• ISSN 1674-8301
  • CN 32-1810/R
Volume 35 Issue 2
Mar.  2021
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Choe Dongwook C., Musunuru Kiran. Base editing: a brief review and a practical example[J]. The Journal of Biomedical Research, 2021, 35(2): 107-114. doi: 10.7555/JBR.34.20200003
Citation: Choe Dongwook C., Musunuru Kiran. Base editing: a brief review and a practical example[J]. The Journal of Biomedical Research, 2021, 35(2): 107-114. doi: 10.7555/JBR.34.20200003

Base editing: a brief review and a practical example

doi: 10.7555/JBR.34.20200003
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  • Corresponding author: Kiran Musunuru, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Building 421, 11-104 Smilow Center for Translational Research, Philadelphia, PA 19104, USA. Tel/Fax: +1-215-573-4717/+1-215-746-7415, E-mail: kiranmusunuru@gmail.com
  • Received: 2020-01-02
  • Revised: 2020-04-29
  • Accepted: 2020-06-10
  • Published: 2020-07-31
  • Issue Date: 2021-03-26
  • Genome editing has undergone rapid development in recent years, yielding new approaches to make precise changes in genes. In this review, we discuss the development of various adenine and cytosine base-editing technologies, which share the ability to make specific base changes at specific sites in the genome. We also describe multiple applications of base editing in vitro and in vivo. Finally, as a practical example, we demonstrate the use of a cytosine base editor and an adenine base editor in human cells to introduce and then correct a prevalent mutation responsible for hereditary tyrosinemia type 1.

     

