Progress in the Application of CRISPR/Cas Family Mediated Third-generation Sequencing Technology

Authors

  • Xizhen Chen

DOI:

https://doi.org/10.54097/a43yhk04

Keywords:

Sequencing Technology; SMRT Technology; Nanopore Sequencing Technology; The CRISPR/Cas Family.

Abstract

The first generation sequencing technology based on the dideoxynucleotide (ddNTP) chain termination method proposed by Sanger was gradually eliminated due to its high cost, low sequencing read length and cumbersome process. The second generation of sequencing technology, called High-throughput sequencing (HTS), which was then developed, still has the problem of fixed read length. In recent years, the third generation sequencing technology represented by SMRT technology and Nanopore sequencing technology has gradually become popular. Compared with the previous two generations of sequencing technology, the most significant advantage of the third generation sequencing technology is its ability to carry out single molecule sequencing. In this process, the infinite length of nucleic acid sequence can be determined theoretically without the help of PCR amplification. This paper first introduces the basic principles, advantages and disadvantages of third-generation sequencing, and introduces in detail the CRISPR/Cas family-mediated SMRT technology and Nanopore sequencing technology in the third-generation sequencing technology. Finally, the research progress and prospects of the combination of the third generation sequencing technology and gene editing technology in the future are analyzed.

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References

[1] Man J C, Cheng J, Zhao L. Effect of Knocking Out HOXA5 Gene by CRISPR-Cas9-Mediated Gene Editing Technique on Proliferation of Acute Myeloid Leukemia Cells[J]. Zhongguo shi yan xue ye xue za zhi, 2024, 32(1): 52-56.

[2] Hu Sihui, Liu Qianyi, Xie Dongchun, et al. Clinical research progress of CRISPR/Cas genome editing in the treatment of human genetic disorders[J]. Life Sciences, 2022,34(10):1250-1263. DOI:10.13376/j.cbls/2022139.

[3] Yingying CHEN, Yang LIU, Junjie SHI, Junying MA, Jianhua JU. CRISPR/Cas systems and their applications in gene editing with filamentous fungi[J]. Synthetic Biology Journal, 2024, 5(3): 672-693.

[4] Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol. 2015 May;33(5):538-42. doi: 10.1038/nbt.3190. Epub 2015 Mar 23. Erratum in: Nat Biotechnol. 2016 Feb;34(2):210. doi: 10.1038/nbt0216-210c. PMID: 25798939; PMCID: PMC4618510.

[5] Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res. 2018 Mar 16;46(5):2159-2168. doi: 10.1093/ nar/ gky066. PMID: 29401301; PMCID: PMC5861413.

[6] Kraft F, Kurth I. Long-read sequencing to understand genome biology and cell function. Int J Biochem Cell Biol. 2020 Sep;126:105799. doi: 10.1016/j.biocel.2020.105799. Epub 2020 Jul 3. PMID: 32629027.

[7] Liu YH, Wang L, Yu L. The principle and application of the single-molecule real-time sequencing technology. Yi Chuan = Hereditas. 2015 Mar;37(3):259-268. DOI: 10.16288/j.yczz.14-323. PMID: 25787000.

[8] Hestand MS, Ameur A. The Versatility of SMRT Sequencing. Genes (Basel). 2019 Jan 4;10(1):24. doi: 10.3390/genes 1001 0024. PMID: 30621217; PMCID: PMC6357146.

[9] Feng L, Lou J. DNA Methylation Analysis. Methods Mol Biol. 2019;1894:181-227. doi: 10.1007/978-1-4939-8916-4_12. PMID: 30547463.

[10] Searle B, Müller M, Carell T, Kellett A. Third-Generation Sequencing of Epigenetic DNA. Angew Chem Int Ed Engl. 2023 Mar 27;62(14):e202215704. doi: 10.1002/anie. 20221 5704. Epub 2023 Jan 25. PMID: 36524852.

[11] Shi ZX, Chen ZC, Zhong JY, Hu KH, Zheng YF, Chen Y, Xie SQ, Bo XC, Luo F, Tang C, Xiao CL, Liu YZ. High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing. Nat Commun. 2023 May 6;14(1):2631. doi: 10.1038/s41467-023-38324-9. PMID: 37149708; PMCID: PMC10164132.

[12] Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat Biotechnol 34, 518–524 (2016). https://doi.org/10.1038/nbt.3423.

[13] Bing-Yuan Guo, Tao Zeng, Hai-Chen Wu, Recent advances of DNA sequencing via nanopore-based technologies, Science Bulletin, Volume 60, Issue 3, 2015, Pages 287-295, ISSN 2095-9273, https://doi.org/10.1007/s11434-014-0707-6.

[14] Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol. 2021 Nov;39(11):1348-1365. doi: 10.1038/ s41587-021-01108-x. Epub 2021 Nov 8. PMID: 34750572; PMCID: PMC8988251.

