Past, present, and future of CRISPR genome editing technologies

Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria

Nussenzweig, P. M., & Marraffini, L. A. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-022120-112523 · Cited by 219

Gene drives gaining speed

Bier, E. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00386-0 · Cited by 217

Efficient generation of mouse models with the prime editing system

Liu, Y., Li, X., He, S., Huang, S., Li, C., Chen, Y., Liu, Z., Huang, X., & Wang, X. (2020) · Cell Discovery · doi:10.1038/s41421-020-0165-z · Cited by 213

Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases

Yang, D., Scavuzzo, M. A., Chmielowiec, J., Sharp, R., Bajić, A., & Borowiak, M. (2016) · Scientific Reports · doi:10.1038/srep21264 · Cited by 212

Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome

Durrant, M. G., Fanton, A., Tycko, J., Hinks, M. M., Chandrasekaran, S. S., Perry, N. T., Schaepe, J. M., Du, P. P., Lotfy, P., Bassik, M. C., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01494-w · Cited by 212

Precise integration of large DNA sequences in plant genomes using PrimeRoot editors

Sun, C., Yuan, L., Li, B., Gao, Q., Li, Y., Cao, W., Yang, C., Li, H., Wang, Z., Li, Y., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01769-w · Cited by 212

Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

Xiang, X., Corsi, G. I., Anthon, C., Qu, K., Pan, X., Liang, X., Han, P., Dong, Z., Liu, L., Zhong, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23576-0 · Cited by 209

Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase

Tong, H., Wang, X., Liu, Y., Liu, N., Li, Y., Luo, J., Ma, Q., Wu, D., Li, J., Xu, C., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01595-6 · Cited by 205

Multifunctional CRISPR-Cas9 with Engineered Immunosilenced Human T Cell Epitopes

Ferdosi, S. R., Ewaisha, R., Moghadam, F., Krishna, S., Park, J. G., Ebrahimkhani, M. R., Kiani, S., & Anderson, K. S. (2019) · Nature Communications · doi:10.1038/s41467-019-09693-x · Cited by 204

A time-resolved, multi-symbol molecular recorder via sequential genome editing

Choi, J., Chen, W., Minkina, A., Chardon, F. M., Suiter, C. C., Regalado, S. G., Domcke, S., Hamazaki, N., Lee, C., Martin, B., et al. (2022) · Nature · doi:10.1038/s41586-022-04922-8 · Cited by 202

Engineering a precise adenine base editor with minimal bystander editing

Chen, L., Zhang, S., Xue, N., Hong, M., Zhang, X., Zhang, D., Yang, J., Bai, S., Huang, Y., Meng, H., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-022-01163-8 · Cited by 202

Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9

Anders, C., Bargsten, K., & Jinek, M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.020 · Cited by 201

Prediction of the sequence-specific cleavage activity of Cas9 variants

Kim, N., Kim, H. K., Lee, S., Seo, J. H., Choi, J. W., Park, J., Min, S., Yoon, S., Cho, S.-R., & Kim, H. H. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0537-9 · Cited by 198 · cited 1×

Structural basis for Cas9 off-target activity

Pacesa, M., Lin, C.-H., Cléry, A., Saha, A., Arantes, P. R., Bargsten, K., Irby, M. J., Allain, F. H.-T., Palermo, G., Cameron, P., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.026 · Cited by 198

Strategies for nonviral nanoparticle‐based delivery of CRISPR/Cas9 therapeutics

Chen, F., Alphonse, M., & Liu, Q. (2020) · WIREs Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.1609 · Cited by 197

Highly Parallel Profiling of Cas9 Variant Specificity

Schmid-Burgk, J. L., Gao, L., Li, D., Gardner, Z., Strecker, J., Lash, B., & Zhang, F. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.02.023 · Cited by 197

Controlling and enhancing CRISPR systems

Shivram, H., Cress, B. F., Knott, G. J., & Doudna, J. A. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-00700-7 · Cited by 194

