Efficient high-precision transgene knock-in by Recombinases (Redα/β)-enhanced DNA integration-CRISPR-Cas9 (RED-CRISPR)

References

Pickar-Oliver, A. & Gersbach, C. A. The next generation of CRISPR-Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 20, 490–507 (2019).

Google Scholar
Carroll, D. Genome engineering with targetable nucleases. Annu Rev. Biochem 83, 409–439 (2014).

Google Scholar
Nambiar, T. S., Baudrier, L., Billon, P. & Ciccia, A. CRISPR-based genome editing through the lens of DNA repair. Mol. Cell 82, 348–388 (2022).

Google Scholar
Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat. Cell Biol. 21, 1468–1478 (2019).

Google Scholar
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

Google Scholar
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

Google Scholar
Maruyama, T. et al. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol. 33, 538–542 (2015).

Google Scholar
Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910–918 (2013).

Google Scholar
Campenhout, C. V. et al. Guidelines for optimized gene knockout using CRISPR/Cas9. Biotechniques 66, 295–302 (2019).

Google Scholar
Jensen, N. M. et al. An update on targeted gene repair in mammalian cells: methods and mechanisms. J. Biomed. Sci. 18, 10 (2011).

Google Scholar
Branzei, D. & Foiani, M. Regulation of DNA repair throughout the cell cycle. Nat. Rev. Mol. Cell Biol. 9, 297–308 (2008).

Google Scholar
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 47, 320–329 (2012).

Google Scholar
Riesenberg, S. et al. Efficient high-precision homology-directed repair-dependent genome editing by HDRobust. Nat. Methods 20, 1388–1399 (2023).

Google Scholar
Banan, M. Recent advances in CRISPR/Cas9-mediated knock-ins in mammalian cells. J. Biotechnol. 308, 1–9 (2020).

Google Scholar
Morrical, S. W. DNA-pairing and annealing processes in homologous recombination and homology-directed repair. Cold Spring Harb. Perspect. Biol. 7, a016444 (2015).

Google Scholar
Robert, F., Barbeau, M., Ethier, S., Dostie, J. & Pelletier, J. Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing. Genome Med. 7, 93 (2015).

Google Scholar
Riesenberg, S. & Maricic, T. Targeting repair pathways with small molecules increases precise genome editing in pluripotent stem cells. Nat. Commun. 9, 2164 (2018).

Google Scholar
Wimberger, S. et al. Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing. Nat. Commun. 14, 4761 (2023).

Google Scholar
Song, J. et al. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat. Commun. 7, 10548 (2016).

Google Scholar
Zhang, W. et al. A high-throughput small molecule screen identifies farrerol as a potentiator of CRISPR/Cas9-mediated genome editing. Elife 9, e56008 (2020).

Google Scholar
Paulsen, B. S. et al. Ectopic expression of RAD52 and dn53BP1 improves homology-directed repair during CRISPR-Cas9 genome editing. Nat. Biomed. Eng. 1, 878–888 (2017).

Google Scholar
Charpentier, M. et al. CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair. Nat. Commun. 9, 1133 (2018).

Google Scholar
Cai, Y. et al. In vivo genome editing rescues photoreceptor degeneration via a Cas9/RecA-mediated homology-directed repair pathway. Sci. Adv. 5, eaav3335 (2019).

Google Scholar
Wang, C. et al. Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. Nucleic Acids Res. 49, e36 (2021).

Google Scholar
Wang, C. et al. dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nat. Cell Biol. 24, 268–278 (2022).

Google Scholar
Gutschner, T., Haemmerle, M., Genovese, G., Draetta, G. F. & Chin, L. Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair. Cell Rep. 14, 1555–1566 (2016).

Google Scholar
Han, W. et al. Efficient precise integration of large DNA sequences with 3′-overhang dsDNA donors using CRISPR/Cas9. Proc. Natl Acad. Sci. USA 120, e2221127120 (2023).

