Single-strand deaminase-assisted editing for functional RNA manipulation – Nature Biotechnology
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).
Google Scholar
Porto, E. M., Komor, A. C., Slaymaker, I. M. & Yeo, G. W. Base editing: advances and therapeutic opportunities. Nat. Rev. Drug Discov. 19, 839–859 (2020).
Google Scholar
Pfeiffer, L. S. & Stafforst, T. Precision RNA base editing with engineered and endogenous effectors. Nat. Biotechnol. 41, 1526–1542 (2023).
Google Scholar
Song, J., Zhuang, Y. & Yi, C. Programmable RNA base editing via targeted modifications. Nat. Chem. Biol. 20, 277–290 (2024).
Google Scholar
Cox, D. B. T. et al. RNA editing with CRISPR–Cas13. Science 358, 1019–1027 (2017).
Google Scholar
Rauch, S. et al. Programmable RNA-guided RNA effector proteins built from human parts. Cell 178, 122–134 (2019).
Google Scholar
Yi, Z. et al. Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo. Nat. Biotechnol. 40, 946–955 (2022).
Google Scholar
Katrekar, D. et al. Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs. Nat. Biotechnol. 40, 938–945 (2022).
Google Scholar
Qian, Y. et al. Programmable RNA sensing for cell monitoring and manipulation. Nature 610, 713–721 (2022).
Google Scholar
Jiang, K. et al. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nat. Biotechnol. 41, 698–707 (2022).
Google Scholar
Kaseniit, K. E. et al. Modular, programmable RNA sensing using ADAR editing in living cells. Nat. Biotechnol. 41, 482–487 (2022).
Google Scholar
Reautschnig, P. et al. CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo. Nat. Biotechnol. 40, 759–768 (2022).
Google Scholar
Ojha, N., Diaz Quiroz, J. F. & Rosenthal, J. J. C. In vitro and in cellula site-directed RNA editing using the λNDD-BoxB system. Methods Enzymol. 658, 335–358 (2021).
Google Scholar
Abudayyeh, O. O. et al. A cytosine deaminase for programmable single-base RNA editing. Science 365, 382–386 (2019).
Google Scholar
Huang, X. et al. Programmable C-to-U RNA editing using the human APOBEC3A deaminase. EMBO J. 39, e104741 (2020).
Google Scholar
Latifi, N., Mack, A. M., Tellioglu, I., Di Giorgio, S. & Stafforst, T. Precise and efficient C-to-U RNA base editing with SNAP-CDAR-S. Nucleic Acids Res. 51, e84 (2023).
Google Scholar
Bhakta, S., Sakari, M. & Tsukahara, T. RNA editing of BFP, a point mutant of GFP, using artificial APOBEC1 deaminase to restore the genetic code. Sci. Rep. 10, 17304 (2020).
Google Scholar
Han, W. et al. Programmable RNA base editing with a single gRNA-free enzyme. Nucleic Acids Res. 50, 9580–9595 (2022).
Google Scholar
Stroppel, A. S. et al. Harnessing self-labeling enzymes for selective and concurrent A-to-I and C-to-U RNA base editing. Nucleic Acids Res. 49, e95 (2021).
Google Scholar
Liu, Z., Jillette, N., Robson, P. & Cheng, A. W. Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold. Nucleic Acids Res. 51, e77 (2023).
Google Scholar
Song, J. et al. CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons. Mol. Cell 83, 139–155 (2023).
Google Scholar
Adachi, H. et al. Targeted pseudouridylation: an approach for suppressing nonsense mutations in disease genes. Mol. Cell 83, 637–651 (2023).
Google Scholar
Luo, N. et al. Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons. Nat. Biotechnol. 43, 114–123 (2025).
Google Scholar
Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).
Google Scholar
Tahmasebi, S., Khoutorsky, A., Mathews, M. B. & Sonenberg, N. Translation deregulation in human disease. Nat. Rev. Mol. Cell Biol. 19, 791–807 (2018).
Google Scholar
Sun, H. X., Li, K., Liu, C. & Yi, C. Q. Regulation and functions of non-m6A mRNA modifications. Nat. Rev. Mol. Cell Biol. 24, 714–731 (2023).
Google Scholar
Fu, X. D. Non-coding RNA: a new frontier in regulatory biology. Natl Sci. Rev. 1, 190–204 (2014).
Google Scholar
Ha, M. & Kim, V. N. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 15, 509–524 (2014).