Drug delivery systems for CRISPR-based genome editors

Madigan, V. J., Zhang, F., & Dahlman, J. E. (2023) · Nature Reviews Drug Discovery · doi:10.1038/s41573-023-00762-x · Cited by 193

Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion

Shou, J., Li, J., Liu, Y., & Wu, Q. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.021 · Cited by 192

Genome-wide target specificity of CRISPR RNA-guided adenine base editors

Kim, D., Kim, D.-E., Lee, G., Cho, S.-I., & Kim, J. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0050-1 · Cited by 192

GalNAc-Lipid nanoparticles enable non-LDLR dependent hepatic delivery of a CRISPR base editing therapy

Kasiewicz, L. N., Biswas, S., Beach, A., Ren, H., Dutta, C., Mazzola, A. M., Rohde, E., Chadwick, A. C., Cheng, C., Garcia, S. P., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37465-1 · Cited by 192

SIRT6 deficiency results in developmental retardation in cynomolgus monkeys

Zhang, W., Wan, H., Feng, G., Qu, J. T., Wang, J., Jing, Y., Ren, R., Liu, Z., Zhang, L., Chen, Z., et al. (2018) · Nature · doi:10.1038/s41586-018-0437-z · Cited by 191

Development of CRISPR-Cas systems for genome editing and beyond

Zhang, F. (2019) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583519000052 · Cited by 188

Human pluripotent reprogramming with CRISPR activators

Weltner, J., Balboa, D., Katayama, S., Bespalov, M., Krjutškov, K., Jouhilahti, E.-M., Trokovic, R., Kere, J., & Otonkoski, T. (2018) · Nature Communications · doi:10.1038/s41467-018-05067-x · Cited by 181

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair

Savić, N., Ringnalda, F. C. A. S., Lindsay, H. A., Berk, C., Bargsten, K., Li, Y., Neri, D., Robinson, M. D., Ciaudo, C., Hall, J., et al. (2018) · eLife · doi:10.7554/elife.33761 · Cited by 179

Efficient targeted insertion of large DNA fragments without DNA donors

Wang, J., Zhou, H., Wang, G., Zhang, R., Duan, J., Gao, P., Lei, X., Qiu, H.-Y., Zhang, C., Zhang, Y., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01399-1 · Cited by 178

Push back to respond better: regulatory inhibition of the DNA double-strand break response

Panier, S., & Durocher, D. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3659 · Cited by 177

R-loop formation and conformational activation mechanisms of Cas9

Pačesa, M., Loeff, L., Querques, I., Muckenfuss, L. M., Sawicka, M., & Jínek, M. (2022) · Nature · doi:10.1038/s41586-022-05114-0 · Cited by 176

Validation of microinjection methods for generating knockout mice by CRISPR/Cas-mediated genome engineering

Horii, T., Arai, Y., Yamazaki, M., Morita, S., Kimura, M., Itoh, M., Abe, Y., & Hatada, I. (2014) · Scientific Reports · doi:10.1038/srep04513 · Cited by 175

Cas9-specific immune responses compromise local and systemic AAV CRISPR therapy in multiple dystrophic canine models

Hakim, C. H., Kumar, S. R. P., Pérez-López, D. O., Wasala, N. B., Zhang, D., Yue, Y., Teixeira, J., Pan, X., Zhang, K., Million, E. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26830-7 · Cited by 175

RNA editing: Expanding the potential of RNA therapeutics

Booth, B. J., Nourreddine, S., Katrekar, D., Savva, Y., Bose, D., Long, T. J., Huss, D. J., & Mali, P. (2023) · Molecular Therapy · doi:10.1016/j.ymthe.2023.01.005 · Cited by 171

Assembly of CRISPR ribonucleoproteins with biotinylated oligonucleotides via an RNA aptamer for precise gene editing

Carlson-Stevermer, J., Abdeen, A. A., Kohlenberg, L., Goedland, M., Molugu, K., Lou, M., & Saha, K. (2017) · Nature Communications · doi:10.1038/s41467-017-01875-9 · Cited by 170

