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Compact RNA editors with small Cas13 proteins

  • 1.

    Terns, M. P. CRISPR-based technologies: impact of RNA-targeting systems. Mol. Cell 72, 404–412 (2018).

    CAS 
    Article 

    Google Scholar 

  • 2.

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

    Article 

    Google Scholar 

  • 3.

    Abudayyeh, O. O. et al. A cytosine deaminase for programmable single-base RNA editing. Science 365, 382–386 (2019).

    CAS 
    Article 

    Google Scholar 

  • 4.

    Dong, J. Y., Fan, P. D. & Frizzel, R. A. Quantitative analysis of the packaging capacity of recombinant adeno-associated virus. Hum. Gene Ther. 7, 2101–2112 (1996).

    CAS 
    Article 

    Google Scholar 

  • 5.

    Wu, Z., Yang, H. & Colosi, P. Effect of genome size on AAV vector packaging. Mol. Ther. 18, 80–86 (2010).

    CAS 
    Article 

    Google Scholar 

  • 6.

    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 (2017).

    CAS 
    Article 

    Google Scholar 

  • 7.

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

    Article 

    Google Scholar 

  • 8.

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

    CAS 
    Article 

    Google Scholar 

  • 9.

    Matthews, M. M. et al. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat. Struct. Mol. Biol. 23, 426–433 (2016).

    CAS 
    Article 

    Google Scholar 

  • 10.

    MacDonald, B. T., Tamai, K. & He, X. Wnt/β-catenin signaling: components, mechanisms, and diseases. Dev. Cell 17, 9–26 (2009).

    CAS 
    Article 

    Google Scholar 

  • 11.

    Apte, U. et al. Beta-catenin activation promotes liver regeneration after acetaminophen-induced injury. Am. J. Pathol. 175, 1056–1065 (2009).

    CAS 
    Article 

    Google Scholar 

  • 12.

    Bhushan, B. et al. 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).

    CAS 
    Article 

    Google Scholar 

  • 13.

    Kattenhorn, L. M. et al. Adeno-associated virus gene therapy for liver disease. Hum. Gene Ther. 27, 947–961 (2016).

    CAS 
    Article 

    Google Scholar 

  • 14.

    Chan, K. Y. et al. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat. Neurosci. 20, 1172–1179 (2017).

    CAS 
    Article 

    Google Scholar 

  • 15.

    Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004).

    CAS 
    Article 

    Google Scholar 

  • 16.

    Keegan, K. P., Glass, E. M. & Meyer, F. MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol. Biol. 1399, 207–233 (2016).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Nordberg, H. et al. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 42, 26–31 (2014).

    Article 

    Google Scholar 

  • 18.

    Chen, I. M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, D751–D763 (2020).

    Article 

    Google Scholar 

  • 19.

    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 
    Article 

    Google Scholar 

  • 20.

    Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

    CAS 
    Article 

    Google Scholar 

  • 21.

    Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).

    CAS 
    Article 

    Google Scholar 

  • 22.

    Steinegger, M. & Söding, J. Clustering huge protein sequence sets in linear time. Nat. Commun. 9, 2542 (2018).

    Article 

    Google Scholar 

  • 23.

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    CAS 
    Article 

    Google Scholar 

  • 24.

    Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 1–15 (2019).

    CAS 
    Article 

    Google Scholar 

  • 25.

    Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2019).

    Article 

    Google Scholar 

  • 26.

    Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 

    Google Scholar 

  • 27.

    Joung, J. et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828–863 (2017).

    CAS 
    Article 

    Google Scholar 

  • 28.

    Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759–771 (2015).

    CAS 
    Article 

    Google Scholar 

  • 29.

    Schmittgen, T. D. & Livak, K. J. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3, 1101–1108 (2008).

    CAS 
    Article 

    Google Scholar 

  • 30.

    Hrvatin, S., Deng, F., O’Donnell, C. W., Gifford, D. K. & Melton, D. A. MARIS: method for analyzing RNA following intracellular sorting. PLoS ONE 9, e89459 (2014).

    Article 

    Google Scholar 

  • 31.

    Veeman, M. T., Slusarski, D. C., Kaykas, A., Louie, S. H. & Moon, R. T. Zebrafish Prickle, a modulator of noncanonical Wnt/Fz signaling, regulates gastrulation movements. Curr. Biol. 13, 680–685 (2003).

    CAS 
    Article 

    Google Scholar 

  • 32.

    Glusman, G., Caballero, J., Mauldin, D. E., Hood, L. & Roach, J. C. Kaviar: an accessible system for testing SNV novelty. Bioinformatics 27, 3216–3217 (2011).

    CAS 
    Article 

    Google Scholar 

  • 33.

    Shen, S., Troupes, A. N., 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).

    CAS 
    Article 

    Google Scholar 

  • 34.

    Grieger, J. C., Choi, V. W. & Samulski, R. J. Production and characterization of adeno-associated viral vectors. Nat. Protoc. 1, 1412–1428 (2006).

    CAS 
    Article 

    Google Scholar 

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