{"id":164303,"date":"2025-09-23T20:34:07","date_gmt":"2025-09-23T20:34:07","guid":{"rendered":"https:\/\/www.newsbeep.com\/au\/164303\/"},"modified":"2025-09-23T20:34:07","modified_gmt":"2025-09-23T20:34:07","slug":"fueling-chromosomal-gene-diversification-and-artificial-evolution-with-crispr-genome-biology","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/au\/164303\/","title":{"rendered":"Fueling chromosomal gene diversification and artificial evolution with CRISPR | Genome Biology"},"content":{"rendered":"

Wilson DS, Keefe AD. Random mutagenesis by PCR. Curr Protoc Mol Biol. 2001;51:8\u20133.<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Reetz MT, Wu S. Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. Chem Commun (Camb). 2008;43:5499\u2013501.<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yu H, Ye C, Wang Y, Wang Z, Fang S, Jin H, et al. Enhancing substrate preference of iridoid synthase via focused polarity-steric mutagenesis scanning. Chem Bio Eng. 2024;1:826\u201335.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Stemmer WP. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A. 1994;91:10747\u201351.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. 1995;164:49\u201353.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Packer MS, Liu DR. Methods for the directed evolution of proteins. Nat Rev Genet. 2015;16:379\u201394.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Fryer T, Wolff DS, Overath MD, Sch\u00e4fer E, Laustsen AH, Jenkins TP, et al. Post-assembly plasmid amplification for increased transformation yields in E. coli and S. cerevisiae. Chem Bio Eng. 2025;2:87\u201396.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, et al. In vivo hypermutation and continuous evolution. Nat Rev Methods Primers. 2022;2:36.<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chen X, Zhang J. The genomic landscape of position effects on protein expression level and noise in yeast. Cell Syst. 2016;2:347\u201354.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

James JS, Dai J, Chew WL, Cai Y. The design and engineering of synthetic genomes. Nat Rev Genet. 2025;26:298\u2013319.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Erdogan M, Fabritius A, Basquin J, Griesbeck O. Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells. Cell Chem Biol. 2020;27:610-621.e615.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lynch M, Ackerman MS, Gout JF, Long H, Sung W, Thomas WK, et al. Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet. 2016;17:704\u201314.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lewis JA, Morran LT. Advantages of laboratory natural selection in the applied sciences. J Evol Biol. 2022;35:5\u201322.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wannier TM, Ciaccia PN, Ellington AD, Filsinger GT, Isaacs FJ, Javanmardi K, et al. Recombineering and MAGE. Nat Rev Methods Primers. 2021;1:7.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 2009;460:894\u20138.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nat Methods. 2012;9:591\u20133.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, et al. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res. 2012;40:e132.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nyerges \u00c1, Cs\u00f6rg\u0151 B, Nagy I, B\u00e1lint B, Bihari P, L\u00e1z\u00e1r V, et al. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species. Proc Natl Acad Sci U S A. 2016;113:2502\u20137.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Barbieri EM, Muir P, Akhuetie-Oni BO, Yellman CM, Isaacs FJ. Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes. Cell. 2017;171:1453-1467.e1413.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