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  • [1]
    Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes[J]. Nat Biotechnol, 2014, 32(4): 347–355. doi: 10.1038/nbt.2842
    [2]
    Adli M. The CRISPR tool kit for genome editing and beyond[J]. Nat Commun, 2018, 9(1): 1911. doi: 10.1038/s41467-018-04252-2
    [3]
    Komor AC, Kim YB, Packer MS, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage[J]. Nature, 2016, 533(7603): 420–424. doi: 10.1038/nature17946
    [4]
    Rees HA, Komor AC, Yeh WH, et al. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery[J]. Nat Commun, 2017, 8(1): 15790. doi: 10.1038/ncomms15790
    [5]
    Kim YB, Komor AC, Levy JM, et al. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions[J]. Nat Biotechnol, 2017, 35(4): 371–376. doi: 10.1038/nbt.3803
    [6]
    Nishida K, Arazoe T, Yachie N, et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems[J]. Science, 2016, 353(6305): aaf8729. doi: 10.1126/science.aaf8729
    [7]
    Li XS, Wang Y, Liu YJ, et al. Base editing with a Cpf1-cytidine deaminase fusion[J]. Nat Biotechnol, 2018, 36(4): 324–327. doi: 10.1038/nbt.4102
    [8]
    Komor AC, Zhao KT, Packer MS, et al. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity[J]. Sci Adv, 2017, 3(8): eaao4774. doi: 10.1126/sciadv.aao4774
    [9]
    Gaudelli NM, Komor AC, Rees HA, et al. Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage[J]. Nature, 2017, 551(7681): 464–471. doi: 10.1038/nature24644
    [10]
    Koblan LW, Doman JL, Wilson C, et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction[J]. Nat Biotechnol, 2018, 36(9): 843–846. doi: 10.1038/nbt.4172
    [11]
    Huang TP, Zhao KT, Miller SM, et al. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors[J]. Nat Biotechnol, 2019, 37(6): 626–631. doi: 10.1038/s41587-019-0134-y
    [12]
    Kim D, Lim K, Kim ST, et al. Genome-wide target specificities of CRISPR RNA-guided programmable deaminases[J]. Nat Biotechnol, 2017, 35(5): 475–480. doi: 10.1038/nbt.3852
    [13]
    Liang PP, Xie XW, Zhi SY, et al. Genome-wide profiling of adenine base editor specificity by EndoV-seq[J]. Nat Commun, 2019, 10(1): 67. doi: 10.1038/s41467-018-07988-z
    [14]
    Kim D, Kim DE, Lee G, et al. Genome-wide target specificity of CRISPR RNA-guided adenine base editors[J]. Nat Biotechnol, 2019, 37(4): 430–435. doi: 10.1038/s41587-019-0050-1
    [15]
    Zuo EW, Sun YD, Wei W, et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos[J]. Science, 2019, 364(6437): 289–292. doi: 10.1126/science.aav9973
    [16]
    Jin S, Zong Y, Gao Q, et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice[J]. Science, 2019, 364(6437): 292–295. doi: 10.1126/science.aaw7166
    [17]
    Grünewald J, Zhou RH, Garcia SP, et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors[J]. Nature, 2019, 569(7756): 433–437. doi: 10.1038/s41586-019-1161-z
    [18]
    Grünewald J, Zhou RH, Iyer S, et al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities[J]. Nat Biotechnol, 2019, 37(9): 1041–1048. doi: 10.1038/s41587-019-0236-6
    [19]
    Zhou CY, Sun YD, Yan R, et al. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis[J]. Nature, 2019, 571(7764): 275–278. doi: 10.1038/s41586-019-1314-0
    [20]
    Ma YQ, Zhang JY, Yin WJ, et al. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells[J]. Nat Methods, 2016, 13(12): 1029–1035. doi: 10.1038/nmeth.4027
    [21]
    Hess GT, Frésard L, Han K, et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells[J]. Nat Methods, 2016, 13(12): 1036–1042. doi: 10.1038/nmeth.4038
    [22]
    Chadwick AC, Wang X, Musunuru K. In vivo base editing of PCSK9 (proprotein convertase subtilisin/kexin type 9) as a therapeutic alternative to genome editing[J]. Arterioscler Thromb Vasc Biol, 2017, 37(9): 1741–1747. doi: 10.1161/ATVBAHA.117.309881
    [23]
    Chadwick AC, Evitt NH, Lv WJ, et al. Reduced blood lipid levels with in vivo CRISPR-Cas9 base editing of ANGPTL3[J]. Circulation, 2018, 137(9): 975–977. doi: 10.1161/CIRCULATIONAHA.117.031335
    [24]
    Rossidis AC, Stratigis JD, Chadwick AC, et al. In utero CRISPR-mediated therapeutic editing of metabolic genes[J]. Nat Med, 2018, 24(10): 1513–1518. doi: 10.1038/s41591-018-0184-6
    [25]
    Yeh WH, Chiang H, Rees HA, et al. In vivo base editing of post-mitotic sensory cells[J]. Nat Commun, 2018, 9(1): 2184. doi: 10.1038/s41467-018-04580-3
    [26]
    Villiger L, Grisch-Chan HM, Lindsay H, et al. Treatment of a metabolic liver disease by in vivo genome base editing in adult mice[J]. Nat Med, 2018, 24(10): 1519–1525. doi: 10.1038/s41591-018-0209-1
    [27]
    Ryu SM, Koo T, Kim K, et al. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy[J]. Nat Biotechnol, 2018, 36(6): 536–539. doi: 10.1038/nbt.4148
    [28]
    Song CQ, Jiang TT, Richter M, et al. Adenine base editing in an adult mouse model of tyrosinaemia[J]. Nat Biomed Eng, 2020, 4(1): 125–130. doi: 10.1038/s41551-019-0357-8
    [29]
    Liang PP, Ding CH, Sun HW, et al. Correction of β-thalassemia mutant by base editor in human embryos[J]. Protein Cell, 2017, 8(11): 811–822. doi: 10.1007/s13238-017-0475-6
    [30]
    Morrow G, Tanguay RM. Biochemical and clinical aspects of hereditary tyrosinemia type 1[M]//Tanguay RM. Hereditary Tyrosinemia: Pathogenesis, Screening and Management. Cham: Springer, 2017: 9–21.
    [31]
    De Braekeleer M, Larochelle J. Genetic epidemiology of hereditary tyrosinemia in Quebec and in Saguenay-Lac-St-Jean[J]. Am J Hum Genet, 1990, 47(2): 302–307. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1683702/
    [32]
    Anzalone AV, Randolph PB, Davis JR, et al. Search-and-replace genome editing without double-strand breaks or donor DNA[J]. Nature, 2019, 576(7785): 149–157. doi: 10.1038/s41586-019-1711-4
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