A split prime editor with untethered reverse transcriptase and circular RNA template

Liu, B., Dong, X., Cheng, H., Zheng, C., Chen, Z., Rodríguez, T., Liang, S., Xue, W., & Sontheimer, E. J. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01255-9 · Cited by 169

Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

Wroblewska, A., Dhainaut, M., Ben-Zvi, B., Rose, S. A., Park, E. S., Amir, E.-A. D., Bektesevic, A., Baccarini, A., Merad, M., Rahman, A. H., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.022 · Cited by 168

Predicting prime editing efficiency and product purity by deep learning

Mathis, N., Allam, A., Kissling, L., Marquart, K. F., Schmidheini, L., Solari, C., Balázs, Z., Krauthammer, M. O., & Schwank, G. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01613-7 · Cited by 167

Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering

Altae-Tran, H., Kannan, S., Suberski, A. J., Mears, K. S., Demircioglu, F. E., Moeller, L., Kocalar, S., Oshiro, R., Makarova, K. S., Macrae, R. K., et al. (2023) · Science · doi:10.1126/science.adi1910 · Cited by 167

Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System

Xu, W., Zhang, C., Yang, Y., Zhao, S., Kang, G., He, X., Song, J., & Yang, J. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.03.012 · Cited by 165

Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing

Chen, L., Zhu, B., Ru, G., Meng, H., Yan, Y., Hong, M., Zhang, D., Luan, C., Zhang, S., Wu, H., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01532-7 · Cited by 156

Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases

Lampe, G. D., King, R. T., Halpin-Healy, T. S., Klompe, S. E., Hogan, M. I., Vo, P. L. H., Tang, S., Chavez, A., & Sternberg, S. H. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01748-1 · Cited by 154

Structural basis for the altered PAM specificities of engineered CRISPR-cas9

Hirano, S., Nishimasu, H., Ishitani, R., & Nureki, O. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.018 · Cited by 152

Enhancement of target specificity of CRISPR–Cas12a by using a chimeric DNA–RNA guide

Kim, H., Lee, W.-J., Oh, Y., Kang, S.-H., Hur, J. K., Lee, H., Song, W., Lim, K. S., Park, Y., Song, B., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa605 · Cited by 151

Transcriptional recording by CRISPR spacer acquisition from RNA

Schmidt, F., Cherepkova, M. Y., & Platt, R. J. (2018) · Nature · doi:10.1038/s41586-018-0569-1 · Cited by 149

Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases

Tóth, E., Varga, É., Kulcsár, P. I., Kocsis-Jutka, V., Krausz, S. L., Nyeste, A., Welker, Z., Huszár, K., Ligeti, Z., Tálas, A., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa110 · Cited by 147

Base editing rescue of spinal muscular atrophy in cells and in mice

Arbab, M., Matuszek, Ż., Kray, K. M., Du, A., Newby, G. A., Blatnik, A. J., Raguram, A., Richter, M. F., Zhao, K. T., Levy, J. M., et al. (2023) · Science · doi:10.1126/science.adg6518 · Cited by 144

Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes

Foss, D. V., Muldoon, J. J., Nguyen, D. N., Carr, D., Sahu, S. U., Hunsinger, J. M., Wyman, S. K., Krishnappa, N., Mendonsa, R., Schanzer, E. V., et al. (2023) · Nature Biomedical Engineering · doi:10.1038/s41551-023-01032-2 · Cited by 143

DNA stretching induces Cas9 off-target activity

Newton, M. D., Taylor, B., Driessen, R. P. C., Roos, L., Cvetešić, N., Allyjaun, S., Lenhard, B., Cuomo, M. E., & Rueda, D. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0188-z · Cited by 142

Improved cytosine base editors generated from TadA variants

Lam, D. K., Feliciano, P. R., Arif, A., Bohnuud, T., Fernandez, T. P., Gehrke, J. M., Grayson, P., Lee, K. D., Ortega, M. A., Sawyer, C. B., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01611-9 · Cited by 140

Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors

Al-Shayeb, B., Skopintsev, P., Soczek, K. M., Stahl, E. C., Li, Z., Groover, E. D., Smock, D. C. J., Eggers, A. R., Pausch, P., Cress, B. F., et al. (2022) · Cell · doi:10.1016/j.cell.2022.10.020 · Cited by 138

Prediction of on-target and off-target activity of CRISPR–Cas13d guide RNAs using deep learning

Wessels, H., Stirn, A., Méndez‐Mancilla, A., Kim, E. J., Hart, S. K., Knowles, D. A., & Sanjana, N. E. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01830-8 · Cited by 136

High-performance CRISPR-Cas12a genome editing for combinatorial genetic screening

Gier, R. A., Budinich, K. A., Evitt, N. H., Cao, Z., Freilich, E., Chen, Q., Qi, J., Lan, Y., Kohli, R. M., & Shi, J. (2020) · Nature Communications · doi:10.1038/s41467-020-17209-1 · Cited by 135

Adenine transversion editors enable precise, efficient A•T-to-C•G base editing in mammalian cells and embryos

Chen, L., Hong, M., Luan, C., Gao, H., Ru, G., Guo, X., Zhang, D., Zhang, S., Li, C., Wu, J., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01821-9 · Cited by 135

Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions

Han, J. S. (2010) · Mobile DNA · doi:10.1186/1759-8753-1-15 · Cited by 132

Massively parallel kinetic profiling of natural and engineered CRISPR nucleases

Jones, S. K., Hawkins, J. A., Johnson, N. V., Jung, C., Hu, K., Rybarski, J. R., Chen, J. S., Doudna, J. A., Press, W. H., & Finkelstein, I. J. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0646-5 · Cited by 131

An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis

Hino, T., Omura, S. N., Nakagawa, R., Togashi, T., Takeda, S. N., Hiramoto, T., Tasaka, S., Hirano, H., Tokuyama, T., Uosaki, H., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.031 · Cited by 131

Massively parallel base editing to map variant effects in human hematopoiesis

Martin-Rufino, J. D., Castano, N., Pang, M., Grody, E. I., Joubran, S. R., Caulier, A., Wahlster, L., Li, T., Qiu, X., Riera-Escandell, A. M., et al. (2023) · Cell · doi:10.1016/j.cell.2023.03.035 · Cited by 130

Genome editing in large animals: current status and future prospects

Zhao, J., Lai, L., Ji, W., & Zhou, Q. (2019) · National Science Review · doi:10.1093/nsr/nwz013 · Cited by 129

Precise cut-and-paste DNA insertion using engineered type V-K CRISPR-associated transposases

Tou, C. J., Orr, B. C., & Kleinstiver, B. P. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01574-x · Cited by 126

Editing the genome of hiPSC with CRISPR/Cas9: disease models

Bassett, A. R. (2017) · Mammalian Genome · doi:10.1007/s00335-017-9684-9 · Cited by 125

A new age in protein design empowered by deep learning

Khakzad, H., Igashov, I., Schneuing, A., Goverde, C. A., Bronstein, M. M., & Correia, B. E. (2023) · Cell Systems · doi:10.1016/j.cels.2023.10.006 · Cited by 121

CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity

Joung, J., Kirchgatterer, P. C., Singh, A., Cho, J. H., Nety, S. P., Larson, R. C., Macrae, R. K., Deasy, R., Tseng, Y., Maus, M. V., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29205-8 · Cited by 119

Ectopic expression of RAD52 and dn53BP1 improves homology-directed repair during CRISPR–Cas9 genome editing

Paulsen, B. S., Mandal, P. K., Frock, R. L., Boyraz, B., Yadav, R., Upadhyayula, S., Gutierrez‐Martinez, P., Ebina, W., Fasth, A. L., Kirchhausen, T. L., et al. (2017) · Nature Biomedical Engineering · doi:10.1038/s41551-017-0145-2 · Cited by 117