DiCarlo JE, Conley AJ, Penttil\u00e4 M, J\u00e4ntti J, Wang HH, Church GM. Yeast oligo-mediated genome engineering (YOGE). ACS Synth Biol. 2013;2:741\u20139.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ciaccia PN, Liang Z, Schweitzer AY, Metzner E, Isaacs FJ. Enhanced eMAGE applied to identify genetic factors of nuclear hormone receptor dysfunction via combinatorial gene editing. Nat Commun. 2024;15:5218.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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. Nat Rev Microbiol. 2020;18:67\u201383.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816\u201321.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR\/Cas systems. Science. 2013;339:819\u201323.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152:1173\u201383.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013;31:833\u20138.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Xu X, Qi LS. A CRISPR-dCas toolbox for genetic engineering and synthetic biology. J Mol Biol. 2019;431:34\u201347.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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;533:420\u20134.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149\u201357.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A. 1996;93:1156\u201360.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, et al. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res. 2011;39:359\u201372.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kim Y, Kweon J, Kim A, Chon JK, Yoo JY, Kim HJ, et al. A library of TAL effector nucleases spanning the human genome. Nat Biotechnol. 2013;31:251\u20138.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kim YK, Wee G, Park J, Kim J, Baek D, Kim JS, et al. TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol. 2013;20:1458\u201364.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, et al. A universal deep-learning model for zinc finger design enables transcription factor reprogramming. Nat Biotechnol. 2023;41:1117\u201329.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Scherer S, Davis RW. Replacement of chromosome segments with altered DNA sequences constructed in vitro. Proc Natl Acad Sci U S A. 1979;76:4951\u20135.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Brown AD, Claybon AB, Bishop AJ. A conditional mouse model for measuring the frequency of homologous recombination events in vivo in the absence of essential genes. Mol Cell Biol. 2011;31:3593\u2013602.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rouet P, Smih F, Jasin M. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol. 1994;14:8096\u2013106.<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature. 2014;513:120\u20133.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature. 2018;562:217\u201322.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Radford EJ, Tan HK, Andersson MHL, Stephenson JD, Gardner EJ, Ironfield H, et al. Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation. Nat Commun. 2023;14:7702.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sahu S, Sullivan TL, Mitrophanov AY, Galloux M, Nousome D, Southon E, et al. Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants. PLoS Genet. 2023;19:e1010940.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Waters AJ, Brendler-Spaeth T, Smith D, Offord V, Tan HK, Zhao Y, et al. Saturation genome editing of BAP1 functionally classifies somatic and germline variants. Nat Genet. 2024;56:1434\u201345.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Olvera-Le\u00f3n R, Zhang F, Offord V, Zhao Y, Tan HK, Gupta P, et al. High-resolution functional mapping of RAD51C by saturation genome editing. Cell. 2024;187:5719-5734.e5719.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Buckley M, Terwagne C, Ganner A, Cubitt L, Brewer R, Kim DK, et al. Saturation genome editing maps the functional spectrum of pathogenic VHL alleles. Nat Genet. 2024;56:1446\u201355.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Huang H, Hu C, Na J, Hart SN, Gnanaolivu RD, Abozaid M, et al. Functional evaluation and clinical classification of BRCA2 variants. Nature. 2025;638:528\u201337.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Jako\u010di\u016bnas T, Pedersen LE, Lis AV, Jensen MK, Keasling JD. CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR\/Cas9. Metab Eng. 2018;48:288\u201396.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Garst AD, Bassalo MC, Pines G, Lynch SA, Halweg-Edwards AL, Liu R, et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol. 2017;35:48\u201355.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Bao Z, Xiao H, Liang J, Zhang L, Xiong X, Sun N, et al. Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth Biol. 2015;4:585\u201394.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Bao Z, HamediRad M, Xue P, Xiao H, Tasan I, Chao R, et al. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. Nat Biotechnol. 2018;36:505\u20138.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Roy KR, Smith JD, Vonesch SC, Lin G, Tu CS, Lederer AR, et al. Multiplexed precision genome editing with trackable genomic barcodes in yeast. Nat Biotechnol. 2018;36:512\u201320.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Guo X, Chavez A, Tung A, Chan Y, Kaas C, Yin Y, et al. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nat Biotechnol. 2018;36:540\u20136.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sharon E, Chen SA, Khosla NM, Smith JD, Pritchard JK, Fraser HB. Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. Cell. 2018;175:544-557.e516.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Deng L, Zhou YL, Cai Z, Zhu J, Li Z, Bao Z. Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast. Sci Adv. 2024;10:eadj9382.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Mavrommati M, Daskalaki A, Papanikolaou S, Aggelis G. Adaptive laboratory evolution principles and applications in industrial biotechnology. Biotechnol Adv. 2022;54:107795.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Storici F, Bebenek K, Kunkel TA, Gordenin DA, Resnick MA. RNA-templated DNA repair. Nature. 2007;447:338\u201341.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Jensen ED, Laloux M, Lehka BJ, Pedersen LE, Jako\u010di\u016bnas T, Jensen MK, et al. A synthetic RNA-mediated evolution system in yeast. Nucleic Acids Res. 2021;49:e88.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Crook N, Abatemarco J, Sun J, Wagner JM, Schmitz A, Alper HS. In vivo continuous evolution of genes and pathways in yeast. Nat Commun. 2016;7:13051.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ravikumar A, Arzumanyan GA, Obadi MKA, Javanpour AA, Liu CC. Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds. Cell. 2018;175:1946-1957.e1913.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kosicki M, Tomberg K, Bradley A. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol. 2018;36:765\u201371.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cullot G, Boutin J, Toutain J, Prat F, Pennamen P, Rooryck C, et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nat Commun. 2019;10:1136.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cullot G, Aird EJ, Schlapansky MF, Yeh CD, van de Venn L, Vykhlyantseva I, Kreutzer S, Mail\u00e4nder D, Lewk\u00f3w B, Klermund J, et al. Genome editing with the HDR-enhancing DNA-PKcs inhibitor AZD7648 causes large-scale genomic alterations. Nat Biotechnol. 2024. https:\/\/doi.org\/10.1038\/s41587-024-02488-6<\/a>.<\/p>\n