[15] Li Z, DU C, Lin Y, et al. [Application of nanopore sequencing in environmental microbiology research]. Sheng wu Gong Cheng xue bao = Chinese Journal of Biotechnology. 2022 Jan;38(1):5-13. DOI: 10.13345/j.cjb.210085. PMID: 35142114.

[16] Zhao X, Liu Y, Chen X, Mi Z, Li W, Wang P, Shan X, Lu X. Detection and Characterization of Single Cisplatin Adducts on DNA by Nanopore Sequencing. ACS Omega. 2021 Jun 22;6 (26):17027-17034. doi: 10.1021/acsomega.1c02106. PMID: 34250360; PMCID: PMC8264939.

[17] Niamh Nic Daeid, Lucina Hackman, Rob Ogden, Nina Vasiljevic, Stefan Prost; Nanopore sequencing in non-human forensic genetics. Emerg Top Life Sci 24 September 2021; 5 (3): 465–473. doi: https://doi.org/10.1042/ETLS20200287.

[18] Bu Xuan, Xiao Guiqing. Application of single molecule sequencing technology in agriculture and forestry related plants [J]. Biochemistry, 2023,43(06):881-887.DOI:10. 13488/j. smhx. 20230063.

[19] Namkung S, Tran NT, Manokaran S, He R, Su Q, Xie J, Gao G, Tai PWL. Direct ITR-to-ITR Nanopore Sequencing of AAV Vector Genomes. Hum Gene Ther. 2022 Nov;33(21-22):1187-1196. doi: 10.1089/hum.2022.143. PMID: 36178359; PMCID: PMC9700346.

[20] Lewandowski K, Xu Y, Pullan ST, Lumley SF, Foster D, Sanderson N, Vaughan A, Morgan M, Bright N, Kavanagh J, Vipond R, Carroll M, Marriott AC, Gooch KE, Andersson M, Jeffery K, Peto TEA, Crook DW, Walker AS, Matthews PC. Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples. J Clin Microbiol. 2019 Dec 23;58(1):e00963-19. doi: 10.1128/JCM.00963-19. PMID: 31666364; PMCID: PMC6935926.

[21] Chen J, Xu F. Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections. Mol Diagn Ther. 2023 Nov;27(6):685-701. doi: 10.1007/s40291-023-00669-8. Epub 2023 Aug 11. PMID: 37563539; PMCID: PMC 10590290.

[22] Solcova M, Demnerova K, Purkrtova S. Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts. Microorganisms. 2021 Apr 27;9(5):937. doi: 10.3390/microorganisms9050937. PMID: 33925711; PMCID: PMC8146283.

[23] Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ. Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting. Hum Mutat. 2020 Sep;41 (9): 1671-1679. doi: 10.1002/humu.24063. Epub 2020 Jun 29. PMID: 32516842; PMCID: PMC7496172.

[24] Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS; University of Washington Center for Mendelian Genomics; King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet. 2021 Aug 5;108(8):1436-1449. doi: 10.1016/ j.ajhg. 2021.06.006. Epub 2021 Jul 2. PMID: 34216551; PM CID: PMC8387463.

[25] Phan, M.; Gomes, M.A.; Stinnett, V.; Morsberger, L.; Hoppman, N.L.; Pearce, K.E.; Smith, K.; Phan, B.; Jiang, L.; Zou, Y.S. An Integrated Approach Including CRISPR/Cas9-Mediated Nanopore Sequencing, Mate Pair Sequencing, and Cytogenomic Methods to Characterize Complex Structural Rearrangements in Acute Myeloid Leukemia. Biomedicines 2024, 12, 598. https://doi.org/10.3390/biomedicines12030598.

[26] Hafford-Tear NJ, Tsai YC, Sadan AN, Sanchez-Pintado B, Zarouchlioti C, Maher GJ, Liskova P, Tuft SJ, Hardcastle AJ, Clark TA, Davidson AE. CRISPR/Cas9-targeted enrichment and long-read sequencing of the Fuchs endothelial corneal dystrophy-associated TCF4 triplet repeat. Genet Med. 2019 Sep;21(9):2092-2102. doi: 10.1038/s41436-019-0453-x. Epub 2019 Feb 8. PMID: 30733599; PMCID: PMC6752322.

[27] Höijer I, Johansson J, Gudmundsson S, Chin CS, Bunikis I, Häggqvist S, Emmanouilidou A, Wilbe M, den Hoed M, Bondeson ML, Feuk L, Gyllensten U, Ameur A. Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity. Genome Biol. 2020 Dec 1;21(1):290. doi: 10.1186/s13059-020-02206-w. PMID: 33261 648; PMCID: PMC7706270.