Google Scholar
Xiang, J. S., Schafer, D. M., Rothamel, K. L. & Yeo, G. W. Decoding protein–RNA interactions using CLIP-based methodologies. Nat. Rev. Genet. 25, 879–895 (2024).
Google Scholar
Bass, B. L. & Weintraub, H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell 55, 1089–1098 (1988).
Google Scholar
Wagner, R. W., Smith, J. E., Cooperman, B. S. & Nishikura, K. A double-stranded-RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian-cells and Xenopus eggs. Proc. Natl Acad. Sci. USA 86, 2647–2651 (1989).
Google Scholar
Melcher, T. et al. A mammalian RNA editing enzyme. Nature 379, 460–464 (1996).
Google Scholar
Salter, J. D., Bennett, R. P. & Smith, H. C. The APOBEC protein family: united by structure, divergent in function. Trends Biochem. Sci. 41, 578–594 (2016).
Google Scholar
Pecori, R., Di Giorgio, S., Lorenzo, J. P. & Papavasiliou, F. N. Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination. Nat. Rev. Genet. 23, 505–518 (2022).
Google Scholar
Wolf, J., Gerber, A. P. & Keller, W. tadA, an essential tRNA-specific adenosine deaminase from. EMBO J. 21, 3841–3851 (2002).
Google Scholar
Losey, H. C., Ruthenburg, A. J. & Verdine, G. L. Crystal structure of tRNA adenosine deaminase TadA in complex with RNA. Nat. Struct. Mol. Biol. 13, 153–159 (2006).
Google Scholar
Yang, L. H. et al. Engineering and optimising deaminase fusions for genome editing. Nat. Commun. 7, 13330 (2016).
Google Scholar
Lam, D. K. et al. Improved cytosine base editors generated from TadA variants. Nat. Biotechnol. 41, 686–697 (2023).
Google Scholar
Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).
Google Scholar
Lapinaite, A. et al. DNA capture by a CRISPR–Cas9-guided adenine base editor. Science 369, 566–571 (2020).
Google Scholar
Rees, H. A., Wilson, C., Doman, J. L. & Liu, D. R. Analysis and minimization of cellular RNA editing by DNA adenine base editors. Sci. Adv. 5, eaax5717 (2019).
Google Scholar
Li, J. A. et al. Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity. Nat. Commun. 12, 2287 (2021).
Google Scholar
Grunewald, J. et al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat. Biotechnol. 37, 1041–1048 (2019).
Google Scholar
Zhou, C. Y. et al. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 571, 275–278 (2019).
Google Scholar
Jeong, Y. K. et al. Adenine base editor engineering reduces editing of bystander cytosines. Nat. Biotechnol. 39, 1426–1433 (2021).
Google Scholar
Gaudelli, N. M. et al. Directed evolution of adenine base editors with increased activity and therapeutic application. Nat. Biotechnol. 38, 892–U899 (2020).
Google Scholar
Mort, M., Ivanov, D., Cooper, D. N. & Chuzhanova, N. A. A meta-analysis of nonsense mutations causing human genetic disease. Hum. Mutat. 29, 1037–1047 (2008).
Google Scholar
Stenson, P. D. et al. The Human Gene Mutation Database: 2008 update. Genome Med. 1, 13 (2009).
Google Scholar
Bidou, L., Allamand, V., Rousset, J. P. & Namy, O. Sense from nonsense: therapies for premature stop codon diseases. Trends Mol. Med. 18, 679–688 (2012).
Google Scholar
Bidou, L. et al. Premature stop codons involved in muscular dystrophies show a broad spectrum of readthrough efficiencies in response to gentamicin treatment. Gene Ther. 11, 619–627 (2004).
Google Scholar
Martins-Dias, P. & Romao, L. Nonsense suppression therapies in human genetic diseases. Cell. Mol. Life Sci. 78, 4677–4701 (2021).
Google Scholar
Welch, E. M. et al. PTC124 targets genetic disorders caused by nonsense mutations. Nature 447, 87–91 (2007).
Google Scholar
Shi, N. et al. Restoration of dystrophin expression in mice by suppressing a nonsense mutation through the incorporation of unnatural amino acids. Nat. Biomed. Eng. 6, 195–206 (2022).
Google Scholar
Lueck, J. D. et al. Engineered transfer RNAs for suppression of premature termination codons. Nat. Commun. 10, 822 (2019).
Google Scholar
Albers, S. et al. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 618, 842–848 (2023).
Google Scholar
Wang, J. M. et al. AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice. Nature 604, 343–348 (2022).