Google Scholar
Cruz-Becerra, G. & Kadonaga, J. T. Enhancement of homology-directed repair with chromatin donor templates in cells. Elife 9, e55780 (2020).

Google Scholar
Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34, 339–344 (2016).

Google Scholar
Renaud, J. B. et al. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases. Cell Rep. 14, 2263–2272 (2016).

Google Scholar
Ghasemi, H. I. et al. Interstrand crosslinking of homologous repair template DNA enhances gene editing in human cells. Nat. Biotechnol. 41, 1398–1404 (2023).

Google Scholar
Shy, B. R. et al. High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails. Nat. Biotechnol. 41, 521–531 (2023).

Google Scholar
Nguyen, D. N. et al. Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency. Nat. Biotechnol. 38, 44–49 (2020).

Google Scholar
Wienert, B. et al. Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair. Nat. Commun. 11, 2109 (2020).

Google Scholar
Moller, L. et al. Recursive Editing improves homology-directed repair through retargeting of undesired outcomes. Nat. Commun. 13, 4550 (2022).

Google Scholar
Bodai, Z., Bishop, A. L., Gantz, V. M. & Komor, A. C. Targeting double-strand break indel byproducts with secondary guide RNAs improves Cas9 HDR-mediated genome editing efficiencies. Nat. Commun. 13, 2351 (2022).

Google Scholar
Chen, E. et al. Decorating chromatin for enhanced genome editing using CRISPR-Cas9. Proc. Natl Acad. Sci. USA 119, e2204259119 (2022).

Google Scholar
O’Driscoll, M. et al. DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Mol. Cell 8, 1175–1185 (2001).

Google Scholar
Woodbine, L., Gennery, A. R. & Jeggo, P. A. The clinical impact of deficiency in DNA non-homologous end-joining. DNA Repair (Amst.) 16, 84–96 (2014).

Google Scholar
Tao, J., Bauer, D. E. & Chiarle, R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat. Commun. 14, 212 (2023).

Google Scholar
Wang, J. et al. Efficient targeted insertion of large DNA fragments without DNA donors. Nat. Methods 19, 331–340 (2022).

Google Scholar
Gaudelli, N. M. et al. Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

Google Scholar
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

Google Scholar
Chen, P. J. & Liu, D. R. Prime editing for precise and highly versatile genome manipulation. Nat. Rev. Genet. 24, 161–177 (2023).

Google Scholar
Durrant, M. G. et al. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat. Biotechnol. 41, 488–499 (2023).

Google Scholar
Yarnall, M. T. N. et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2023).

Google Scholar
Iyer, L. M., Koonin, E. V. & Aravind, L. Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics 3, 8 (2002).

Google Scholar
Bell, J. C. & Kowalczykowski, S. C. RecA: Regulation and Mechanism of a Molecular Search Engine. Trends Biochem Sci. 41, 491–507 (2016).

Google Scholar
Lin, Z., Kong, H., Nei, M. & Ma, H. Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proc. Natl Acad. Sci. USA 103, 10328–10333 (2006).

Google Scholar
Murphy, K. C. Phage recombinases and their applications. Adv. Virus Res. 83, 367–414 (2012).

Google Scholar
Kuzminov, A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol. Biol. Rev. 63, 751–813 (1999).

Google Scholar
Caldwell, B. J. & Bell, C. E. Structure and mechanism of the Red recombination system of bacteriophage lambda. Prog. Biophys. Mol. Biol. 147, 33–46 (2019).

Google Scholar
Muyrers, J. P., Zhang, Y., Buchholz, F. & Stewart, A. F. RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners. Genes Dev. 14, 1971–1982 (2000).

Google Scholar
Mistry, J. et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).

Google Scholar
Lopes, A., Amarir-Bouhram, J., Faure, G., Petit, M. A. & Guerois, R. Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. Nucleic Acids Res. 38, 3952–3962 (2010).

