Recent progress and perspectives on development of gene editing tools

Authors

Zixian LIU, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Center for Life Sciences, Tsinghua University, Beijing 100084, ChinaFollow
Chengping LI, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Center for Life Sciences, Tsinghua University, Beijing 100084, China
Gogo Jun-Jie LIU, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Center for Life Sciences, Tsinghua University, Beijing 100084, ChinaFollow

Keywords

gene editing; CRISPR-Cas systems; transposons; ribozymes; future directions

Document Type

Biomanufacturing: Retrospect and Prospects

Abstract

The gene editing field has witnessed remarkable advancements in recent years, leading to the establishment and refinement of multidimensional gene editing platforms. These innovations have enabled precise targeted gene knockout, repair, and insertion. These tools have stimulated significant progress in fundamental research, therapeutics, agriculture, environment protection, and industrial applications. In this review, we provide a comprehensive overview of the milestones in gene editing tool development and offer perspectives on potential future directions for this rapidly evolving field.

First page

14

Last Page

24

Language

Chinese

Publisher

Bulletin of Chinese Academy of Sciences

References

1 Durmaz A A, Karaca E, Demkow U, et al. Evolution of genetic techniques: Past, present, and beyond. BioMed Research International, 2015, doi: 10.1155/2015/461524.

2 Scherer S, Davis R W. Replacement of chromosome segments with altered DNA sequences constructed in vitro. PNAS, 1979, 76(10): 4951-4955.

3 Capecchi M R. The new mouse genetics: Altering the genome by gene targeting. Trends in Genetics, 1989, 5: 70-76.

4 Jasin M. Genetic manipulation of genomes with rare-cutting endonucleases. Trends in Genetics, 1996, 12(6): 224-228.

5 Ménoret S, Fontanière S, Jantz D, et al. Generation of Rag1-knockout immunodeficient rats and mice using engineered meganucleases. FASEB Journal, 2013, 27(2): 703-711.

6 Gao H R, Smith J, Yang M Z, et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant Journal, 2010, 61(1): 176-187.

7 Kim Y G, Cha J, Chandrasegaran S. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. PNAS, 1996, 93(3): 1156-1160.

8 Deng D, Yan C Y, Pan X J, et al. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science, 2012, 335: 720-723.

9 Yang J J, Zhang Y, Yuan P F, et al. Complete decoding of TAL effectors for DNA recognition. Cell Research, 2014, 24(5): 628-631.

10 Gaj T, Gersbach C A, Barbas C F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 2013, 31(7): 397-405.

11 Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012, 337: 816-821.

12 Cong L, Ann Ran F, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013, 339: 819-823.

13 Mali P, Yang L H, Esvelt K M, et al. RNA-guided human genome engineering via Cas9. Science, 2013, 339: 823-826.

14 Makarova K S, Wolf Y I, Iranzo J, et al. Evolutionary classification of CRISPR-cas systems: A burst of class 2 and derived variants. Nature Reviews Microbiology, 2020, 18(2): 67-83.

15 Li T X, Yang Y Y, Qi H Z, et al. CRISPR/Cas9 therapeutics: Progress and prospects. Signal Transduction and Targeted Therapy, 2023, 8: 36.

16 Liu J J, Orlova N, Oakes B L, et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature, 2019, 566: 218-223.

17 Karvelis T, Bigelyte G, Young J K, et al. PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Research, 2020, 48(9): 5016-5023.

18 Kong X F, Zhang H N, Li G L, et al. Engineered CRISPR-OsCas12f1 and RhCas12f1 with robust activities and expanded target range for genome editing. Nature Communications, 2023, 14(1): 2046.

19 Sun A, Li C P, Chen Z H, et al. The compact Casπ (Cas12l) ‘bracelet’ provides a unique structural platform for DNA manipulation. Cell Research, 2023, 33(3): 229-244.

20 Lee J K, Jeong E, Lee J, et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nature Communications, 2018, 9(1): 3048.

21 Slaymaker I M, Gao L Y, Zetsche B, et al. Rationally engineered Cas9 nucleases with improved specificity. Science, 2016, 351: 84-88.

22 Kleinstiver B P, Pattanayak V, Prew M S, et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature, 2016, 529: 490-495.

23 Chen J S, Dagdas Y S, Kleinstiver B P, et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature, 2017, 550: 407-410.

24 Kleinstiver B P, Sousa A A, Walton R T, et al. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature Biotechnology, 2019, 37(3): 276-282.

25 Tsuchida C A, Zhang S Y, Doost M S, et al. Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Molecular Cell, 2022, 82(6): 1199-1209.

26 Riesenberg S, Helmbrecht N, Kanis P, et al. Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage. Nature Communications, 2022, 13(1): 489.

27 Zhang S Y, Sun A, Qian J M, et al. Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Nature, 2024, 630: 484-492.

28 Komor A C, Kim Y B, Packer M S, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 2016, 533: 420-424.

29 Komor A C, Zhao K T, Packer M S, 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. Science Advances, 2017, 3(8): eaao4774.

