Science and Nature

Compact RNA editors with small Cas13 proteins

Abstract

CRISPR–Cas13 programs have been developed for accurate RNA enhancing, and might potentially be feeble therapeutically when rapid-timeframe modifications are desirable or when DNA enhancing is fascinating. Now we have identified and characterised an ultrasmall family of Cas13b proteins—Cas13bt—that can mediate mammalian transcript knockdown. Now 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 inside of a single adeno-related virus.

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Data availability

Deep sequencing facts from whole-transcriptome sequencing had been deposited as a BioProject below Mission ID PRJNA641934. Data from the principle figures are available in within the Supplementary Data.

Code availability

All Python scripts feeble for facts prognosis are available in in a GitHub repository chanced on at https://github.com/fengzhanglab/Cas13bt-prognosis.

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Acknowledgements

We thank E. Eloe-Fadrosh for generously sharing JGI facts from admire Ga0114919; D. L. Valentine and J. Tarn for generously sharing JGI facts from admire Ga0180434; E. Puccio for assistance with AAV manufacturing; F. E. Demircioglu for assistance with protein purification; participants of the laboratory of F.Z. for advice and discussions, R. Macrae for dialogue and enhancing of the manuscript, and R. Belliveau for technical reinforce. S.Okay. is supported by a National Science Foundation Graduate Learn Fellowship. F.Z. is supported by NIH grants (1R01-HG009761, 1R01-MH110049 and 1DP1-HL141201), HHMI, Birth Philanthropy, The G. Harold and Leila Y. Mathers Charitable, Bill and Melinda Gates, and Edward Mallinckrodt, Jr Foundations, the Poitras Middle for Psychiatric Disorders Learn at MIT, the Hock E. Tan and Okay. Lisa Yang Middle for Autism Learn at MIT, the Yang-Tan Middle for Molecular Therapeutics, and by L. Yang, the Phillips family and J. and P. Poitras.

Creator facts

Creator notes

  1. These authors contributed equally: Soumya Kannan, Han Altae-Tran.

Affiliations

  1. Howard Hughes Scientific Institute, Cambridge, MA, USA

    Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J. Madigan, Rachel Oshiro & Feng Zhang

  2. Huge Institute of MIT and Harvard, Cambridge, MA, USA

    Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J. Madigan, Rachel Oshiro & Feng Zhang

  3. McGovern Institute for Brain Learn at MIT, Massachusetts Institute of Know-how, Cambridge, MA, USA

    Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J. Madigan, Rachel Oshiro & Feng Zhang

  4. Department of Organic Engineering, Massachusetts Institute of Know-how, Cambridge, MA, USA

    Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J. Madigan, Rachel Oshiro & Feng Zhang

  5. Department of Brain and Cognitive Science, Massachusetts Institute of Know-how, Cambridge, MA, USA

    Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J. Madigan, Rachel Oshiro & Feng Zhang

  6. Society of Fellows, Harvard University, Cambridge, MA, USA

    Xin Jin

  7. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA

    Xin Jin

  8. National Middle for Biotechnology Data, National Library of Treatment, National Institutes of Successfully being, Bethesda, MD, USA

    Kira S. Makarova & Eugene V. Koonin

Contributions

S.Okay., H.A.-T. and F.Z. conceived the mission and designed the computational pipeline and experiments. H.A.-T. completed computational taking a peek and phylogenetic prognosis with input from Okay.S.M. and E.V.Okay. S.Okay. and H.A.-T. completed the general gene conceal conceal experiment and H.A.-T. analyzed the implications. X.J. completed the transcriptome-wide specificity sequencing experiment, and S.Okay. analyzed the implications. V.M. produced AAV and assisted with operate of AAV constructs and experiments. S.Okay. completed and analyzed outcomes from all other experiments with the reduction of X.J., R.O. and V.M. S.Okay., H.A.-T. and F.Z. drafted the manuscript with input from all authors.

Corresponding author

Correspondence to
Feng Zhang.

Ethics declarations

Competing interests

F.Z. is a co-founder of Editas Treatment, Beam Therapeutics, Pairwise Plants, Arbor Biotechnologies and Sherlock Biosciences. S.Okay., H.A.-T. and F.Z. are co-inventors on US provisional patent application 62/905,645 regarding the Cas proteins described on this manuscript. The final authors show no competing interests.

Additional facts

Explore overview facts Nature Biotechnology thanks Magdy Mahfouz, Mitchell O’Connell and the opposite, anonymous, reviewer(s) for their contribution to the behold overview of this work.

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Kannan, S., Altae-Tran, H., Jin, X. et al. Compact RNA editors with small Cas13 proteins.
Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-01030-2

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