Article
Biotechnology & Applied Microbiology
Hui Kwon Kim, Goosang Yu, Jinman Park, Seonwoo Min, Sungtae Lee, Sungroh Yoon, Hyongbum Henry Kim
Summary: This study identified factors affecting PE2 efficiency through high-throughput evaluation and developed three computational models to predict pegRNA efficiency, which can be applied to edits of various types and positions. Spearman's correlations between 0.47 and 0.81 were found when testing the accuracy of the predictions using independent test data sets.
NATURE BIOTECHNOLOGY
(2021)
Article
Biology
Toshitsugu Fujita, Shoko Nagata, Hodaka Fujii
Summary: This study explores the use of blocking RPA method to detect gene mutations and examine DNA epigenetic status through nucleic acid blockers and CRISPR ribonucleoproteins. Moreover, it demonstrates that Methyl-CpG binding proteins can inhibit DNA polymerase elongation on CpG-methylated template DNA, enabling the detection of methylated CpG islands in RPA reactions at low temperatures.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Analytical
Pintao Li, Xiaowei Zeng, Huajie Xue, Xin Ye, Bin Yang, Jilie Kong, Liping Yin, Xueen Fang
Summary: DNA barcode identification has wide applications and great potential in various fields. The development of a CRISPR-microfluidic array allows for rapid and accurate identification of DNA barcodes, achieving consistent results with morphological identification in real-field seed detection.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Physical
Songcheng Yu, Shengnan Cao, Sitian He, Kaixiang Zhang
Summary: DNA methylation is an important epigenetic characteristic that can result in heritable and revisable changes in phenotype without altering the DNA sequence. Aberrant methylation at specific loci has been linked to various diseases. The use of Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems as biosensors has shown potential for detecting locus-specific DNA methylation.
Article
Biotechnology & Applied Microbiology
Dongdong Zhao, Ju Li, Siwei Li, Xiuqing Xin, Muzi Hu, Marcus A. Price, Susan J. Rosser, Changhao Bi, Xueli Zhang
Summary: This study presents new glycosylase base editors (GBEs) that can induce C-to-A and C-to-G transversions in bacteria and mammalian cells, respectively. The GBEs can serve as a complement to existing adenine and cytidine base editors (ABE and CBE) and have the potential to target G/C disease-causing mutations.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dongdong Zhao, Ju Li, Siwei Li, Xiuqing Xin, Muzi Hu, Marcus A. Price, Susan J. Rosser, Changhao Bi, Xueli Zhang
Summary: The study introduces novel glycosylase base editors (GBEs) that can induce C-to-A and C-to-G transversions in Escherichia coli and mammalian cells, respectively. The new editors exhibit high editing specificity and efficiency, making them potential tools for targeting G/C disease-causing mutations.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lisa Simirenko, Jan-Fang Cheng, Ian Blaby
Summary: High-throughput genetic screening, with the use of pooled guide RNA libraries and sequencing-based assays, allows for rapid association of genes with phenotypes and establishment of sequence-function relationships. A new in silico design workflow, called gRNA-SeqRET, has been developed to assist in the construction of pooled gRNA assemblies. This tool automates the design of gRNA libraries targeting specific regions or whole genomes of any prokaryote or eukaryote, and also aids in the design of homology arms for insertion or deletion constructs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Dieter K. K. Lam, Patricia R. R. Feliciano, Amena Arif, Tanggis Bohnuud, Thomas P. P. Fernandez, Jason M. M. Gehrke, Phil Grayson, Kin D. D. Lee, Manuel A. A. Ortega, Courtney Sawyer, Noah D. D. Schwaegerle, Leila Peraro, Lauren Young, Seung-Joo Lee, Giuseppe Ciaramella, Nicole M. M. Gaudelli