Karanam K, Kafri R, Loewer A, Lahav G. Quantitative live cell imaging reveals a gradual shift between DNA repair mechanisms and a maximal use of HR in mid S phase. Mol Cell. 2012;47:320\u20139.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ploessl D, Zhao Y, Cao M, Ghosh S, Lopez C, Sayadi M, et al. A repackaged CRISPR platform increases homology-directed repair for yeast engineering. Nat Chem Biol. 2022;18:38\u201346.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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. 2016;353:aaf8729.<\/p>\n

Wang L, Jackson WC, Steinbach PA, Tsien RY. Evolution of new nonantibody proteins via iterative somatic hypermutation. Proc Natl Acad Sci U S A. 2004;101:16745\u20139.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, et al. Programmable base editing of A\u2022T to G\u2022C in genomic DNA without DNA cleavage. Nature. 2017;551:464\u201371.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat Methods. 2016;13:1029\u201335.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hess GT, Fr\u00e9sard L, Han K, Lee CH, Li A, Cimprich KA, et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods. 2016;13:1036\u201342.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li C, Zhang R, Meng X, Chen S, Zong Y, Lu C, et al. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat Biotechnol. 2020;38:875\u201382.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhang X, Zhu B, Chen L, Xie L, Yu W, Wang Y, et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat Biotechnol. 2020;38:856\u201360.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gr\u00fcnewald J, Zhou R, Lareau CA, Garcia SP, Iyer S, Miller BR, et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat Biotechnol. 2020;38:861\u20134.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sakata RC, Ishiguro S, Mori H, Tanaka M, Tatsuno K, Ueda H, et al. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat Biotechnol. 2020;38:865\u20139.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tao W, Liu Q, Huang S, Wang X, Qu S, Guo J, et al. CABE-RY: a PAM-flexible dual-mutation base editor for reliable modeling of multi-nucleotide variants. Mol Ther. 2021;26:114\u201321.<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Neugebauer ME, Hsu A, Arbab M, Krasnow NA, McElroy AN, Pandey S, et al. Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity. Nat Biotechnol. 2023;41:673\u201385.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lam DK, Feliciano PR, Arif A, Bohnuud T, Fernandez TP, Gehrke JM, et al. Improved cytosine base editors generated from TadA variants. Nat Biotechnol. 2023;41:686\u201397.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Liang Y, Xie J, Zhang Q, Wang X, Gou S, Lin L, et al. AGBE: a dual deaminase-mediated base editor by fusing CGBE with ABE for creating a saturated mutant population with multiple editing patterns. Nucleic Acids Res. 2022;50:5384\u201399.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhang A, Shan T, Sun Y, Chen Z, Hu J, Hu Z, et al. Directed evolution rice genes with randomly multiplexed sgRNAs assembly of base editors. Plant Biotechnol J. 2023;21:2597\u2013610.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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. Nat Biotechnol. 2021;39:41\u20136.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhao D, Li J, Li S, Xin X, Hu M, Price MA, et al. Glycosylase base editors enable C-to-A and C-to-G base changes. Nat Biotechnol. 2021;39:35\u201340.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kweon J, Jang A-H, Shin HR, See J-E, Lee W, Lee JW, et al. A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants. Oncogene. 2020;39:30\u20135.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Huang C, Li G, Wu J, Liang J, Wang X. Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction. Genome Biol. 2021;22:80.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hanna RE, Hegde M, Fagre CR, DeWeirdt PC, Sangree AK, Szegletes Z, et al. Massively parallel assessment of human variants with base editor screens. Cell. 2021;184:1064-1080.e1020.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

