Preloader

CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo

  • 1.

    Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018).

    CAS 
    Article 

    Google Scholar 

  • 2.

    Stafforst, T. & Schneider, M. F. An RNA-deaminase conjugate selectively repairs point mutations. Angew. Chem. Int. Ed. Engl. 51, 11166–11169 (2012).

    CAS 
    Article 

    Google Scholar 

  • 3.

    Montiel-Gonzalez, M. F. et al. Correction of mutations within the cystic fibrosis transmembrane conductance regulator by site-directed RNA editing. Proc. Natl Acad. Sci. USA 110, 18285–18290 (2013).

    CAS 
    Article 

    Google Scholar 

  • 4.

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

  • 5.

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

    CAS 
    Article 

    Google Scholar 

  • 6.

    Vogel, P. & Stafforst, T. Critical review on engineering deaminases for site-directed RNA editing. Curr. Opin. Biotechnol. 55, 74–80 (2018).

    Article 

    Google Scholar 

  • 7.

    Vallecillo-Viejo, I. C. et al., Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme. RNA Biol. 15, 104–114 (2017).

  • 8.

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

    CAS 
    Article 

    Google Scholar 

  • 9.

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

    CAS 
    Article 

    Google Scholar 

  • 10.

    Kim, D. et al. Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat. Biotechnol. 37, 430–435 (2019).

    CAS 
    Article 

    Google Scholar 

  • 11.

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

  • 12.

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

    CAS 
    Article 

    Google Scholar 

  • 13.

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

  • 14.

    Nishikura, K. Functions and regulation of RNA editing by ADAR deaminases. Annu. Rev. Biochem. 79, 321–349 (2010).

    CAS 
    Article 

    Google Scholar 

  • 15.

    Wettengel, J. et al. Harnessing human ADAR2 for RNA repair – recoding a PINK1 mutation rescues mitophagy. Nucleic Acids Res. 45, 2797–2808 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • 16.

    Bennett, C. F. et al. Pharmacology of antisense drugs. Annu. Rev. Pharmacol. Toxicol. 57, 81–105 (2017).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Heep, M. et al. Applying human ADAR1p110 and ADAR1p150 for site-directed RNA editing-G/C substitution stabilizes guideRNAs against editing. Genes (Basel) 8, 34 (2017).

  • 18.

    Tan, M. H. et al. Dynamic landscape and regulation of RNA editing in mammals. Nature 550, 249–254 (2017).

    Article 

    Google Scholar 

  • 19.

    Lundstrom, K. & Boulikas, T. Viral vectors in gene therapy: technology development and clinical trials. Technol. Cancer Res. Treat. 2, 471–486 (2003).

  • 20.

    Conrad, N. K. The emerging role of triple helices in RNA biology. Wiley Interdiscip. Rev. RNA 5, 15–29 (2014).

    CAS 
    Article 

    Google Scholar 

  • 21.

    Tomatsu, S. et al. Mutations and polymorphisms in GUSB gene in mucopolysaccharidosis VII (Sly Syndrome). Hum. Mutat. 30, 511–519 (2009).

    CAS 
    Article 

    Google Scholar 

  • 22.

    BasuRay, S. et al. Rab7 mutants associated with Charcot–Marie–Tooth disease cause delayed growth factor receptor transport and altered endosomal and nuclear signaling. J. Biol. Chem. 288, 1135–1149 (2013).

    CAS 
    Article 

    Google Scholar 

  • 23.

    Vogel, P., Hanswillemenke, A. & Stafforst, T. Switching protein localization by site-directed RNA editing under control of light. ACS Synth. Biol. 6, 1642–1649 (2017).

    CAS 
    Article 

    Google Scholar 

  • 24.

    McCaffrey, A. P. et al. RNA interference in adult mice. Nature 418, 38–39 (2002).

    CAS 
    Article 

    Google Scholar 

  • 25.

    Vabret, N., Bhardwaj, N. & Greenbaum, B. D. Sequence-specific sensing of nucleic acids. Trends Immunol. 38, 53–65 (2017).

    CAS 
    Article 

    Google Scholar 

  • 26.

    Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019).

    CAS 
    Article 

    Google Scholar 

  • 27.

    Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).

    Article 

    Google Scholar 

  • 28.

    Wang, Y., Zhu, W. & Levy, D. E. Nuclear and cytoplasmic mRNA quantification by SYBR green based real-time RT-PCR. Methods 39, 356–362 (2006).

    CAS 
    Article 

    Google Scholar 

  • 29.

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

    CAS 
    Article 

    Google Scholar 

  • 30.

    Merkle, T. & Stafforst, T. New frontiers for site-directed RNA editing: harnessing endogenous ADARs. Methods Mol. Biol. 2181, 331–349 (2021).

    CAS 
    Article 

    Google Scholar 

  • 31.

    Ramaswami, G. et al. Accurate identification of human Alu and non-Alu RNA editing sites. Nat. Methods 9, 579–581 (2012).

    CAS 
    Article 

    Google Scholar 

  • 32.

    Ramaswami, G. et al. Identifying RNA editing sites using RNA sequencing data alone. Nat. Methods 10, 128–132 (2013).

    CAS 
    Article 

    Google Scholar 

  • 33.

    Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    CAS 
    Article 

    Google Scholar 

  • 34.

    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 

    Google Scholar 

  • 35.

    McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    CAS 
    Article 

    Google Scholar 

  • 36.

    Kent, W. J. BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 37.

    Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).

    Article 

    Google Scholar 

  • 38.

    Ramaswami, G. & Li, J. B. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 42, D109–D113 (2014).

    Article 

    Google Scholar 

  • 39.

    Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).

    CAS 
    Article 

    Google Scholar 

  • 40.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article 

    Google Scholar 

  • Source link