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Cited by 176CRISPR and Genetic EngineeringRNA regulation and diseaseRNA Interference and Gene Delivery

Compact RNA editors with small Cas13 proteins

Open access
Kannan, Soumya, Altae-Tran, Han, Jin, Xin, Madigan, Victoria J., Oshiro, Rachel, Makarova, Kira S., Koonin, Eugene V., Zhang, Feng·2022·Nature Biotechnology
DOI 10.1038/s41587-021-01030-2PMC PMC8929162
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Abstract

CRISPR-Cas13 systems have been developed for precise RNA editing, and can potentially be used therapeutically when temporary changes are desirable or when DNA editing is challenging. We have identified and characterized an ultrasmall family of Cas13b proteins-Cas13bt-that can mediate mammalian transcript knockdown. We have engineered compact variants of REPAIR and RESCUE RNA editors by functionalizing Cas13bt with adenosine and cytosine deaminase domains, and demonstrated packaging of the editors within a single adeno-associated virus.

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  • Hypercompact Cas13bt3 (Cas13X) enzymes range at 775 amino acids.

    “More recently, hypercompact Cas13bt3 (also reported as Cas13X) enzymes were described, ranging even smaller at 775 amino acids (11, 12).”

    From Characterization of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina (2024) · cites this paper as [12]

    The Abstract describes Cas13bt proteins as ultra-compact and gives 775–804 amino acids for the smallest members; it also identifies Cas13bt3 as one of the proteins studied. It does not establish that Cas13bt3 specifically is 775 amino acids or that Cas13bt3 is also called Cas13X. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

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References 35 · Cited by 176

