CRISPR/Cas9, a decade of genome editing tools to fix the DNA

by Lúcia Santos


    1. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (1979). 2012;337(6096). 
    2. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nature Protocols. 2013;8(11):2281–308. 
    3. Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Vol. 9, Nature Reviews Microbiology. 2011. 
    4. Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Vol. 18, Nature Reviews Microbiology. 2020. 
    5. Bhaya D, Davison M, Barrangou R. CRISPR-cas systems in bacteria and archaea: Versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics. 2011;45. 
    6. Hynes AP, Villion M, Moineau S. Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages. Nature Communications.  2014;5. 
    7. Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Vol. 19, Microbial Cell Factories. 2020.
    8. Jiang F, Doudna JA. CRISPR-Cas9 Structures and Mechanisms. Vol. 46, Annual Review of Biophysics. 2017. 
    9. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature. 2016;529(7587). 
    10. Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science (1979). 2016;351(6268). 
    11. Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature. 2017;550(7676). 
    12. Casini A, Olivieri M, Petris G, Montagna C, Reginato G, Maule G, et al. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nature Biotechnology. 2018;36(3). 
    13. Lee JK, Jeong E, Lee J, Jung M, Shin E, Kim Y hoon, et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nature Communications. 2018;9(1). 
    14. Vakulskas CA, Dever DP, Rettig GR, Turk R, Jacobi AM, Collingwood MA, et al. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nature Medicine. 2018;24(8):1216–24. 
    15. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science (1979). 2014;343(6176).    
    16. Trevino AE, Zhang F. Genome editing using cas9 nickases. Methods in Enzymology. 2014. 
    17. Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 2015;520(7546). 
    18. Müller M, Lee CM, Gasiunas G, Davis TH, Cradick TJ, Siksnys V, et al. Streptococcus thermophilus CRISPR-Cas9 systems enable specific editing of the human genome. Molecular Therapy. 2016;24(3). 
    19. Lee CM, Cradick TJ, Bao G. The neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells. Molecular Therapy. 2016;24(3). 
    20. Kim E, Koo T, Park SW, Kim D, Kim K, Cho HY, et al. In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nature Communications. 2017;8. 
    21. Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, et al. Structure and Engineering of Francisella novicida Cas9. Cell. 2016;164(5).  
    22. Kleinstiver BP, Prew MS, Tsai SQ, Topkar V v., Nguyen NT, Zheng Z, et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015;523(7561). 
    23. Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, et al. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science (1979). 2018;361(6408). 
    24. Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018;556(7699).               
    25. Walton RT, Christie KA, Whittaker MN, Kleinstiver BP. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science (1979). 2020;368(6488). 
    26. Kosicki M, Tomberg K, Bradley A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology. 2018;36(8).   
    27. Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J. CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nature Medicine. 2018;24(7). 
    28. Ihry RJ, Worringer KA, Salick MR, Frias E, Ho D, Theriault K, et al. P53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nature Medicine. 2018;24(7).  
    29. Saleh-Gohari N, Helleday T. Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle un human cells. Nucleic Acids Research. 2004;32(12).
    30. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420–4. 
    31. Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science (1979). 2016;353(6305). 
    32. Carrington B, Weinstein RN, Sood R. BE4max and AncBE4max Are Efficient in Germline Conversion of C:G to T:A Base Pairs in Zebrafish. Cells. 2020;9(7). 
    33. Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nature Biotechnology. 2017;35(4). 
    34. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, et al. Programmable base editing of T to G C in genomic DNA without DNA cleavage. Nature. 2017 Nov 23;551(7681):464–71. 
    35. Gaudelli NM, Lam DK, Rees HA, Solá-Esteves NM, Barrera LA, Born DA, et al. Directed evolution of adenine base editors with increased activity and therapeutic application. Nature Biotechnology. 2020;38(7).   
    36. Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nature Biotechnology. 2020;38(7). 
    37. Arbab M, Shen MW, Mok B, Wilson C, Matuszek Ż, Cassa CA, et al. Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning. Cell. 2020;182(2). 
    38. Kurt IC, Zhou R, Iyer S, Garcia SP, Miller BR, Langner LM, et al. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nature Biotechnology. 2021;39(1). 
    39. Anzalone A v., Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Vol. 576, Nature. 2019. 149–157 p. 
    40. Scholefield J, Harrison PT. Prime editing – an update on the field. Gene Therapy. 2021. 
    41. Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen PF, et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22). 
    42. Nidhi S, Anand U, Oleksak P, Tripathi P, Lal JA, Thomas G, et al. Molecular Sciences Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives. International Journal of Molecular Sciences. 2021;22(3327):1-41. 
    43. Anzalone A v., Koblan LW, Liu DR. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Vol. 38, Nature Biotechnology. 2020.