30 Koblan L W, Doman J L, Wilson C, et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nature Biotechnology, 2018, 36(9): 843-846.

31 Gaudelli N M, Komor A C, Rees H A, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 2017, 551: 464-471.

32 Huang J Y, Lin Q P, Fei H Y, et al. Discovery of deaminase functions by structure-based protein clustering. Cell, 2023, 186(15): 3182-3195.e14.

33 Ye L J, Zhao D D, Li J, et al. Glycosylase-based base editors for efficient T-to-G and C-to-G editing in mammalian cells. Nature Biotechnology, 2024, 42(10): 1538-1547.

34 Tong H W, Wang H Q, Wang X C, et al. Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase. Nature Communications, 2024, 15(1): 4897.

35 Yi Z Y, Zhang X X, Wei X X, et al. Programmable DNA pyrimidine base editing via engineered uracil-DNA glycosylase. Nature Communications, 2024, 15(1): 6397.

36 Rees H A, Liu D R. Base editing: Precision chemistry on the genome and transcriptome of living cells. Nature Reviews Genetics, 2018, 19(12): 770-788.

37 Molla K A, Sretenovic S, Bansal K C, et al. Precise plant genome editing using base editors and prime editors. Nature Plants, 2021, 7(9): 1166-1187.

38 Porto E M, Komor A C, Slaymaker I M, et al. Base editing: Advances and therapeutic opportunities. Nature Reviews Drug Discovery, 2020, 19(12): 839-859.

39 Anzalone A V, Randolph P B, Davis J R, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 2019, 576: 149-157.

40 Chen P J, Hussmann J A, Yan J, et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell, 2021, 184(22): 5635-5652.

41 Doman J L, Pandey S, Neugebauer M E, et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell, 2023, 186(18): 3983-4002.

42 Yan J, Oyler-Castrillo P, Ravisankar P, et al. Improving prime editing with an endogenous small RNA-binding protein. Nature, 2024, 628: 639-647.

43 Lin Q P, Zong Y, Xue C X, et al. Prime genome editing in rice and wheat. Nature Biotechnology, 2020, 38(5): 582-585.

44 Jin S, Lin Q P, Luo Y F, et al. Genome-wide specificity of prime editors in plants. Nature Biotechnology, 2021, 39(10): 1292-1299.

45 Lin Q P, Jin S, Zong Y, et al. High-efficiency prime editing with optimized, paired pegRNAs in plants. Nature Biotechnology, 2021, 39(8): 923-927.

46 Zong Y, Liu Y J, Xue C X, et al. An engineered prime editor with enhanced editing efficiency in plants. Nature Biotechnology, 2022, 40(9): 1394-1402.

47 Zhao Z H, Shang P, Mohanraju P, et al. Prime editing: Advances and therapeutic applications. Trends in Biotechnology, 2023, 41(8): 1000-1012.

48 FDA clears prime editors for testing in humans. Nature Biotechnology, 2024, 42(5): 691.

49 Zheng C W, Liu B, Dong X L, et al. Template-jumping prime editing enables large insertion and exon rewriting in vivo. Nature Communications, 2023, 14(1): 3369.

50 Deng P J, Tan S Q, Yang Q Y, et al. Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon. Cell, 2023, 186(13): 2865-2879.

51 Wilkinson M E, Frangieh C J, MacRae R K, et al. Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription. Science, 2023, 380: 301-308.

52 Chen Y C, Luo S Q, Hu Y P, et al. All-RNA-mediated targeted gene integration in mammalian cells with rationally engineered R2 retrotransposons. Cell, 2024, 187(17): 4674-4689.

53 Zhang X Z, Van Treeck B, Horton C A, et al. Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci. Nature Biotechnology, 2024, doi: 10.1038/s41587-10.1038/s41024-02137-y.

54 Strecker J, Ladha A, Gardner Z, et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science, 2019, 365: 48-53.

55 Klompe S E, Vo P L H, Halpin-Healy T S, et al. Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature, 2019, 571: 219-225.

56 Wang X T, Xu G X, Johnson W A, et al. Long sequence insertion via CRISPR/Cas gene-editing with transposase, recombinase, and integrase. Current Opinion in Biomedical Engineering, 2023, 28: 100491.

57 Durrant M G, Perry N T, Pai J J, et al. Bridge RNAs direct programmable recombination of target and donor DNA. Nature, 2024, 630: 984-993.

58 Zhang T T, Tan S J, Tang N, et al. Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox. Cell, 2024, 187(14): 3741-3760.

59 Liu Z X, Zhang S Y, Zhu H Z, et al. Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage. Science, 2024, 383: eadh4859.

Recommended Citation

LIU, Zixian; LI, Chengping; and LIU, Gogo Jun-Jie (2024) "Recent progress and perspectives on development of gene editing tools," Bulletin of Chinese Academy of Sciences (Chinese Version): Vol. 40 : Iss. 1 , Article 3.
DOI: https://doi.org/10.16418/j.issn.1000-3045.20241230005
Available at: https://bulletinofcas.researchcommons.org/journal/vol40/iss1/3