Engineered amphiphilic peptides enable delivery of proteins and CRISPR-associated nucleases to airway epithelia

Krishnamurthy, S., Wohlford-Lenane, C., KANDIMALLA, S., Sartre, G., Meyerholz, D. K., Théberge, V., Hallée, S., Duperré, A.-M., Del’Guidice, T., Lepetit-Stoffaes, J.-P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12922-y · Cited by 116

Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors

Saunderson, E. A., Stepper, P., Gomm, J. J., Hoa, L., Morgan, A. A., Allen, M. D., Jones, J. L., Gribben, J. G., Jurkowski, T. P., & Ficz, G. (2017) · Nature Communications · doi:10.1038/s41467-017-01078-2 · Cited by 115

CRISPR-based therapeutics: current challenges and future applications

Modell, A. E., Lim, D., Nguyen, T. M., Sreekanth, V., & Choudhary, A. (2021) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2021.10.012 · Cited by 114

Increasing the efficiency and precision of prime editing with guide RNA pairs

Zhuang, Y., Liu, J., Wu, H., Zhu, Q., Yan, Y., Meng, H., Chen, P. R., & Yi, C. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00889-1 · Cited by 112

Engineered CRISPR/Cas9 enzymes improve discrimination by slowing DNA cleavage to allow release of off-target DNA

Liu, M., Gong, S., Yu, H., Jung, K., Johnson, K. A., & Taylor, D. W. (2020) · Nature Communications · doi:10.1038/s41467-020-17411-1 · Cited by 104

CRISPR engineering in organoids for gene repair and disease modelling

Geurts, M. H., & Clevers, H. (2023) · Nature Reviews Bioengineering · doi:10.1038/s44222-022-00013-5 · Cited by 103

Emerging applications for DNA writers and molecular recorders

Farzadfard, F., & Lu, T. K. (2018) · Science · doi:10.1126/science.aat9249 · Cited by 102

Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair

Wienert, B., Nguyen, D. N., Guenther, A., Feng, S. J., Locke, M. N., Wyman, S. K., Shin, J. J., Kazane, K. R., Gregory, G. L., Carter, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15845-1 · Cited by 102

Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens

Marquart, K. F., Allam, A., Janjuha, S., Sintsova, A., Villiger, L., Frey, N., Krauthammer, M., & Schwank, G. (2021) · Nature Communications · doi:10.1038/s41467-021-25375-z · Cited by 102

The miniature CRISPR-Cas12m effector binds DNA to block transcription

Wu, W. Y., Mohanraju, P., Liao, C., Adiego-Pérez, B., Creutzburg, S. C. A., Makarova, K. S., Keessen, K., Lindeboom, T. A., Khan, T. S., Prinsen, S. H. P., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.11.003 · Cited by 102

CRISPR‐Net: A Recurrent Convolutional Network Quantifies CRISPR Off‐Target Activities with Mismatches and Indels

Lin, J., Zhang, Z., Zhang, S., Chen, J., & Wong, K. (2020) · Advanced Science · doi:10.1002/advs.201903562 · Cited by 101

A universal deep-learning model for zinc finger design enables transcription factor reprogramming

Ichikawa, D. M., Abdin, O., Alerasool, N., Kogenaru, M., Mueller, A. L., Wen, H., Giganti, D. O., Goldberg, G. W., Adams, S., Spencer, J. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01624-4 · Cited by 101

Tissue-restricted genome editing in vivo specified by microRNA-repressible anti-CRISPR proteins

Lee, J., Mou, H., Ibraheim, R., Liang, S.-Q., Liu, P., Xue, W., & Sontheimer, E. J. (2019) · RNA · doi:10.1261/rna.071704.119 · Cited by 100

Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein

Tetter, S., Terasaka, N., Steinauer, A., Bingham, R. J., Clark, S., Scott, A. J. P., Patel, N., Leibundgut, M., Wroblewski, E., Ban, N., et al. (2021) · Science · doi:10.1126/science.abg2822 · Cited by 100

Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression

Wiegand, T., Karambelkar, S., Bondy‐Denomy, J., & Wiedenheft, B. (2020) · Annual Review of Microbiology · doi:10.1146/annurev-micro-020518-120107 · Cited by 97

CRISPR–Cas9 bends and twists DNA to read its sequence

Cofsky, J. C., Soczek, K. M., Knott, G. J., Nogales, E., & Doudna, J. A. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00756-0 · Cited by 91

Noninvasive assessment of gut function using transcriptional recording sentinel cells

Schmidt, F., Zimmermann, J., Tanna, T., Farouni, R., Conway, T., Macpherson, A. J., & Platt, R. J. (2022) · Science · doi:10.1126/science.abm6038 · Cited by 91

Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints

Chen, Q., Chuai, G., Zhang, H., Tang, J., Duan, L., Guan, H., Li, W., Li, W., Wen, J., Zuo, E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42695-4 · Cited by 89

Calcium dysregulation contributes to neurodegeneration in FTLD patient iPSC-derived neurons

Imamura, K., Sahara, N., Kanaan, N. M., Tsukita, K., Kondo, T., Kutoku, Y., Ohsawa, Y., Sunada, Y., Kawakami, K., Hotta, A., et al. (2016) · Scientific Reports · doi:10.1038/srep34904 · Cited by 88

Efficient high-precision homology-directed repair-dependent genome editing by HDRobust

Riesenberg, S., Kanis, P., Macak, D., Wollny, D., Düsterhöft, D., Kowalewski, J., Helmbrecht, N., Maričić, T., & Pääbo, S. (2023) · Nature Methods · doi:10.1038/s41592-023-01949-1 · Cited by 87

Bi-PE: bi-directional priming improves CRISPR/Cas9 prime editing in mammalian cells

Tao, R. X., Wang, Y., Jiao, Y., Hu, Y. F., Li, L., Jiang, L., Zhou, L., Qu, J., Chen, Q., & Yao, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac506 · Cited by 86

Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases

da Silva, J. F., Tou, C. J., King, E. M., Eller, M. L., Rufino‐Ramos, D., Ma, L., Cromwell, C. R., Metović, J., Benning, F. M. C., Chao, L. H., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02324-x · Cited by 86

Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA

Dmytrenko, O., Neumann, G. C., Hallmark, T., Keiser, D., Crowley, V. M., Vialetto, E., Mougiakos, I., Wandera, K. G., Domgaard, H., Weber, J., et al. (2023) · Nature · doi:10.1038/s41586-022-05559-3 · Cited by 85

RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2

Bravo, J. P. K., Hallmark, T., Naegle, B., Beisel, C. L., Jackson, R. N., & Taylor, D. W. (2023) · Nature · doi:10.1038/s41586-022-05560-w · Cited by 85

Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex

Kato, K., Zhou, W., Okazaki, S., Isayama, Y., Nishizawa, T., Gootenberg, J. S., Abudayyeh, O. O., & Nishimasu, H. (2022) · Cell · doi:10.1016/j.cell.2022.05.003 · Cited by 84

Transcriptional linkage analysis with in vivo AAV-Perturb-seq

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Target site selection and remodelling by type V CRISPR-transposon systems

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Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans

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UK first to approve CRISPR treatment for diseases: what you need to know

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Structures of the holo CRISPR RNA-guided transposon integration complex

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Lineage tracing and analog recording in mammalian cells by single-site DNA writing

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Inducible and reversible RNA N6-methyladenosine editing

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Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

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Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription

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Enhancement of Precise Gene Editing by the Association of Cas9 With Homologous Recombination Factors

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MIC-Drop: A platform for large-scale in vivo CRISPR screens

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Structural basis for the assembly of the type V CRISPR-associated transposon complex

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CRISPR/Cas9-mediated ApoE-/- and LDLR-/- double gene knockout in pigs elevates serum LDL-C and TC levels

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Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease

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High-throughput PRIME-editing screens identify functional DNA variants in the human genome

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Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells

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Cas9-directed immune tolerance in humans—a model to evaluate regulatory T cells in gene therapy?

