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Search-and-replace genome editing without double-strand breaks or donor DNA

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  1. You-Jeong Kim & Dayoung Yun & Jungjoon K. Lee & Cheulhee Jung & Aram J. Chung, 2024. "Highly efficient CRISPR-mediated genome editing through microfluidic droplet cell mechanoporation," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  2. Hongyuan Zhang & Jiacheng Ma & Zhaowei Wu & Xiaoyang Chen & Yangyang Qian & Weizhong Chen & Zhipeng Wang & Ya Zhang & Huanhu Zhu & Xingxu Huang & Quanjiang Ji, 2024. "BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
  3. Mu Li & Aaron Zhong & Youjun Wu & Mega Sidharta & Michael Beaury & Xiaolan Zhao & Lorenz Studer & Ting Zhou, 2022. "Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  4. Jaesuk Lee & Kayeong Lim & Annie Kim & Young Geun Mok & Eugene Chung & Sung-Ik Cho & Ji Min Lee & Jin-Soo Kim, 2023. "Prime editing with genuine Cas9 nickases minimizes unwanted indels," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  5. Ronghao Chen & Yu Cao & Yajing Liu & Dongdong Zhao & Ju Li & Zhihui Cheng & Changhao Bi & Xueli Zhang, 2023. "Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
  6. Michelle L. Johnson & Bruce A. Hay & Maciej Maselko, 2024. "Altering traits and fates of wild populations with Mendelian DNA sequence modifying Allele Sails," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  7. Xiaoguang Pan & Kunli Qu & Hao Yuan & Xi Xiang & Christian Anthon & Liubov Pashkova & Xue Liang & Peng Han & Giulia I. Corsi & Fengping Xu & Ping Liu & Jiayan Zhong & Yan Zhou & Tao Ma & Hui Jiang & J, 2022. "Massively targeted evaluation of therapeutic CRISPR off-targets in cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  8. Huawei Tong & Haoqiang Wang & Xuchen Wang & Nana Liu & Guoling Li & Danni Wu & Yun Li & Ming Jin & Hengbin Li & Yinghui Wei & Tong Li & Yuan Yuan & Linyu Shi & Xuan Yao & Yingsi Zhou & Hui Yang, 2024. "Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  9. Jeonghun Kwon & Minyoung Kim & Seungmin Bae & Anna Jo & Youngho Kim & Jungjoon K. Lee, 2022. "TAPE-seq is a cell-based method for predicting genome-wide off-target effects of prime editor," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  10. You Li & Zhiqiang Li & Ruiling Chen & Min Lian & Hanxiao Wang & Yiran Wei & Zhengrui You & Jun Zhang & Bo Li & Yikang Li & Bingyuan Huang & Yong Chen & Qiaoyan Liu & Zhuwan Lyu & Xueying Liang & Qi Mi, 2023. "A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  11. Peter N. Ciaccia & Zhuobin Liang & Anabel Y. Schweitzer & Eli Metzner & Farren J. Isaacs, 2024. "Enhanced eMAGE applied to identify genetic factors of nuclear hormone receptor dysfunction via combinatorial gene editing," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  12. Kun Jia & Yan-ru Cui & Shisheng Huang & Peihong Yu & Zhengxing Lian & Peixiang Ma & Jia Liu, 2022. "Phage peptides mediate precision base editing with focused targeting window," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  13. Arianna Moiani & Gil Letort & Sabrina Lizot & Anne Chalumeau & Chloe Foray & Tristan Felix & Diane Clerre & Sonal Temburni-Blake & Patrick Hong & Sophie Leduc & Noemie Pinard & Alan Marechal & Eduardo, 2024. "Non-viral DNA delivery and TALEN editing correct the sickle cell mutation in hematopoietic stem cells," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  14. Jonathan Tellechea-Luzardo & Leanne Hobbs & Elena Velázquez & Lenka Pelechova & Simon Woods & Víctor Lorenzo & Natalio Krasnogor, 2022. "Versioning biological cells for trustworthy cell engineering," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  15. Sébastien Levesque & Diana Mayorga & Jean-Philippe Fiset & Claudia Goupil & Alexis Duringer & Andréanne Loiselle & Eva Bouchard & Daniel Agudelo & Yannick Doyon, 2022. "Marker-free co-selection for successive rounds of prime editing in human cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  16. Lisa Maria Riedmayr & Klara Sonnie Hinrichsmeyer & Stefan Bernhard Thalhammer & David Manuel Mittas & Nina Karguth & Dina Yehia Otify & Sybille Böhm & Valentin Johannes Weber & Michael David Bartosche, 2023. "mRNA trans-splicing dual AAV vectors for (epi)genome editing and gene therapy," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  17. Marion Rosello & Malo Serafini & Luca Mignani & Dario Finazzi & Carine Giovannangeli & Marina C. Mione & Jean-Paul Concordet & Filippo Del Bene, 2022. "Disease modeling by efficient genome editing using a near PAM-less base