Summary: This study presents a new type of CBEs that utilize engineered variants of TadA to achieve efficient G->A mutations in a sequence-diverse set of genomic loci. These editors exhibit robust activity in primary cells and do not result in elevated genome-wide mutation rate.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
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
Summary: We developed a systematic evaluation approach to assess the off-target effects of base editors (BE3, YE1-BE3-FNLS, and ABE7.10(F148A)) in transgenic mice. The study found that BE3 expression generated de novo mutations in the offspring of transgenic mice. Transcriptome analysis revealed that both BE3 and YE1-BE3-FNLS induced transcriptome-wide single nucleotide variants (SNVs), and the number of RNA SNVs was positively correlated with CBE expression levels. On the other hand, ABE7.10(F148A) showed no detectable off-target DNA or RNA SNVs. Importantly, long-term monitoring revealed abnormal phenotypes such as obesity and developmental delay in mice with permanent genomic BE3 overexpression, highlighting potential overlooked side effects of BE3 in vivo.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Ruijie Cai, Runyu Lv, Xin'e Shi, Gongshe Yang, Jianjun Jin
Summary: CRISPR/Cas9-mediated gene editing has been widely used due to its programmability and specificity, but can also affect genome stability. Recently, fusion proteins with transcriptional activator/inhibitor effects have been developed by linking proteins to dCas9 to regulate gene transcription. These tools have important applications in gene regulation, functional studies, target gene screening, and disease treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Noor Mohammad, Shrinivas S. Katkam, Qingshan Wei
Summary: This study demonstrates a novel CRISPR-Cas12a-based sensing platform for detecting single-stranded DNA targets by quantifying the size reduction of double-stranded DNA as report molecules. It is simple, inexpensive, non-optical, and exhibits high sensitivity compared to fluorescent methods.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biotechnology & Applied Microbiology
Nahye Kim, Sungchul Choi, Sungjae Kim, Myungjae Song, Jung Hwa Seo, Seonwoo Min, Jinman Park, Sung-Rae Cho, Hyongbum Henry Kim
Summary: A deep learning model is used to predict the best base editor for specific applications. Seven base editors and nine Cas9 variants were systematically compared to determine their editing windows, outcomes, and preferred motifs. Two computational models, DeepCas9variants and DeepBE, were developed to predict the efficiency and outcomes of base editors, resulting in significantly higher efficiency for DeepBE-designed editors compared to rational design.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Min Qing, Sheng Liang Chen, Zhe Sun, Yi Fan, Hong Qun Luo, Nian Bing Li
Summary: The study introduced the CRISPR/Cas system into an electrochemical biosensing platform for sensitive and specific detection of disease-related molecules. By utilizing modular rolling circle amplification and CRISPR/Cas12a, signal amplification was achieved. The flexibility and programmability of this strategy allow for the detection of various targets.
ANALYTICAL CHEMISTRY
(2021)
Review
Microbiology
Genki Sato, Kouichi Kuroda
Summary: Modification of the yeast Saccharomyces cerevisiae genome using the CRISPR-Cas9 system has great potential in biological research and biotechnology. Overcoming the limitations of the conventional system, this review focuses on developments in reducing unintended editing and inducing desired changes in the target region's epigenetic state. Moreover, the expansion of the CRISPR-Cas9 system to edit genomes within intracellular organelles like mitochondria is discussed, highlighting the key role of yeast cells in driving advancements in genome editing.