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Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement

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Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates

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Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity

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Human germline genome editing

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RNA-guided retargeting of Sleeping Beauty transposition in human cells

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Engineering self-deliverable ribonucleoproteins for genome editing in the brain

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Selective TnsC recruitment enhances the fidelity of RNA-guided transposition

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Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses

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Transposon-encoded nucleases use guide RNAs to promote their selfish spread

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PAM-flexible genome editing with an engineered chimeric Cas9

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Heritable human genome editing: Research progress, ethical considerations, and hurdles to clinical practice

Turocy, J. M., Adashi, E. Y., & Egli, D. M. (2021) · Cell · doi:10.1016/j.cell.2021.02.036 · Cited by 56

Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

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Genome editing in large animal models

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Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility

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An Engineered Cas-Transposon System for Programmable and Site-Directed DNA Transpositions

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Pig-to-baboon lung xenotransplantation: Extended survival with targeted genetic modifications and pharmacologic treatments

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Electroporation and genetic supply of Cas9 increase the generation efficiency of CRISPR/Cas9 knock-in alleles in C57BL/6J mouse zygotes

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Blackjack mutations improve the on-target activities of increased fidelity variants of SpCas9 with 5′ G-extended sgRNAs

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Targeting double-strand break indel byproducts with secondary guide RNAs improves Cas9 HDR-mediated genome editing efficiencies

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Preclinical safety and biodistribution of CRISPR targeting SIV in non-human primates

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RNA-guided piggyBac transposition in human cells

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Generation of ApoE deficient dogs via combination of embryo injection of CRISPR/Cas9 with somatic cell nuclear transfer

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Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes

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DNA repair protein RAD51 enhances the CRISPR/Cas9-mediated knock-in efficiency in brain neurons

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Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

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RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications

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Mutations in MYLPF Cause a Novel Segmental Amyoplasia that Manifests as Distal Arthrogryposis

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Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector

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Targeted DNA transposition in vitro using a dCas9-transposase fusion protein

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RNA recording in single bacterial cells using reprogrammed tracrRNAs

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UBR7 functions with UBR5 in the Notch signaling pathway and is involved in a neurodevelopmental syndrome with epilepsy, ptosis, and hypothyroidism

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Molecular recording: transcriptional data collection into the genome

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New Tools for Lineage Tracing in Cancer In Vivo

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Genome editing with retroelements

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Proteasome impairment in neural cells derived from HMSN-P patient iPSCs

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Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicingPreprint

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Recursive Editing improves homology-directed repair through retargeting of undesired outcomes

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Reconstructing cell lineage trees with genomic barcoding: approaches and applications

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Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy, and periventricular calcifications

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An ultra-compact promoter drives widespread neuronal expression in mouse and monkey brains

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Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment

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Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domainsPreprint

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Emerging applications of gene editing technologies for the development of climate-resilient crops

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Efficient Multiplex Genome Editing of the Cyanobacterium Synechocystis sp. PCC6803 via CRISPR‐Cas12a

Du, W., Meister, L. L., van Grinsven, T., & Branco dos Santos, F. (2025) · Biotechnology and Bioengineering · doi:10.1002/bit.28910 · Cited by 7

Unintended CRISPR-Cas9 editing outcomes: a review of the detection and prevalence of structural variants generated by gene-editing in human cells

Hunt, J., Samson, C., du Rand, A., & Sheppard, H. M. (2023) · Human Genetics · doi:10.1007/s00439-023-02561-1 · Cited by 141

Strategies for Optimization of the Clustered Regularly Interspaced Short Palindromic Repeat-Based Genome Editing System for Enhanced Editing Specificity

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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review

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CRISPR/Cas9 system: A promising technology for the treatment of inherited and neoplastic hematological diseases

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Temperature effect on CRISPR-Cas9 mediated genome editing

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