editor in vivo," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  18. Yuting Chen & Eriona Hysolli & Anlu Chen & Stephen Casper & Songlei Liu & Kevin Yang & Chenli Liu & George Church, 2022. "Multiplex base editing to convert TAG into TAA codons in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  19. Xiangfeng Kong & Hainan Zhang & Guoling Li & Zikang Wang & Xuqiang Kong & Lecong Wang & Mingxing Xue & Weihong Zhang & Yao Wang & Jiajia Lin & Jingxing Zhou & Xiaowen Shen & Yinghui Wei & Na Zhong & W, 2023. "Engineered CRISPR-OsCas12f1 and RhCas12f1 with robust activities and expanded target range for genome editing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  20. Minja Velimirovic & Larissa C. Zanetti & Max W. Shen & James D. Fife & Lin Lin & Minsun Cha & Ersin Akinci & Danielle Barnum & Tian Yu & Richard I. Sherwood, 2022. "Peptide fusion improves prime editing efficiency," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
  21. Roberta Esposito & Andrés Lanzós & Tina Uroda & Sunandini Ramnarayanan & Isabel Büchi & Taisia Polidori & Hugo Guillen-Ramirez & Ante Mihaljevic & Bernard Mefi Merlin & Lia Mela & Eugenio Zoni & Lusin, 2023. "Tumour mutations in long noncoding RNAs enhance cell fitness," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  22. Xiangyang Li & Guiquan Zhang & Shisheng Huang & Yao Liu & Jin Tang & Mingtian Zhong & Xin Wang & Wenjun Sun & Yuan Yao & Quanjiang Ji & Xiaolong Wang & Jianghuai Liu & Shiqiang Zhu & Xingxu Huang, 2023. "Development of a versatile nuclease prime editor with upgraded precision," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  23. J. Ferreira da Silva & G. P. Oliveira & E. A. Arasa-Verge & C. Kagiou & A. Moretton & G. Timelthaler & J. Jiricny & J. I. Loizou, 2022. "Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  24. Péter István Kulcsár & András Tálas & Zoltán Ligeti & Sarah Laura Krausz & Ervin Welker, 2022. "SuperFi-Cas9 exhibits remarkable fidelity but severely reduced activity yet works effectively with ABE8e," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  25. Maria Pallarès-Masmitjà & Dimitrije Ivančić & Júlia Mir-Pedrol & Jessica Jaraba-Wallace & Tommaso Tagliani & Baldomero Oliva & Amal Rahmeh & Avencia Sánchez-Mejías & Marc Güell, 2021. "Find and cut-and-transfer (FiCAT) mammalian genome engineering," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
  26. Ju-Chan Park & Yun-Jeong Kim & Gue-Ho Hwang & Chan Young Kang & Sangsu Bae & Hyuk-Jin Cha, 2024. "Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  27. Hongzhi Zeng & Qichen Yuan & Fei Peng & Dacheng Ma & Ananya Lingineni & Kelly Chee & Peretz Gilberd & Emmanuel C. Osikpa & Zheng Sun & Xue Gao, 2023. "A split and inducible adenine base editor for precise in vivo base editing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  28. Friedrich Fauser & Bhakti N. Kadam & Sebastian Arangundy-Franklin & Jessica E. Davis & Vishvesha Vaidya & Nicola J. Schmidt & Garrett Lew & Danny F. Xia & Rakshaa Mureli & Colman Ng & Yuanyue Zhou & N, 2024. "Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  29. Ting Fu & Kofi Amoah & Tracey W. Chan & Jae Hoon Bahn & Jae-Hyung Lee & Sari Terrazas & Rockie Chong & Sriram Kosuri & Xinshu Xiao, 2024. "Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  30. Tian Zhou & Xinyi Zhu & Zhizhong Ye & Yong-Fei Wang & Chao Yao & Ning Xu & Mi Zhou & Jianyang Ma & Yuting Qin & Yiwei Shen & Yuanjia Tang & Zhihua Yin & Hong Xu & Yutong Zhang & Xiaoli Zang & Huihua D, 2022. "Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  31. Charlotte Cautereels & Jolien Smets & Jonas De Saeger & Lloyd Cool & Yanmei Zhu & Anna Zimmermann & Jan Steensels & Anton Gorkovskiy & Thomas B. Jacobs & Kevin J. Verstrepen, 2024. "Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  32. Dominique L. Brooks & Manuel J. Carrasco & Ping Qu & William H. Peranteau & Rebecca C. Ahrens-Nicklas & Kiran Musunuru & Mohamad-Gabriel Alameh & Xiao Wang, 2023. "Rapid and definitive treatment of phenylketonuria in variant-humanized mice with corrective editing," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
  33. Chunwei Zheng & Bin Liu & Xiaolong Dong & Nicholas Gaston & Erik J. Sontheimer & Wen Xue, 2023. "Template-jumping prime editing enables large insertion and exon rewriting in vivo," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
  34. Matin Qaim, 2020. "Role of New Plant Breeding Technologies for Food Security and Sustainable Agricultural Development," Applied Economic Perspectives and Policy, John Wiley & Sons, vol. 42(2), pages 129-150, June.