Article
Biology
Zhiquan Liu, Siyu Chen, Wanhua Xie, Hao Yu, Liangxue Lai, Zhanjun Li
Summary: Researchers have revisited and engineered a compact Cas9 orthologue derived from Neisseria cinerea (NcCas9) for efficient genome editing in mammal cells. NcCas9 can recognize a PAM sequence (N4GYAT) that existing Cas9s cannot, and by optimizing its architecture and spacer length, editing efficacy is improved. NcCas9-derived Base editors can efficiently generate base conversions, and six anti-CRISPR proteins were identified as off-switches for NcCas9. NcCas9 successfully generated efficient editing of mouse embryos by microinjection of NcCas9 mRNA and the corresponding sgRNA.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Aamir Mir, Julia F. Alterman, Matthew R. Hassler, Alexandre J. Debacker, Edward Hudgens, Dimas Echeverria, Michael H. Brodsky, Anastasia Khvorova, Jonathan K. Watts, Erik J. Sontheimer
NATURE COMMUNICATIONS
(2018)
News Item
Microbiology
Alireza Edraki, Erik J. Sontheimer
NATURE MICROBIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Jooyoung Lee, Haiwei Mou, Raed Ibraheim, Shun-Qing Liang, Pengpeng Liu, Wen Xue, Erik J. Sontheimer
Article
Biotechnology & Applied Microbiology
Pranam Chatterjee, Noah Jakimo, Jooyoung Lee, Nadia Amrani, Tomas Rodriguez, Sabrina R. T. Koseki, Emma Tysinger, Rui Qing, Shilei Hao, Erik J. Sontheimer, Joseph Jacobson
NATURE BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo
NATURE COMMUNICATIONS
(2020)
Correction
Biotechnology & Applied Microbiology
Pranam Chatterjee, Noah Jakimo, Jooyoung Lee, Nadia Amrani, Tomas Rodriguez, Sabrina R. T. Koseki, Emma Tysinger, Rui Qing, Shilei Hao, Erik J. Sontheimer, Joseph Jacobson
NATURE BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Krishanu Saha, Erik J. Sontheimer, P. J. Brooks, Melinda R. Dwinell, Charles A. Gersbach, David R. Liu, Stephen A. Murray, Shengdar Q. Tsai, Ross C. Wilson, Daniel G. Anderson, Aravind Asokan, Jillian F. Banfield, Krystof S. Bankiewicz, Gang Bao, Jeff W. M. Bulte, Nenad Bursac, Jarryd M. Campbell, Daniel F. Carlson, Elliot L. Chaikof, Zheng-Yi Chen, R. Holland Cheng, Karl J. Clark, David T. Curiel, James E. Dahlman, Benjamin E. Deverman, Mary E. Dickinson, Jennifer A. Doudna, Stephen C. Ekker, Marina E. Emborg, Guoping Feng, Benjamin S. Freedman, David M. Gamm, Guangping Gao, Ionita C. Ghiran, Peter M. Glazer, Shaoqin Gong, Jason D. Heaney, Jon D. Hennebold, John T. Hinson, Anastasia Khvorova, Samira Kiani, William R. Lagor, Kit S. Lam, Kam W. Leong, Jon E. Levine, Jennifer A. Lewis, Cathleen M. Lutz, Danith H. Ly, Samantha Maragh, Paul B. McCray, Todd C. McDevitt, Oleg Mirochnitchenko, Ryuji Morizane, Niren Murthy, Randall S. Prather, John A. Ronald, Subhojit Roy, Sushmita Roy, Venkata Sabbisetti, W. Mark Saltzman, Philip J. Santangelo, David J. Segal, Mary Shimoyama, Melissa C. Skala, Alice F. Tarantal, John C. Tilton, George A. Truskey, Moriel Vandsburger, Jonathan K. Watts, Kevin D. Wells, Scot A. Wolfe, Qiaobing Xu, Wen Xue, Guohua Yi, Jiangbing Zhou
Summary: The NIH's SCGE Consortium aims to develop safer and more effective methods to edit disease-relevant somatic cell genomes in patients, even in hard-to-reach tissues. Their approach includes rigorous validation of technology through third-party testing in animals to accelerate clinical development of new therapies.