[28] Yang Liu, Yousry A. El-Kassaby, Landscape of Fluid Sets of Hairpin-Derived 21-/24-nt-Long Small RNAs at Seed Set Uncovers Special Epigenetic Features in Picea glauca, Genome Biology and Evolution, Volume 9, Issue 1, January 2017, Pages 82–92, https://doi.org/ 10.1093/ gbe/ evw283.

[29] Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Downs B, Sukumar S, Sedlazeck FJ, Timp W. Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol. 2020 Apr;38(4):433-438. doi: 10.1038/ s41587-020-0407-5. Epub 2020 Feb 10. PMID: 32042167; PMCID: PMC7145730.

[30] Xu S, Shiomi H, Yamashita Y, Koyama S, Horie T, Baba O, Kimura M, Nakashima Y, Sowa N, Hasegawa K, Suzuki A, Suzuki Y, Kimura T, Ono K. CRISPR-Cas9-guided amplification-free genomic diagnosis for familial hypercholesterolemia using nanopore sequencing. PLoS One. 2024 Mar 20;19(3):e0297231. doi: 10.1371/ journal. pone. 0297231. PMID: 38507394; PMCID: PMC10954175.

[31] Geng K, Merino LG, Wedemann L, Martens A, Sobota M, Sanchez YP, Søndergaard JN, White RJ, Kutter C. Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells. Genome Res. 2022 Oct;32 (10):1876-1891. doi: 10.1101/gr.276901.122. Epub 2022 Sep 30. PMID: 36180232; PMCID: PMC9712622.

[32] Lopatriello G, Maestri S, Alfano M, Papa R, Di Vittori V, De Antoni L, Bellucci E, Pieri A, Bitocchi E, Delledonne M, Rossato M. CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions. Int J Mol Sci. 2023 Jan 5;24(2):1076. doi: 10.3390/ijms24021076. PMID: 36674592; PMCID: PMC9863143.

[33] Kim D, Kim J, Hur JK, Been KW, Yoon SH, Kim JS. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol. 2016 Aug;34(8):863-8. doi: 10.1038/ nbt.3609. Epub 2016 Jun 6. Erratum in: Nat Biotechnol. 2016 Aug 9;34(8):888. doi: 10.1038/nbt0816-888a. PMID: 27272384.

[34] Kim Y, Cheong SA, Lee JG, Lee SW, Lee MS, Baek IJ, Sung YH. Generation of knockout mice by Cpf1-mediated gene targeting. Nat Biotechnol. 2016 Aug;34(8):808-10. doi: 10.1038/nbt.3614. Epub 2016 Jun 6. PMID: 27272387.

[35] Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol. 2016 Aug;34(8):869-74. doi: 10.1038/nbt. 3620. Epub 2016 Jun 27. PMID: 27347757; PMCID: PMC 498 0201.

[36] Murugan K, Seetharam AS, Severin AJ, Sashital DG. CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. J Biol Chem. 2020 Apr 24;295(17):5538-5553. doi: 10.1074/ jbc. RA120.012933. Epub 2020 Mar 11. PMID: 32161115; PMCID: PMC7186167.

[37] Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol. 2020 Jul;38(7): 870-874. doi: 10.1038/s41587-020-0513-4. Epub 2020 Apr 16. PMID: 32300245; PMCID: PMC9107629.

[38] Nouri R, Jiang Y, Lian XL, Guan W. Sequence-Specific Recognition of HIV-1 DNA with Solid-State CRISPR-Cas12a-Assisted Nanopores (SCAN). ACS Sens. 2020 May 22;5 (5): 1273-1280. doi: 10.1021/acssensors.0c00497. Epub 2020 May 8. PMID: 32370494.

[39] Naqvi, M.M., Lee, L., Montaguth, O.E.T. et al. CRISPR–Cas12a-mediated DNA clamping triggers target-strand cleavage. Nat Chem Biol 18, 1014–1022 (2022). https://doi. org/ 10.1038/s41589-022-01082-8.

[40] Nouri R, Jiang Y, Tang Z, Lian XL, Guan W. Detection of SARS-CoV-2 with Solid-State CRISPR-Cas12a-Assisted Nanopores. Nano Lett. 2021 Oct 13;21(19):8393-8400. doi: 10. 1021/ acs.nanolett.1c02974. Epub 2021 Sep 20. PMID: 3454 2296.

[41] Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017 Apr 28;356(6336):438-442. doi: 10.1126/science. aam9321. Epub 2017 Apr 13. PMID: 28408723; PMCID: PMC5526198.

[42] Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec; 74(12):5463-7. doi: 10.1073/pnas.74.12.5463. PMID: 271968; PMCID: PMC431765.

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14-09-2024

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How to Cite

Chen, X. (2024). Progress in the Application of CRISPR/Cas Family Mediated Third-generation Sequencing Technology. Academic Journal of Science and Technology, 12(2), 184-190. https://doi.org/10.54097/a43yhk04