact of RNA-targeting systems. Mol Cell 72:404–412PubMedPubMedCentralGoogle Scholar
  17. 17.
    Dugar G et al (2018) CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9. Mol Cell 69:893–905.e7PubMedPubMedCentralGoogle Scholar
  18. 18.
    Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA (2018) RNA-dependent RNA targeting by CRISPR–Cas9. Elife 7:1–17Google Scholar
  19. 19.
    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 69:906–914.e4PubMedPubMedCentralGoogle Scholar
  20. 20.
    Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS (2013) A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497:254–257PubMedPubMedCentralGoogle Scholar
  21. 21.
    Yang L et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826PubMedPubMedCentralGoogle Scholar
  22. 22.
    Fisher M et al (2013) Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis 51:835–843PubMedPubMedCentralGoogle Scholar
  23. 23.
    Yeh J-RJ et al (2013) Efficient genome editing in zebrafish using a CRISPR–Cas system. Nat Biotechnol 31:227–229PubMedPubMedCentralGoogle Scholar
  24. 24.
    Sander JD, Joung JK (2014) CRISPR–Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–350PubMedPubMedCentralGoogle Scholar
  25. 25.
    Li Y et al (2013) Heritable gene targeting in the mouse and rat using a CRISPR–Cas system. Nat Biotechnol.  https://doi.org/10.1038/nbt.2661 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Yang D et al (2014) Effective gene targeting in rabbits using RNA-guided Cas9 nucleases. J Mol Cell Biol 6:97–99PubMedPubMedCentralGoogle Scholar
  27. 27.
    O’Connell MR et al (2014) Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516:263–266PubMedPubMedCentralGoogle Scholar
  28. 28.
    Nelles DA et al (2016) Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165:488–496PubMedPubMedCentralGoogle Scholar
  29. 29.
    Batra R et al (2017) Elimination of toxic microsatellite repeat expansion RNA by RNA-targeting Cas9. Cell 170:899–912.e10PubMedPubMedCentralGoogle Scholar
  30. 30.
    Liu Y, Chen Z, He A, Zhan Y, Li J, Liu L, Wu H, Zhuang C, Lin J, Zhang Q, Huang W (2016) Targeting cellular mRNAs translation by CRISPR-Cas9. Scientific Reports 6(1):29652PubMedPubMedCentralGoogle Scholar
  31. 31.
    Hale CR et al (2009) RNA-guided RNA cleavage by a CRISPR RNA–Cas protein complex. Cell 139:945–956PubMedPubMedCentralGoogle Scholar
  32. 32.
    Neupane N et al (2014) RNA targeting by the type III-A CRISPR–Cas Csm complex of Thermus thermophilus. Mol Cell 56:518–530PubMedPubMedCentralGoogle Scholar
  33. 33.
    Samai P, Pyenson N, Hatoum-Aslan A, Correspondence LAM (2015) Co-transcriptional DNA and RNA cleavage during type III CRISPR–Cas immunity. Cell 161:1164–1174PubMedPubMedCentralGoogle Scholar
  34. 34.
    Tamulaitis G et al (2014) Programmable RNA shredding by the type III-A CRISPR–Cas system of Streptococcus thermophilus. Mol Cell 56:506–517PubMedGoogle Scholar
  35. 35.
    Abudayyeh OO et al (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353:aaf5573PubMedPubMedCentralGoogle Scholar
  36. 36.
    East-Seletsky A et al (2016) Two distinct RNase activities of CRISPR–C2c2 enable guide-RNA processing and RNA detection. Nature 538:270–273PubMedPubMedCentralGoogle Scholar
  37. 37.
    East-Seletsky A, O’Connell MR, Burstein D, Knott GJ, Doudna JA (2017) RNA targeting by functionally orthogonal type VI-A CRISPR–Cas enzymes. Mol Cell 66:373–383.e3PubMedPubMedCentralGoogle Scholar
  38. 38.
    Knott GJ et al (2017) Guide-bound structures of an RNA-targeting A-cleaving CRISPR–Cas13a enzyme. Nat Struct Mol Biol.  https://doi.org/10.1038/nsmb.3466 CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Liu L et al (2017) Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168:121–134.e12PubMedGoogle Scholar
  40. 40.
    Liu L et al (2017) The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170:714–726.e10PubMedGoogle Scholar
  41. 41.
    Effectors TVC et al (2018) Transcriptome engineering with RNA-targeting article transcriptome engineering with RNA-targeting. Cell 173:1–12Google Scholar
  42. 42.
    Zhang C et al (2018) Structural basis for the RNA-guided ribonuclease activity of CRISPR–Cas13d. Cell 175:212–223.e17PubMedPubMedCentralGoogle Scholar
  43. 43.
    Yan WX et al (2018) Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol Cell 70:327–339.e5PubMedPubMedCentralGoogle Scholar
  44. 44.
    Abudayyeh OO et al (2017) RNA targeting with CRISPR–Cas13. Nature.  https://doi.org/10.1038/nature24049 CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Cox DBT et al (2017) RNA editing with CRISPR–Cas13. Science 0180:eaaq0180Google Scholar
  46. 46.
    Gootenberg JS et al (2017) Nucleic acid detection with CRISPR–Cas13a/C2c2. Science 356:438–442PubMedPubMedCentralGoogle Scholar
  47. 47.
