Boore, J. L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767–1780 (1999).
Tuppen, H. A., Blakely, E. L., Turnbull, D. M. & Taylor, R. W. Mitochondrial DNA mutations and human disease. Biochim. Biophys. Acta 1797, 113–128 (2010).
Greaves, L. C., Reeve, A. K., Taylor, R. W. & Turnbull, D. M. Mitochondrial DNA and disease. J. Pathol. 226, 274–286 (2012).
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).
Shan, Q. et al. Targeted genome modification of crop plants using a CRISPR–Cas system. Nat. Biotechnol. 31, 686–688 (2013).
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).
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).
Zong, Y. et al. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat. Biotechnol. 35, 438–440 (2017).
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
Lin, Q. et al. Prime genome editing in rice and wheat. Nat. Biotechnol. 38, 582–585 (2020).
Yarnall, M. T. N. et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2023).
Sun, C. et al. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01769-w (2023).
Mok, B. Y. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637 (2020).
Lee, S., Lee, H., Baek, G. & Kim, J. S. Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors. Nat. Biotechnol. 41, 378–386 (2022).
Kang, B. C. et al. Chloroplast and mitochondrial DNA editing in plants. Nat. Plants 7, 899–905 (2021).
Lei, Z. et al. Mitochondrial base editor induces substantial nuclear off-target mutations. Nature 606, 804–811 (2022).
Cho, S. I. et al. Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases. Cell 185, 1764–1776 (2022).
Yin, L., Shi, K. & Aihara, H. Structural basis of sequence-specific deamination by double-stranded DNA deaminase toxin DddA. Nat. Struct. Mol. Biol. https://doi.org/10.1038/s41594-023-01034-3 (2023).
Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I. & Aggarwal, A. K. Structure of the multimodular endonuclease FokI bound to DNA. Nature 388, 97–100 (1997).
Bitinaite, J., Wah, D. A., Aggarwal, A. K. & Schildkraut, I. FokI dimerization is required for DNA cleavage. Proc. Natl Acad. Sci. USA 95, 10570–10575 (1998).
Miller, J. C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778–785 (2007).
Szczepek, M. et al. Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat. Biotechnol. 25, 786–793 (2007).
Waugh, D. S. & Sauer, R. T. Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease. Proc. Natl Acad. Sci. USA 90, 9596–9600 (1993).
Lee, B. I., Shannon, M., Stubbs, L. & Wilson, D. M. 3rd Expression specificity of the mouse exonuclease 1 (mExo1) gene. Nucleic Acids Res. 27, 4114–4120 (1999).
Certo, M. T. et al. Coupling endonucleases with DNA end-processing enzymes to drive gene disruption. Nat. Methods 9, 973–975 (2012).
Chen, M. J., Ma, S. M., Dumitrache, L. C. & Hasty, P. Biochemical and cellular characteristics of the 3′ → 5′ exonuclease TREX2. Nucleic Acids Res. 35, 2682–2694 (2007).
Zong, Y. et al. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 36, 950–953 (2018).
Gehrke, J. M. et al. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat. Biotechnol. 36, 977–982 (2018).
Sanders, K. L., Catto, L. E., Bellamy, S. R. & Halford, S. E. Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res. 37, 2105–2115 (2009).
Li, R. et al. High-efficiency plastome base-editing in rice with TAL cytosine deaminase. Mol. Plant 14, 1412–1414 (2021).
Nakazato, I. et al. Targeted base editing in the plastid genome of Arabidopsis thaliana. Nat. Plants 7, 906–913 (2021).
Jiang, Z., Yang, M., Zhang, Y., Jackson, A. O. & Li, D. In Encyclopedia of Virology 4th edn, Vol. 3 (eds Bamford, D. H. & Zickerman, M.) 420–429 (Academic Press, 2021).
Bonillo, M., Pfromm, J. & Fischer, M. D. Challenges to gene editing approaches in the retina. Klin. Monbl. Augenheilkd. 239, 275–283 (2022).
Huang, J. et al. Discovery of deaminase functions by structure-based protein clustering. Cell 186, 3182–3195 (2023).
Christian, M. et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186, 757–761 (2010).
Kim, Y. et al. A library of TAL effector nucleases spanning the human genome. Nat. Biotechnol. 31, 251–258 (2013).
Nakazato, I. et al. Targeted base editing in the mitochondrial genome of Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 119, e2121177119 (2022).
Mok, B. Y. et al. CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat. Biotechnol. 40, 1378–1387 (2022).
Mi, L. et al. DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing. Nat. Commun. 14, 874 (2023).
Shimura, M. et al. Development of Leigh syndrome with a high probability of cardiac manifestations in infantile-onset patients with m.14453G> A. Mitochondrion 63, 1–8 (2022).
Wei, Y. et al. Mitochondrial base editor DdCBE causes substantial DNA off-target editing in nuclear genome of embryos. Cell Discov. 8, 27 (2022).
Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935–949 (2014).
Richter, M. F. et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38, 883–891 (2020).
Yi, Z. et al. Strand-selective base editing of human mitochondrial DNA using mitoBEs. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01791-y (2023).
Shan, Q. et al. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol. Plant 6, 1365–1368 (2013).
Jin, S., Lin, Q., Gao, Q. & Gao, C. Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs). Nat. Protoc. 18, 831–853 (2023).
Chen, S. Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2, e107 (2023).
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31, 2032–2034 (2015).
Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinformatics 43, 11.10.1–11.10.33 (2013).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, 1–4 (2021).
Bae, S., Park, J. & Kim, J. S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014).
Hu, J. et al. Strand-selective base editing of organellar and nuclear genomes with TALE fusions. National Center for Biotechnology Information (NCBI) https://www.ncbi.nlm.nih.gov/bioproject/PRJNA957096 (2023).