Google Scholar
Bonilla, B., Hengel, S. R., Grundy, M. K. & Bernstein, K. A. RAD51 Gene Family Structure and Function. Annu Rev. Genet 54, 25–46 (2020).

Google Scholar
Martinsohn, J. T., Radman, M. & Petit, M. A. The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. PLoS Genet 4, e1000065 (2008).

Google Scholar
Pan, X. et al. A Structure-Activity Analysis for Probing the Mechanism of Processive Double-Stranded DNA Digestion by lambda Exonuclease Trimers. Biochemistry 54, 6139–6148 (2015).

Google Scholar
Zakharova, K., Caldwell, B. J., Ta, S., Wheat, C. T. & Bell, C. E. Mutational Analysis of Redbeta Single Strand Annealing Protein: Roles of the 14 Lysine Residues in DNA Binding and Recombination In Vivo. Int J. Mol. Sci. 22, 7758 (2021).

Google Scholar
Yu, Y. et al. An efficient gene knock-in strategy using 5′-modified double-stranded DNA donors with short homology arms. Nat. Chem. Biol. 16, 387–390 (2020).

Google Scholar
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).

Google Scholar
Macville, M. et al. Comprehensive and definitive molecular cytogenetic characterization of HeLa cells by spectral karyotyping. Cancer Res. 59, 141–150 (1999).

Google Scholar
Zhang, J. P. et al. Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage. Genome Biol. 18, 35 (2017).

Google Scholar
Paix, A. et al. Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks. Proc. Natl Acad. Sci. USA 114, E10745–E10754 (2017).

Google Scholar
Lin, S., Staahl, B. T., Alla, R. K. & Doudna, J. A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3, e04766 (2014).

Google Scholar
Yao, X. et al. Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res. 27, 801–814 (2017).

Google Scholar
Rees, H. A., Yeh, W. H. & Liu, D. R. Development of hRad51-Cas9 nickase fusions that mediate HDR without double-stranded breaks. Nat. Commun. 10, 2212 (2019).

Google Scholar
Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015).

Google Scholar
Malinin, N. L. et al. Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq. Nat. Protoc. 16, 5592–5615 (2021).

Google Scholar
Yin, J. et al. Optimizing genome editing strategy by primer-extension-mediated sequencing. Cell Discov. 5, 18 (2019).

Google Scholar
Zhang, L. et al. Guide-specific loss of efficiency and off-target reduction with Cas9 variants. Nucleic Acids Res. 51, 9880–9893 (2023).

Google Scholar
Yin, J. et al. Cas9 exo-endonuclease eliminates chromosomal translocations during genome editing. Nat. Commun. 13, 1204 (2022).

Google Scholar
Turchiano, G. et al. Quantitative evaluation of chromosomal rearrangements in gene-edited human stem cells by CAST-Seq. Cell Stem Cell 28, 1136–1147.e1135 (2021).

Google Scholar
Chou, B. K. et al. Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures. Cell Res. 21, 518–529 (2011).

Google Scholar
Cai, L. et al. A Universal Approach to Correct Various HBB Gene Mutations in Human Stem Cells for Gene Therapy of Beta-Thalassemia and Sickle Cell Disease. Stem Cells Transl. Med. 7, 87–97 (2018).

Google Scholar
Tilgner, K. et al. A human iPSC model of Ligase IV deficiency reveals an important role for NHEJ-mediated-DSB repair in the survival and genomic stability of induced pluripotent stem cells and emerging haematopoietic progenitors. Cell Death Differ. 20, 1089–1100 (2013).

Google Scholar
Eyquem, J. et al. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature 543, 113–117 (2017).

Google Scholar
Webber, B. R. et al. Cas9-induced targeted integration of large DNA payloads in primary human T cells via homology-mediated end-joining DNA repair. Nat. Biomed. Eng. 8, 1553–1570 (2024).