Research works printed but not linked: 30

  1. [1]Terns MP CRISPR-Based Technologies: Impact of RNA-Targeting Systems. Mol. Cell 72, 404– 412 (2018). 30388409 PMC6239212
  2. [2]Cox DBT RNA editing with CRISPR-Cas13. Science (80-.). 1027, 1019– 1027 (2017). PMC5793859 29070703
  3. [3]Abudayyeh OO A cytosine deaminase for programmable single-base RNA editing. Science (80-.). 365, 382– 386 (2019). PMC6956565 31296651
  4. [4]Dong JY, Fan PD & Frizzel RA Quantitative analysis of the packaging capacity of recombinant adeno-associated virus. Hum. Gene Ther 7, 2101– 12 (1996). 8934224
  5. [6]Smargon AA 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). 28065598 PMC5432119
  6. [7]Abudayyeh OO C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. 5573, 1– 17 (2016). PMC5127784 27256883
  7. [8]Gootenberg JS Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a and Csm6. Science (80-.). 360, 439– 444 (2018). PMC5961727 29449508
  8. [9]Matthews MM Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat. Struct. Mol. Biol 23, 426– 433 (2016). 27065196 PMC4918759
  9. [10]MacDonald BT, Tamai K & He X Wnt/β-Catenin Signaling: Components, Mechanisms, and Diseases. Dev. Cell 17, 9– 26 (2009). 19619488 PMC2861485
  10. [11]Apte U Beta-catenin activation promotes liver regeneration after acetaminophen-induced injury. Am. J. Pathol 175, 1056– 1065 (2009). 19679878 PMC2731124
  11. [12]Bhushan B Pro-regenerative signaling after acetaminophen-induced acute liver injury in mice identified using a novel incremental dose model. Am. J. Pathol 184, 3013– 3025 (2014). 25193591 PMC4215032
  12. [14]Chan KY Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat. Neurosci 20, 1172– 1179 (2017). 28671695 PMC5529245
  13. [15]Crooks GE, Hon G, Chandonia JM & Brenner SE WebLogo: A sequence logo generator. Genome Res. 14, 1188– 1190 (2004). 15173120 PMC419797
  14. [16]Keegan KP, Glass EM & Meyer F MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. Methods Mol. Biol 1399, 207– 233 (2016). 26791506
  15. [17]Nordberg H The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 42, 26– 31 (2014). PMC3965075 24225321
  16. [18]Chen IMA The IMG/M data management and analysis system v.6.0: New tools and advanced capabilities. Nucleic Acids Res. 49, D751– D763 (2020). PMC7778900 33119741
  17. [19]Shmakov SA, Makarova KS, Wolf YI, Severinov KV & Koonin EV Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proc. Natl. Acad. Sci. U. S. A 115, E5307– E5316 (2018). 29784811 PMC6003329
  18. [21]Steinegger M & Söding J MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol 35, 1026– 1028 (2017). 29035372
  19. [22]Steinegger M & Söding J Clustering huge protein sequence sets in linear time. Nat. Commun 9, (2018). PMC6026198 29959318
  20. [24]Steinegger M HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 473, 1– 15 (2019). PMC6744700 31521110
  21. [25]Makarova KS Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol 18, (2019). PMC8905525 31857715
  22. [26]Price MN, Dehal PS & Arkin AP FastTree 2 - Approximately maximum-likelihood trees for large alignments. PLoS One 5, (2010). PMC2835736 20224823
  23. [27]Joung J Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat. Protoc 12, 828– 863 (2017). 28333914 PMC5526071
  24. [28]Zetsche B Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell 163, 759– 771 (2015). 26422227 PMC4638220
  25. [29]Schmittgen TD & Livak KJ Analyzing real-time PCR data by the comparative CT method. Nat. Protoc 3, 1101– 1108 (2008). 18546601
  26. [30]Hrvatin S, Deng F, O’Donnell CW, Gifford DK & Melton DA MARIS: Method for analyzing RNA following intracellular sorting. PLoS One 9, 1– 6 (2014). PMC3940959 24594682
  27. [31]Veeman MT, Slusarski DC, Kaykas A, Louie SH & Moon RT Zebrafish Prickle, a Modulator of NoncanonicalWnt/Fz Signaling, Regulates Gastrulation Movements. Curr. Biol 13, 680– 685 (2003). 12699626
  28. [32]Glusman G, Caballero J, Mauldin DE, Hood L & Roach JC Kaviar: An accessible system for testing SNV novelty. Bioinformatics 27, 3216– 3217 (2011). 21965822 PMC3208392
  29. [33]Shen S, Troupes AN, Pulicherla N & Asokan A Multiple Roles for Sialylated Glycans in Determining the Cardiopulmonary Tropism of Adeno-Associated Virus 4. J. Virol 87, 13206– 13213 (2013). 24067974 PMC3838263
  30. [34]Grieger JC, Choi VW & Samulski RJ Production and characterization of adeno-associated viral vectors. Nat. Protoc 1, 1412– 1428 (2006). 17406430

Authors
Kannan, S., Altae-Tran, H., Jin, X., Madigan, V. J., Oshiro, R., Makarova, K. S., Koonin, E. V., & Zhang, F.
Affiliations
  • Broad Institute (US)
  • National Institutes of Health (US)
Corresponding author
Zhang, Feng
ORCID
Venue
Nature Biotechnology
Publisher
Springer Science and Business Media LLC
Published
2021-08-30
Volume
40
Issue
2
Pages
194-197
ISSN
  • 0733-222X (ISSN-L)
  • 1087-0156
  • 1546-1696
DOI
10.1038/s41587-021-01030-2
PMC
PMC8929162
OpenAlex
W3197347308
Cited by
176
References
35
Citations by year
2026: 20 · 2025: 31 · 2024: 51 · 2023: 36 · 2022: 33 · 2021: 5
FWCI
9.81
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Biotechnology (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
Funders
Edward Mallinckrodt, Jr. Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
Keywords
CRISPR-Cas13, RNA editing, adenosine deaminase, cytosine deaminase, adeno-associated virus vectors
MeSH terms
Gene Editing, Adenosine, Adenosine Deaminase, Animals, Mammals, RNA, RNA Editing, CRISPR-Cas Systems

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