Article
Multidisciplinary Sciences
Zsolt Bodai, Alena L. Bishop, Valentino M. Gantz, Alexis C. Komor
Summary: Programmable double-strand DNA breaks (DSBs) can be harnessed for precision genome editing through manipulation of the homology-directed repair (HDR) pathway. This study introduces a general strategy called the double tap method, which improves HDR-mediated precision editing efficiency by taking advantage of the reproducible nature of indel sequences. The method utilizes multiple gRNAs, including a primary gRNA that targets the wild-type genomic sequence and one or more secondary gRNAs that target the most common indel sequence(s).
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xinyi Li, Bing Sun, Hongrun Qian, Jinrong Ma, Magdalena Paolino, Zhiying Zhang
Summary: Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 nuclease (Cas9) is a highly efficient genome editing tool. However, achieving biallelic editing remains a technical challenge. In this study, the authors developed a novel method to enable biallelic editing using CRISPR/Cas9-mediated homology-directed repair (HDR), and enriched the positively targeted cell clones through an integrated selection system. Experimental results on the APP and PSEN1 genes demonstrated high biallelic editing efficiency using this approach.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2022)
Article
Multidisciplinary Sciences
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
Summary: Strategies to improve the specificity of nuclease-based prime editor (PEn) are needed. Here the authors report a 53BP1-inhibitory ubiquitin variant-assisted PEn platform (uPEn) to inhibit NHEJ and enable precise prime editing for generation of insertions, deletions, and replacements.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Guoling Li, Xiaohui Yang, Xinxin Luo, Zhenfang Wu, Huaqiang Yang
Summary: The use of small molecules to synchronize the cell cycle in S and G2/M phases enhances the efficiency of CRISPR/Cas9-mediated homology-directed repair (HDR) in animal cells and embryos. The study reveals the common molecular mechanisms that connect cell cycle progression and HDR activity.
CELL AND BIOSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Zhihan Zhao, Peng Shang, Fanny Sage, Niels Geijsen
Summary: CRISPR/Cas12a is a nuclease that generates sticky-ended DNA double strand breaks, which can be utilized for precise genome editing through a strategy called 'Ligation-Assisted Homologous Recombination' (LAHR). LAHR achieves high editing efficiency by using a short double-stranded DNA repair template with sticky ends and homologous arms. This study expands the repertoire of genome editing technologies and provides insights into DNA repair mechanisms involved in genome editing.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Biochemistry & Molecular Biology
Brett M. Sansbury, Eric B. Kmiec
Summary: The expectations for selectively modifying the human genome have never been higher in the last five years. The development of site-specific nucleases is centerstage in effective molecular therapies, with a focus on correcting genetic mutations that cause cancer and inherited diseases. Homology directed repair, a process for reversing mutations and restoring normal protein function, is a key technique that is being researched for human gene editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Kevin Bloh, Natalia Rivera-Torres
Summary: The mechanism of ssODN-directed gene editing has been a topic of discussion within the field of CRISPR gene editing. The ExACT pathway, based on oligo-driven DNA repair, provides a comprehensive understanding of the different ways DNA repair can occur in the presence of a repair oligonucleotide after CRISPR cleavage, by comparing and challenging other similar DNA repair pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Hiromi Miura, Jurai Imafuku, Aki Kurosaki, Masahiro Sato, Yongjie Ma, Guisheng Zhang, Akiko Mizutani, Kenya Kamimura, Channabasavaiah B. Gurumurthy, Dexi Liu, Masato Ohtsuka
Summary: The CRISPR system is a powerful tool for genome editing that has been widely used in medical research. Researchers have developed and validated DEGFP mouse models for evaluating genome editing tools, demonstrating their utility in assessing both NHEJ and HDR processes. The results suggest that these models can serve as valuable tools for in vivo genome editing evaluation.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Review
Pharmacology & Pharmacy
Adrian B. C. Lee, Meng-How Tan, Christina L. L. Chai
Summary: Using small molecules to increase the efficiency of HDR and decrease NHEJ to improve the efficiency of precise knock-in genome editing.