  35. Zeyu Lu & Lingtian Zhang & Qing Mu & Junyang Liu & Yu Chen & Haoyuan Wang & Yanjun Zhang & Rui Su & Ruijun Wang & Zhiying Wang & Qi Lv & Zhihong Liu & Jiasen Liu & Yunhua Li & Yanhong Zhao, 2024. "Progress in Research and Prospects for Application of Precision Gene-Editing Technology Based on CRISPR–Cas9 in the Genetic Improvement of Sheep and Goats," Agriculture, MDPI, vol. 14(3), pages 1-17, March.
  36. I. F. Schene & I. P. Joore & J. H. L. Baijens & R. Stevelink & G. Kok & S. Shehata & E. F. Ilcken & E. C. M. Nieuwenhuis & D. P. Bolhuis & R. C. M. Rees & S. A. Spelier & H. P. J. Doef & J. M. Beekman, 2022. "Mutation-specific reporter for optimization and enrichment of prime editing," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  37. Afsaneh Sadremomtaz & Robert F. Glass & Jorge Eduardo Guerrero & Dennis R. LaJeunesse & Eric A. Josephs & Reza Zadegan, 2023. "Digital data storage on DNA tape using CRISPR base editors," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
  38. Yi-Li Feng & Qian Liu & Ruo-Dan Chen & Si-Cheng Liu & Zhi-Cheng Huang & Kun-Ming Liu & Xiao-Ying Yang & An-Yong Xie, 2022. "DNA nicks induce mutational signatures associated with BRCA1 deficiency," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  39. Martin Peterka & Nina Akrap & Songyuan Li & Sandra Wimberger & Pei-Pei Hsieh & Dmitrii Degtev & Burcu Bestas & Jack Barr & Stijn Plassche & Patricia Mendoza-Garcia & Saša Šviković & Grzegorz Sienski &, 2022. "Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
  40. Zhenxing Yu & Zhike Lu & Jingjing Li & Yingying Wang & Panfeng Wu & Yini Li & Yangfan Zhou & Bailun Li & Heng Zhang & Yingzheng Liu & Lijia Ma, 2022. "PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  41. Guiquan Zhang & Yao Liu & Shisheng Huang & Shiyuan Qu & Daolin Cheng & Yuan Yao & Quanjiang Ji & Xiaolong Wang & Xingxu Huang & Jianghuai Liu, 2022. "Enhancement of prime editing via xrRNA motif-joined pegRNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  42. Zhaohui Zhong & Guanqing Liu & Zhongjie Tang & Shuyue Xiang & Liang Yang & Lan Huang & Yao He & Tingting Fan & Shishi Liu & Xuelian Zheng & Tao Zhang & Yiping Qi & Jian Huang & Yong Zhang, 2023. "Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  43. Daphne Collias & Elena Vialetto & Jiaqi Yu & Khoa Co & Éva d. H. Almási & Ann-Sophie Rüttiger & Tatjana Achmedov & Till Strowig & Chase L. Beisel, 2023. "Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  44. Xiaosa Li & Lina Zhou & Bao-Qing Gao & Guangye Li & Xiao Wang & Ying Wang & Jia Wei & Wenyan Han & Zixian Wang & Jifang Li & Runze Gao & Junjie Zhu & Wenchao Xu & Jing Wu & Bei Yang & Xiaodong Sun & L, 2022. "Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
  45. Zsolt Bodai & Alena L. Bishop & Valentino M. Gantz & Alexis C. Komor, 2022. "Targeting double-strand break indel byproducts with secondary guide RNAs improves Cas9 HDR-mediated genome editing efficiencies," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  46. Qichen Yuan & Xue Gao, 2022. "Multiplex base- and prime-editing with drive-and-process CRISPR arrays," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  47. Chao Yang & Zhenzhen Ma & Keshan Wang & Xingxiao Dong & Meiyu Huang & Yaqiu Li & Xiagu Zhu & Ju Li & Zhihui Cheng & Changhao Bi & Xueli Zhang, 2023. "HMGN1 enhances CRISPR-directed dual-function A-to-G and C-to-G base editing," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  48. Nana Yan & Hu Feng & Yongsen Sun & Ying Xin & Haihang Zhang & Hongjiang Lu & Jitan Zheng & Chenfei