Google Scholar
Wong, S. K., Sato, S. & Lazinski, D. W. Substrate recognition by ADAR1 and ADAR2. RNA 7, 846–858 (2001).
Google Scholar
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).
Google Scholar
Azad, M. T. A., Bhakta, S. & Tsukahara, T. Site-directed RNA editing by adenosine deaminase acting on RNA for correction of the genetic code in gene therapy. Gene Ther. 24, 779–786 (2017).
Google Scholar
Dugueperoux, I. et al. Cystic fibrosis at the Reunion Island (France): spectrum of mutations and genotype–phenotype for the Y122X mutation. J. Cyst. Fibros. 3, 185–188 (2004).
Google Scholar
Karijolich, J. & Yu, Y. T. Therapeutic suppression of premature termination codons: mechanisms and clinical considerations (review). Int. J. Mol. Med. 34, 355–362 (2014).
Google Scholar
Neugebauer, M. E. et al. Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity. Nat. Biotechnol. 41, 673–685 (2023).
Google Scholar
Chen, L. et al. Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing. Nat. Biotechnol. 41, 663–672 (2023).
Google Scholar
Zhang, E., Neugebauer, M. E., Krasnow, N. A. & Liu, D. R. Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference. Nat. Commun. 15, 1697 (2024).
Google Scholar
Li, Z. Y. et al. dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic Acids Res. 50, D471–D479 (2022).
Google Scholar
Rao, R. S. P. & Moller, I. M. Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins. Biochim. Biophys. Acta 1824, 405–412 (2012).
Google Scholar
Schweiger, R. & Linial, M. Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. Biol. Direct 5, 6 (2010).
Google Scholar
Zheng, L. et al. Phosphorylation of stem-loop binding protein (SLBP) on two threonines triggers degradation of SLBP, the sole cell cycle-regulated factor required for regulation of histone mRNA processing, at the end of S phase. Mol. Cell. Biol. 23, 1590–1601 (2003).
Google Scholar
Doman, J. L., Raguram, A., Newby, G. A. & Liu, D. R. Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors. Nat. Biotechnol. 38, 620–628 (2020).
Google Scholar
Yu, Y. et al. Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity. Nat. Commun. 11, 2052 (2020).
Google Scholar
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).
Google Scholar
Zhang, X. H. et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat. Biotechnol. 38, 856–U810 (2020).
Google Scholar
Li, C. et al. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat. Biotechnol. 38, 875–U866 (2020).
Google Scholar
Grünewald, J. et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat. Biotechnol. 38, 861–U827 (2020).
Google Scholar
Sakata, R. C. et al. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat. Biotechnol. 38, 865–U846 (2020).
Google Scholar
Weber, L. et al. Editing a γ-globin repressor binding site restores fetal hemoglobin synthesis and corrects the sickle cell disease phenotype. Sci. Adv. 6, eaay9392 (2020).
Google Scholar
Antoniou, P. et al. Base-editing-mediated dissection of a γ-globin-regulatory element for the therapeutic reactivation of fetal hemoglobin expression. Nat. Commun. 13, 6618 (2022).
Google Scholar
Lebek, S. et al. Ablation of CaMKIId oxidation by CRISPR–Cas9 base editing as a therapy for cardiac disease. Science 379, 179–185 (2023).
Google Scholar
Yan, H. & Tang, W. Programmed RNA editing with an evolved bacterial adenosine deaminase. Nat. Chem. Biol. 20, 1361–1370 (2024).
Google Scholar
Giudice, G., Sanchez-Cabo, F., Torroja, C. & Lara-Pezzi, E. ATtRACT—a database of RNA-binding proteins and associated motifs. Database (Oxf.) 2016, baw035 (2016).
Google Scholar
Kluesner, M. G. et al. EditR: a method to quantify base editing from Sanger sequencing. CRISPR J. 1, 239–250 (2018).
Google Scholar
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Google Scholar
Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
Google Scholar
Cheng, E. C. K., Lam, J. K. C. & Kwon, S. C. Cytosolic CRISPR RNAs for efficient application of RNA-targeting CRISPR–Cas systems. EMBO Rep. 26, 1891–1912 (2025).
Google Scholar
Lu, B. et al. Transposase assisted tagmentation of RNA/DNA hybrid duplexes. Elife 9, e54919 (2020).
Google Scholar
Lu, B. & Yi, C. TRACE-seq: rapid, low-input, one-tube RNA-seq library construction based on tagmentation of RNA/DNA hybrids. Curr. Protoc. 3, e735 (2023).
Google Scholar