    Smargon AA et al (2017) Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell 65:618–630.e7PubMedPubMedCentralGoogle Scholar
  48. 48.
    Rauch S, He C, Dickinson BC (2018) Targeted m6A reader proteins to study epitranscriptomic regulation of single RNAs. J Am Chem Soc 140:11974–11981PubMedPubMedCentralGoogle Scholar
  49. 49.
    Wang X, McLachlan J, Zamore PD, Hall TMT (2002) Modular recognition of RNA by a human Pumilio-homology domain. Cell 110:501–512PubMedGoogle Scholar
  50. 50.
    Wang X, Zamore PD, Hall TMT (2001) Crystal structure of a Pumilio homology domain. Mol Cell 7:855–865PubMedGoogle Scholar
  51. 51.
    Cheong C-G, Hall TMT (2006) Engineering RNA sequence specificity of Pumilio repeats. Proc Natl Acad Sci 103:13635–13639PubMedGoogle Scholar
  52. 52.
    Choudhury R, Tsai YS, Dominguez D, Wang Y, Wang Z (2012) Engineering RNA endonucleases with customized sequence specificities. Nat Commun 3:1147–1148PubMedPubMedCentralGoogle Scholar
  53. 53.
    Campbell ZT, Valley CT, Wickens M (2014) A protein-RNA specificity code enables targeted activation of an endogenous human transcript. Nat Struct Mol Biol 21:732–738PubMedPubMedCentralGoogle Scholar
  54. 54.
    Wang Y, Ma M, Xiao X, Wang Z (2012) Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat Struct Mol Biol 19:1044–1053PubMedPubMedCentralGoogle Scholar
  55. 55.
    Wang Y, Cheong CG, Hall TMT, Wang Z (2009) Engineering splicing factors with designed specificities. Nat Methods 6:825–830PubMedPubMedCentralGoogle Scholar
  56. 56.
    Filipovska A, Razif MFM, NygÅrd KKA, Rackham O (2011) A universal code for RNA recognition by PUF proteins. Nat Chem Biol 7:425–427PubMedGoogle Scholar
  57. 57.
    Dong S et al (2011) Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains. J Biol Chem 286:26732–26742PubMedPubMedCentralGoogle Scholar
  58. 58.
    Zhao Y-Y et al (2018) Expanding RNA binding specificity and affinity of engineered PUF domains. Nucleic Acids Res 46:4771–4782PubMedPubMedCentralGoogle Scholar
  59. 59.
    Filipovska A, Oliver R (2013) Pentatricopeptide repeats introduction: modularity in molecular recognition. RNA Biol 10:1426–1432PubMedPubMedCentralGoogle Scholar
  60. 60.
    Coquille S et al (2014) An artificial PPR scaffold for programmable RNA recognition. Nat Commun 5:5729.  https://doi.org/10.1038/ncomms6729 CrossRefPubMedGoogle Scholar
  61. 61.
    Hall TMT (2016) De-coding and re-coding RNA recognition by PUF and PPR repeat proteins. Curr Opin Struct Biol 36:116–121PubMedGoogle Scholar
  62. 62.
    Barkan A, Small I (2014) Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol 65:415–442PubMedGoogle Scholar
  63. 63.
    Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13:663–670PubMedGoogle Scholar
  64. 64.
    Yin P et al (2013) Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature 504:168–171PubMedGoogle Scholar
  65. 65.
    Gully BS et al (2015) The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA. Nucleic Acids Res 43:1918–1926PubMedPubMedCentralGoogle Scholar
  66. 66.
    Wei H, Wang Z (2015) Engineering RNA-binding proteins with diverse activities. Wiley Interdiscip Rev RNA 6:597–613PubMedGoogle Scholar
  67. 67.
    Cooke A, Prigge A, Opperman L, Wickens M (2011) Targeted translational regulation using the PUF protein family scaffold. Proc Natl Acad Sci 108:15870–15875PubMedGoogle Scholar
  68. 68.
    Cao J, Arha M, Sudrik C, Schaffer DV, Kane RS (2014) Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. Angew Chemie Int Ed 53:4900–4904Google Scholar
  69. 69.
    Abil Z, Denard CA, Zhao H (2014) Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA. J Biol Eng 8:1–11Google Scholar
  70. 70.
    Lapinaite A, Doudna JA, Cate JHD (2018) Programmable RNA recognition using a CRISPR-associated Argonaute. Proc Natl Acad Sci 115:3368–3373PubMedGoogle Scholar
  71. 71.
    Dayeh DM, Cantara WA, Kitzrow JP, Musier-Forsyth K, Nakanishi K (2018) Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA. Nucleic Acids Res 46:98Google Scholar
  72. 72.
    Ramanathan M et al (2018) RNA–protein interaction detection in living cells. Nat Methods.  https://doi.org/10.1038/nmeth.4601 CrossRefPubMedPubMedCentralGoogle Scholar
  73. 73.
    Rauch S et al (2019) Programmable RNA-guided RNA effector proteins built from human parts. Cell 178:122–134.e12PubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden
  2. 2.Department of Biomedical Sciences, College of Veterinary Medicine and Life SciencesCity University of Hong KongKowloon TongHong Kong

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