S\u00e1nchez-Rivera FJ, Diaz BJ, Kastenhuber ER, Schmidt H, Katti A, Kennedy M, et al. Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Nat Biotechnol. 2022;40:862\u201373.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sangree AK, Griffith AL, Szegletes ZM, Roy P, DeWeirdt PC, Hegde M, et al. Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2. Nat Commun. 2022;13:1318.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kim Y, Lee S, Cho S, Park J, Chae D, Park T, et al. High-throughput functional evaluation of human cancer-associated mutations using base editors. Nat Biotechnol. 2022;40:874\u201384.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lue NZ, Garcia EM, Ngan KC, Lee C, Doench JG, Liau BB. Base editor scanning charts the DNMT3A activity landscape. Nat Chem Biol. 2023;19:176\u201386.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yao Y, Zhou Z, Wang X, Liu Z, Zhai Y, Chi X, et al. SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution. Cell Genom. 2024;4:100583.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tong H, Wang X, Liu Y, Liu N, Li Y, Luo J, et al. Programmable a-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase. Nat Biotechnol. 2023;41:1080\u20134.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Belli O, Karava K, Farouni R, Platt RJ. Multimodal scanning of genetic variants with base and prime editing. Nat Biotechnol. 2024. https:\/\/doi.org\/10.1038\/s41587-024-02439-1<\/a>.<\/p>\n

Hao W, Cui W, Cheng Z, Han L, Suo F, Liu Z, et al. Development of a base editor for protein evolution via in situ mutation in vivo. Nucleic Acids Res. 2021;49:9594\u2013605.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang Y, Cheng H, Liu Y, Liu Y, Wen X, Zhang K, et al. In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing. Nat Commun. 2021;12:678.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hao W, Cui W, Liu Z, Suo F, Wu Y, Han L, et al. A new-generation base editor with an expanded editing window for microbial cell evolution in vivo based on CRISPR-Cas12b engineering. Adv Sci. 2024;11:2309767.<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 2015;169:931\u201345.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ran Y, Liang Z, Gao C. Current and future editing reagent delivery systems for plant genome editing. Sci China Life Sci. 2017;60:490\u2013505.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kuang Y, Li S, Ren B, Yan F, Spetz C, Li X, et al. Base-editing-mediated artificial evolution of OsALS1 in planta to develop novel herbicide-tolerant rice germplasms. Mol Plant. 2020;13:565\u201372.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang X, Pan W, Sun C, Yang H, Cheng Z, Yan F, et al. Creating large-scale genetic diversity in Arabidopsis via base editing-mediated deep artificial evolution. Genome Biol. 2024;25:215.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13:722\u201336.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Morisaka H, Yoshimi K, Okuzaki Y, Gee P, Kunihiro Y, Sonpho E, et al. CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun. 2019;10:5302.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zimmermann A, Prieto-Vivas JE, Cautereels C, Gorkovskiy A, Steensels J, Van de Peer Y, et al. A Cas3-base editing tool for targetable in vivo mutagenesis. Nat Commun. 2023;14:3389.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chen XD, Chen Z, Wythes G, Zhang Y, Orr BC, Sun G, et al. Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes. Science. 2024;386:eadn5876.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cs\u00f6rg\u0151 B, Le\u00f3n LM, Chau-Ly IJ, Vasquez-Rifo A, Berry JD, Mahendra C, et al. A compact cascade-Cas3 system for targeted genome engineering. Nat Methods. 2020;17:1183\u201390.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Whitford CM, Gockel P, Faurdal D, Gren T, Sigrist R, Weber T. Cascade-Cas3 enables highly efficient genome engineering in Streptomyces species. Nucleic Acids Res. 2025. https:\/\/doi.org\/10.1093\/nar\/gkaf214<\/a>.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhou Q, Zhao Y, Ke C, Wang H, Gao S, Li H, et al. Repurposing endogenous type I-E CRISPR-Cas systems for natural product discovery in Streptomyces. Nat Commun. 2024;15:9833.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, et al. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell. 2019;74:936-950.e935.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tan R, Krueger RK, Gramelspacher MJ, Zhou X, Xiao Y, Ke A, et al. Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems. Mol Cell. 2022;82:852-867.e855.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Guo J, Gong L, Yu H, Li M, An Q, Liu Z, et al. Engineered minimal type I CRISPR-Cas system for transcriptional activation and base editing in human cells. Nat Commun. 2024;15:7277.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li Y, Huang B, Chen J, Huang L, Xu J, Wang Y, et al. Targeted large fragment deletion in plants using paired crRNAs with type I CRISPR system. Plant Biotechnol J. 2023;21:2196\u2013208.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang J, Zhao D, Li J, Hu M, Xin X, Price MA, et al. Helicase-AID: a novel molecular device for base editing at random genomic loci. Metab Eng. 2021;67:396\u2013402.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Xu R, Liu X, Li J, Qin R, Wei P. Identification of herbicide resistance OsACC1 mutations via in planta prime-editing-library screening in rice. Nat Plants. 2021;7:888\u201392.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Erwood S, Bily TMI, Lequyer J, Yan J, Gulati N, Brewer RA, et al. Saturation variant interpretation using CRISPR prime editing. Nat Biotechnol. 2022;40:885\u201395.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, et al. High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Mol Cell. 2023;83:4633-4645.e4639.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kim Y, Oh HC, Lee S, Kim HH. Saturation profiling of drug-resistant genetic variants using prime editing. Nat Biotechnol. 2024. https:\/\/doi.org\/10.1038\/s41587-024-02465-z<\/a><\/p>\n