DRUG DISCOVERY TODAY
(2022)
Review
Biochemistry & Molecular Biology
Svetlana A. Smirnikhina, Milyausha I. Zaynitdinova, Vasilina A. Sergeeva, Alexander V. Lavrov
Summary: This article investigates the use of methods that influence the cell cycle in genome editing experiments to improve the efficiency of gene editing. Despite the reversible effects on the cell cycle, caution is still needed to prevent cell mutations and malignant transformation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Igor Petkovic, Johannes Bischof, Thomas Kocher, Oliver Patrick March, Bernadette Liemberger, Stefan Hainzl, Dirk Strunk, Anna Maria Raninger, Heide-Marie Binder, Julia Reichelt, Christina Guttmann-Gruber, Verena Wally, Josefina Pinon Hofbauer, Johann Wolfgang Bauer, Ulrich Koller
Summary: In this study, researchers used CRISPR/Cas9 gene editing technique to successfully correct a causal pathogenic frameshift mutation in the COL17A1 gene, which leads to junctional epidermolysis bullosa. By inducing both end-joining repair and HDR-mediated pathways, they achieved efficient gene repair and observed improved cellular functions and structures in the corrected cells.
FRONTIERS IN MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Christopher E. Denes, Alexander J. Cole, Yagiz Alp Aksoy, Geng Li, Graham Gregory Neely, Daniel Hesselson
Summary: Genome modification holds great potential for disease prevention or treatment, with CRISPR/Cas9 techniques showing promise in altering disease-relevant genes. Competition among DNA repair pathways can lead to undesirable editing outcomes, but small molecule modulators and engineered CRISPR/Cas proteins have been shown to enhance precision editing efficacy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Qian Wang, Jin Liu, Josephine M. Janssen, Manuel A. F. Goncalves
Summary: Homology-directed recombination (HDR) allows for precise genomic edits in mammalian cells, but programmable nucleases can also cause unintended modifications. In trans paired nicking (ITPN) using CRISPR-Cas9 nickases enables seamless genome editing. This study identified high-specificity CRISPR-Cas9 nucleases for precise genome editing and demonstrated the compatibility of ITPN with these nickases, leading to editing of essential and recurrent sequences without activating negative DNA damage responses in human iPSCs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jiantao Tan, Yaxi Wang, Shuifu Chen, Zhansheng Lin, Yanchang Zhao, Yang Xue, Yuyu Luo, Yao-Guang Liu, Qinlong Zhu
Summary: This study developed a CRISPR/Cas9-mediated HDR auto-excision method using a rice promoter, Pssi, to efficiently remove marker genes from transgenic plants. The results demonstrated that this method achieved a high proportion of homozygous marker-excised plants in a short time, providing a time-saving and efficient strategy for gene marker removal in transgenic plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
John Murray Topp Hunt, Christopher Allan Samson, Alex du Rand, Hilary M. Sheppard
Summary: The CRISPR-Cas gene-editing system is a valuable tool for research purposes and has made significant advancements in human clinical trials. However, our understanding of the editing outcomes has not kept pace with the developments in generating edits. Comprehensive validation of on- and off-target effects is necessary to ensure reproducibility and accurately assess safety in future editing applications.