He & Zhenrui Zuo & Tanglong Yuan & Nana Li & Long Xie & Wu Wei & Yidi Sun & Erwei Zuo, 2023. "Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  49. Michael Kosicki & Felicity Allen & Frances Steward & Kärt Tomberg & Yangyang Pan & Allan Bradley, 2022. "Cas9-induced large deletions and small indels are controlled in a convergent fashion," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  50. Luke Hoberecht & Pirunthan Perampalam & Aaron Lun & Jean-Philippe Fortin, 2022. "A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  51. Péter István Kulcsár & András Tálas & Zoltán Ligeti & Eszter Tóth & Zsófia Rakvács & Zsuzsa Bartos & Sarah Laura Krausz & Ágnes Welker & Vanessza Laura Végi & Krisztina Huszár & Ervin Welker, 2023. "A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  52. Jianli Tao & Qi Wang & Carlos Mendez-Dorantes & Kathleen H. Burns & Roberto Chiarle, 2022. "Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  53. Maarten H. Geurts & Shashank Gandhi & Matteo G. Boretto & Ninouk Akkerman & Lucca L. M. Derks & Gijs Son & Martina Celotti & Sarina Harshuk-Shabso & Flavia Peci & Harry Begthel & Delilah Hendriks & Pa, 2023. "One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  54. Udaya Subedi & Kazi Kader & Kethmi N. Jayawardhane & Hari Poudel & Guanqun Chen & Surya Acharya & Luiz S. A. Camargo & Daniela Matias de C. Bittencourt & Stacy D. Singer, 2022. "The Potential of Novel Gene Editing-Based Approaches in Forages and Rumen Archaea for Reducing Livestock Methane Emissions," Agriculture, MDPI, vol. 12(11), pages 1-21, October.
  55. András Tálas & Dorottya A. Simon & Péter I. Kulcsár & Éva Varga & Sarah L. Krausz & Ervin Welker, 2021. "BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  56. Chao Chen & Zhenxing Zhang & Caiyun Liu & Bin Wang & Ping Liu & Shu Fang & Fan Yang & Yongping You & Xinjian Li, 2022. "ATF4-dependent fructolysis fuels growth of glioblastoma multiforme," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  57. Yanik Weber & Desirée Böck & Anastasia Ivașcu & Nicolas Mathis & Tanja Rothgangl & Eleonora I. Ioannidi & Alex C. Blaudt & Lisa Tidecks & Máté Vadovics & Hiromi Muramatsu & Andreas Reichmuth & Kim F. , 2024. "Enhancing prime editor activity by directed protein evolution in yeast," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  58. Guanhua Xun & Zhixin Zhu & Nilmani Singh & Jingxia Lu & Piyush K. Jain & Huimin Zhao, 2024. "Harnessing noncanonical crRNA for highly efficient genome editing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  59. Patrizia Tornabene & Rita Ferla & Manel Llado-Santaeularia & Miriam Centrulo & Margherita Dell’Anno & Federica Esposito & Elena Marrocco & Emanuela Pone & Renato Minopoli & Carolina Iodice & Edoardo N, 2022. "Therapeutic homology-independent targeted integration in retina and liver," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  60. Duško Lainšček & Vida Forstnerič & Veronika Mikolič & Špela Malenšek & Peter Pečan & Mojca Benčina & Matjaž Sever & Helena Podgornik & Roman Jerala, 2022. "Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  61. Raed Ibraheim & Phillip W. L. Tai & Aamir Mir & Nida Javeed & Jiaming Wang & Tomás C. Rodríguez & Suk Namkung & Samantha Nelson & Eraj Shafiq Khokhar & Esther Mintzer & Stacy Maitland & Zexiang Chen &, 2021. "Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
  62. Karinne Ludlow, 2024. "Implications of Law’s Response to Mitochondrial Donation," Laws, MDPI, vol. 13(2), pages 1-15, March.
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