Gould SI, Wuest AN, Dong K, Johnson GA, Hsu A, Narendra VK, Atwa O, Levine SS, Liu DR, S\u00e1nchez Rivera FJ. High-throughput evaluation of genetic variants with prime editing sensor libraries. Nat Biotechnol. 2024. https:\/\/doi.org\/10.1038\/s41587-024-02172-9<\/a><\/p>\n

Martyn GE, Montgomery MT, Jones H, Guo K, Doughty BR, Linder J, et al. Rewriting regulatory DNA to dissect and reprogram gene expression. Cell. 2025. https:\/\/doi.org\/10.1016\/j.cell.2025.03.034<\/a>.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Xie J, Xiang J, Shen Y, Shao S. Mechanistic insights into the tools for intracellular protein delivery. Chem Bio Eng. 2025;2:132\u201355.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Halperin SO, Tou CJ, Wong EB, Modavi C, Schaffer DV, Dueber JE. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature. 2018;560:248\u201352.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tou CJ, Schaffer DV, Dueber JE. Targeted diversification in the S. cerevisiae genome with CRISPR-guided DNA polymerase I. ACS Synth Biol. 2020;9:1911\u20136.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Qi L, Sui Y, Tang XX, McGinty RJ, Liang XZ, Dominska M, et al. Shuffling the yeast genome using CRISPR\/Cas9-generated DSBs that target the transposable Ty1 elements. PLoS Genet. 2023;19:e1010590.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Koeppel J, Ferreira R, Vanderstichele T, Riedmayr LM, Peets EM, Girling G, et al. Randomizing the human genome by engineering recombination between repeat elements. Science. 2025;387:eado3979.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Koeppel J, Murat P, Girling G, Peets EM, Gouley M, Rebernig V, Maheshwari A, Hepkema J, Weller J, Johnkingsly Jebaraj JH, et al. Resolution of a human super-enhancer by targeted genome randomisation. bioRxiv 2025:2025.2001.2014.632548.<\/p>\n

Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: recent advances and applications. Biotechnol Adv. 2024;72:108343.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Xu J, Sun Y, Wu J, Yang S, Yang L. Chromosome recombination and modification by LoxP-mediated evolution in Vibrio natriegens using CRISPR-associated transposases. Biotechnol Bioeng. 2024;121(3):1163\u201372.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Choi J, Chen W, Suiter CC, Lee C, Chardon FM, Yang W, et al. Precise genomic deletions using paired prime editing. Nat Biotechnol. 2022;40:218\u201326.<\/p>\n

Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, et al. High-content CRISPR screening. Nat Rev Methods Primers. 2022;2:9.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pinglay S, Lalanne J-B, Daza RM, Kottapalli S, Quaisar F, Koeppel J, et al. Multiplex generation and single-cell analysis of structural variants in mammalian genomes. Science. 2025;387:eado5978.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cai Z, Xie W, Bao Z. Broadening the targetable space: engineering and discovery of PAM-flexible Cas proteins. Trends Microbiol. 2024;32:728\u201331.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kim HK, Lee S, Kim Y, Park J, Min S, Choi JW, et al. High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells. Nat Biomed Eng. 2020;4:111\u201324.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yang C, Zhou Z, Sun X, Ju H, Yue X, Rao S, et al. PAMless spRY exhibits a preference for the seed region for efficient targeting. Cell Rep. 2024;43:114225.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Jiang W, Feng S, Huang S, Yu W, Li G, Yang G, et al. BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity. Cell Res. 2018;28:855\u201361.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang Y, Zhou L, Liu N, Yao S. BE-PIGS: a base-editing tool with deaminases inlaid into Cas9 PI domain significantly expanded the editing scope. Signal Transduct Target Ther. 2019;4:36.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Villiger L, Schmidheini L, Mathis N, Rothgangl T, Marquart K, Schwank G. Replacing the SpCas9 HNH domain by deaminases generates compact base editors with an alternative targeting scope. Mol Ther Nucleic Acids. 2021;26:502\u201310.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019;365:48\u201353.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH. Transposon-encoded CRISPR-cas systems direct RNA-guided DNA integration. Nature. 2019;571:219\u201325.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yarnall MTN, Ioannidi EI, Schmitt-Ulms C, Krajeski RN, Lim J, Villiger L, et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol. 2023;41:500\u201312.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chen F, Lian M, Ma B, Gou S, Luo X, Yang K, et al. Multiplexed base editing through Cas12a variant-mediated cytosine and adenine base editors. Commun Biol. 2022;5:1163.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Geurts MH, Gandhi S, Boretto MG, Akkerman N, Derks LLM, van Son G, et al. One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids. Nat Commun. 2023;14:4998.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wu Y, Li Y, Liu Y, Xiu X, Liu J, Zhang L, et al. Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor. Nucleic Acids Res. 2024;52:4739\u201355.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gupta A, Liu B, Raza S, Chen QJ, Yang B. Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice. Plant Commun. 2024;5:100741.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Si T, Chao R, Min Y, Wu Y, Ren W, Zhao H. Automated multiplex genome-scale engineering in yeast. Nat Commun. 2017;8:15187.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li S, An J, Li Y, Zhu X, Zhao D, Wang L, et al. Automated high-throughput genome editing platform with an AI learning in situ prediction model. Nat Commun. 2022;13:7386.<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n","protected":false},"excerpt":{"rendered":"Wilson DS, Keefe AD. Random mutagenesis by PCR. Curr Protoc Mol Biol. 2001;51:8\u20133. Google Scholar\u00a0 Reetz MT, Wu…\n","protected":false},"author":2,"featured_media":164304,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[25],"tags":[7003,64,63,15373,1619,2931,9866,17818,108223,336,7001,17255,108224,17256,128],"class_list":{"0":"post-164303","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetics","8":"tag-animal-genetics-and-genomics","9":"tag-au","10":"tag-australia","11":"tag-bioinformatics","12":"tag-crispr","13":"tag-evolution","14":"tag-evolutionary-biology","15":"tag-functional-genomics","16":"tag-gene-diversification","17":"tag-genetics","18":"tag-human-genetics","19":"tag-microbial-genetics-and-genomics","20":"tag-organism-engineering","21":"tag-plant-genetics-and-genomics","22":"tag-science"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/posts\/164303","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/comments?post=164303"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/posts\/164303\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/media\/164304"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/media?parent=164303"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/categories?post=164303"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/au\/wp-json\/wp\/v2\/tags?post=164303"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}