Article
Developmental Biology
Takuya Nakayama, Marilyn Fisher, Keisuke Nakajima, Akinleye O. Odeleye, Keith B. Zimmerman, Margaret B. Fish, Yoshio Yaoita, Jena L. Chojnowski, James D. Lauderdale, Peter A. Netland, Robert M. Grainger
DEVELOPMENTAL BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Adam M. Session, Yoshinobu Uno, Taejoon Kwon, Jarrod A. C. Hapman, Atsushi Toyoda, Shuji Takahashi, Akimasa Fukui, Akira Hikosaka, Atsushi Suzuki, Mariko Kondo, Simon J. van Heeringen, Ian Quigley, Sven Heinz, Hajime Ogino, Haruki Ochi, Uffe Hellsten, Jessica B. . Lyons, Oleg Simakov, Nicholas Putnam, Jonathan Stites, Yoko Kuroki, Toshiaki Tanaka, Tatsuo Michiue, Minoru Watanabe, Ozren B. Ogdanovic, Ryan Lister, Georgios Georgiou, Sarita S. Paranjpe, Ila Van Kruijsbergen, Shengquiang Shu, Joseph Carlson, Tsutomu Kinoshita, Yuko Ohta, Shuuji Mawaribuchi, Jerry Jenkins, Jane Grimwood, Jeremy Schmutz, Therese Mitros, Sahar V. Mozaffari, Yutaka Suzuki, Yoshikazu Haramoto, Takamasa S. Yamamoto, Chiyo Takagi, Rebecca Heald, Kelly Miller, Christian Haudenschild, Jacob Kitzman, Takuya Nakayama, Yumi I. Zutsu, Jacques Robert, Joshua Fortriede, Kevin Burns, Vaneet Lotay, Kamran Karimi, Yuuri Yasuoka, Darwin S. Dichmann, Martin F. Flajnik, Douglas W. Houston, Jay Shendure, Louis DuPasquier, Peter D. Vize, Aaron M. Zorn, Michihiko Ito, Edward M. Marcotte, John B. . Wallingford, Yuzuru Ito, Makoto Asashima, Naoto Ueno, Yoichi Matsuda, Gert Jan C. . Veenstra, Asao Fujiyama, Richard M. Harland, Masanori Taira, Daniel S. Rokhsar
Article
Biochemistry & Molecular Biology
Emmanuel Tadjuidje, Matthew Kofron, Adnan Mir, Christopher Wylie, Janet Heasman, Sang-Wook Cha
Article
Developmental Biology
Shuo Wei, Guofeng Xu, Lance C. Bridges, Phoebe Williams, Takuya Nakayama, Anoop Shah, Robert M. Grainger, Judith M. White, Douglas W. DeSimone
DEVELOPMENTAL BIOLOGY
(2012)
Article
Developmental Biology
Margaret B. Fish, Takuya Nakayama, Marilyn Fisher, Nicolas Hirsch, Amanda Cox, Rollin Reeder, Samantha Carruthers, Amanda Hall, Derek L. Stemple, Robert M. Grainger
DEVELOPMENTAL BIOLOGY
(2014)
Article
Developmental Biology
Margaret B. Fish, Takuya Nakayama, Robert M. Grainger
Article
Developmental Biology
Takuya Nakayama, Margaret B. Fish, Marilyn Fisher, Jamina Oomen-Hajagos, Gerald H. Thomsen, Robert M. Grainger
Article
Biochemical Research Methods
Mei Zeng, Marissa S. Kuzirian, Lamia Harper, Suzanne Paradis, Takuya Nakayama, Nelson C. Lau
Article
Multidisciplinary Sciences
Yuta Mishima, Changshan Wang, Satoru Miyagi, Atsunori Saraya, Hiroyuki Hosokawa, Makiko Mochizuki-Kashio, Yaeko Nakajima-Takagi, Shuhei Koide, Masamitsu Negishi, Goro Sashida, Taku Naito, Tomoyuki Ishikura, Atsushi Onodera, Toshinori Nakayama, Daniel G. Tenen, Naoto Yamaguchi, Haruhiko Koseki, Ichiro Taniuchi, Atsushi Iwama
NATURE COMMUNICATIONS
(2014)
Article
Developmental Biology
Yetki Aslan, Emmanuel Tadjuidje, Aaron M. Zorn, Sang-Wook Cha
Article
Developmental Biology
Tatsuo Michiue, Takayoshi Yamamoto, Yuuri Yasuoka, Toshiyasu Goto, Takafumi Ikeda, Kei Nagura, Takuya Nakayama, Masanori Taira, Tsutomu Kinoshita
DEVELOPMENTAL BIOLOGY
(2017)
Article
Developmental Biology
Takuya Nakayama, Keisuke Nakajima, Amanda Cox, Marilyn Fisher, Mary Howell, Margaret B. Fish, Yoshio Yaoita, Robert M. Grainger
DEVELOPMENTAL BIOLOGY
(2017)