Article
Multidisciplinary Sciences
Pengpeng Liu, Shun-Qing Liang, Chunwei Zheng, Esther Mintzer, Yan G. Zhao, Karthikeyan Ponnienselvan, Aamir Mir, Erik J. Sontheimer, Guangping Gao, Terence R. Flotte, Scot A. Wolfe, Wen Xue
Summary: The study introduces an NLS-optimized SpCas9-based prime editor that enhances genome editing efficiency and demonstrates the potential to induce tumor formation and correct pathogenic mutations in adult mice through somatic cell editing. The use of dual adeno-associated virus (AAVs) for delivery of a split-intein prime editor further establishes the capability of this system for in vivo installation of sequence modifications with important implications for disease modeling and correction.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Zexiang Chen, Gitali Devi, Amena Arif, Phillip D. Zamore, Erik J. Sontheimer, Jonathan K. Watts
Summary: This study reports a tetrazine ligation method for the synthesis of sgRNA, which enables the formation of sgRNA under mild conditions by introducing corresponding moieties on the ends of crRNA and tracrRNA. This method allows efficient genome editing in human cells.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Bin Liu, Xiaolong Dong, Haoyang Cheng, Chunwei Zheng, Zexiang Chen, Tomas C. Rodriguez, Shun-Qing Liang, Wen Xue, Erik J. Sontheimer
Summary: This study reports a split prime editor (sPE) that can efficiently perform genome editing and shows potential therapeutic effects in a mouse model. Compared to previous split prime editors, this system reduces the complexity of the constructs and improves efficiency.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Shun-Qing Liang, Pengpeng Liu, Karthikeyan Ponnienselvan, Sneha Suresh, Zexiang Chen, Christian Kramme, Pranam Chatterjee, Lihua Julie Zhu, Erik J. Sontheimer, Wen Xue, Scot A. Wolfe
Summary: PE-tag is a genome-wide approach for identifying potential off-target sites of prime editors, enabling high-throughput profiling and safety evaluation.
Article
Multidisciplinary Sciences
Chunwei Zheng, Bin Liu, Xiaolong Dong, Nicholas Gaston, Erik J. Sontheimer, Wen Xue
Summary: Targeted insertion of large DNA fragments using prime editing (PE) has shown promise for genome engineering and gene therapy. However, the efficiency of inserting larger fragments (>400bp) remains low and in vivo application has not been demonstrated. Inspired by retrotransposons, researchers have developed a template-jumping (TJ) PE approach which allows for the insertion of large DNA fragments with high efficiency and without double-stranded DNA breaks.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Carolyn Kraus, Erik J. Sontheimer
Summary: In the ten years since the discovery of the first anti-CRISPR (Acr) proteins, the number of validated Acrs has rapidly expanded, along with our understanding of the diverse mechanisms they use to suppress natural CRISPR-Cas immunity. Acr proteins can directly interact with Cas protein effectors, allowing them to modulate the activities and properties of CRISPR-Cas effectors. These abilities have been harnessed for a wide range of biotechnological applications, primarily for controlling and improving genome editing systems.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Carolyn Kraus, Erik J. Sontheimer
Summary: Bacteria and archaea use RNA-guided defences to destroy viruses, but the viruses can produce RNA mimics to counteract these defences.
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Marena Trinidad, Daniel Bellieny-Rabelo, Elaine Zhang, Hannah M. Karp, Petr Skopintsev, Brittney W. Thornton, Rachel F. Weissman, Peter H. Yoon, Linxing Chen, Tomas Hessler, Amy R. Eggers, David Colognori, Ron Boger, Erin E. Doherty, Connor A. Tsuchida, Ryan Tran, Laura Hofman, Honglue Shi, Kevin M. Wasko, Zehan Zhou, Chenglong Xia, Muntathar J. Al-Shimary, Jaymin R. Patel, Vienna C. J. X. Thomas, Rithu Pattali, Matthew J. Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F. Maxwell, Andrew G. Murdock, Glenn C. Ramit, Hope R. Henderson, Roland W. Calvert, Rebecca S. Bamert, Gavin J. Knott, Audrone Lapinaite, Patrick Pausch, Joshua C. Cofsky, Erik J. Sontheimer, Blake Wiedenheft, Peter C. Fineran, Stan J. J. Brouns, Dipali G. Sashital, Brian C. Thomas, Christopher T. Brown, Daniela S. A. Goltsman, Rodolphe Barrangou, Virginius Siksnys, Jillian F. Banfield, David F. Savage, Jennifer A. Doudna
Summary: CRISPR-Cas enzymes play a crucial role in bacterial immunity and genome editing. CasPEDIA is a comprehensive database that summarizes the enzymatic properties of Cas enzymes, providing valuable resources for researchers.
NUCLEIC ACIDS RESEARCH
(2023)