Google Scholar
Zou, R. S. et al. Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. Nat. Methods 20, 706–713 (2023).

Google Scholar
Donohoue, P. D. et al. Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol. Cell 81, 3637–3649.e3635 (2021).

Google Scholar
Zhao, B., Rothenberg, E., Ramsden, D. A. & Lieber, M. R. The molecular basis and disease relevance of non-homologous DNA end joining. Nat. Rev. Mol. Cell Biol. 21, 765–781 (2020).

Google Scholar
Xue, C. & Greene, E. C. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 37, 639–656 (2021).

Google Scholar
Peabody, D. S. & Lim, F. Complementation of RNA binding site mutations in MS2 coat protein heterodimers. Nucleic Acids Res 24, 2352–2359 (1996).

Google Scholar
Huang, F. et al. Identification of specific inhibitors of human RAD51 recombinase using high-throughput screening. ACS Chem. Biol. 6, 628–635 (2011).

Google Scholar
Datta, S., Costantino, N., Zhou, X. & Court, D. L. Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc. Natl Acad. Sci. USA 105, 1626–1631 (2008).

Google Scholar
Richardson, R. R. et al. Enhancing Precision and Efficiency of Cas9-Mediated Knockin Through Combinatorial Fusions of DNA Repair Proteins. CRISPR J. 6, 447–461 (2023).

Google Scholar
Lin, L. et al. Fusion of SpCas9 to E. coli Rec A protein enhances CRISPR-Cas9 mediated gene knockout in mammalian cells. J. Biotechnol. 247, 42–49 (2017).

Google Scholar
Hackley, C. R. A Novel Set of Cas9 Fusion Proteins to Stimulate Homologous Recombination: Cas9-HRs. CRISPR J. 4, 253–263 (2021).

Google Scholar
Wilde, J. J. et al. Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair. Cell 184, 3267–3280.e3218 (2021).

Google Scholar
Ellis, H. M., Yu, D., DiTizio, T. & Court, D. L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl Acad. Sci. USA 98, 6742–6746 (2001).

Google Scholar
Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA 97, 5978–5983 (2000).

Google Scholar
Charles, M., Radding, J. R., Richards, F. & Cassuto, E. Appendix: Separation And Characterization Of Exonuclease, β Protein, and A Complex Of Both. J. Biol. Chem. 246, 2510–2512 (1971).
Carter, D. M. & Radding, C. M. The role of exonuclease and beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease. J. Biol. Chem. 246, 2502–2512 (1971).

Google Scholar
Radding, C. M. & Carter, D. M. The role of exonuclease and beta protein of phage lambda in genetic recombination. 3. Binding to deoxyribonucleic acid. J. Biol. Chem. 246, 2513–2518 (1971).

Google Scholar
Caldwell, B. J. et al. Crystal structure of the Redbeta C-terminal domain in complex with lambda Exonuclease reveals an unexpected homology with lambda Orf and an interaction with Escherichia coli single stranded DNA binding protein. Nucleic Acids Res. 47, 1950–1963 (2019).

Google Scholar
Filsinger, G. T. et al. Characterizing the portability of phage-encoded homologous recombination proteins. Nat. Chem. Biol. 17, 394–402 (2021).

Google Scholar
Miyaoka, Y. et al. Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Sci. Rep. 6, 23549 (2016).

Google Scholar
Xu, Z. et al. Carrier strategies boost the application of CRISPR/Cas system in gene therapy. Exploration (Beijing) 2, 20210081 (2022).

Google Scholar
Xin, C. et al. Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption. Nat. Commun. 13, 5623 (2022).

Google Scholar
Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374, 57–65 (2021).

Google Scholar
Han, D. et al. Development of miniature base editors using engineered IscB nickase. Nat. Methods 20, 1029–1036 (2023).

Google Scholar
Xiang, G. et al. Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors. Nat. Biotechnol. 42, 745–757 (2023).

Google Scholar