Article
Multidisciplinary Sciences
Xiaolong Cheng, Zexu Li, Ruocheng Shan, Zihan Li, Shengnan Wang, Wenchang Zhao, Han Zhang, Lumen Chao, Jian Peng, Teng Fei, Wei Li
Summary: A major challenge in the application of the CRISPR-Cas13d system is accurately predicting its guide-dependent on-target and off-target effects. In this study, researchers used CRISPR-Cas13d proliferation screens and developed a deep learning model called DeepCas13 to predict on-target activity based on guide sequences and secondary structures. DeepCas13 outperformed existing methods in predicting the efficiency of guides targeting both protein-coding and non-coding RNAs.
NATURE COMMUNICATIONS
(2023)
Review
Biotechnology & Applied Microbiology
Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo
Summary: Gene editing involves precise changes to specific nucleic acid sequences. The CRISPR/Cas9 system has revolutionized gene editing, making it efficient, convenient, and programmable. However, off-target effects remain a major concern, leading to unexpected alterations in the genome. Various methods have been developed to detect and mitigate these off-target effects, advancing the precision of CRISPR/Cas9 derivatives. This review summarizes these technological advancements and discusses the challenges in managing off-target effects for future gene therapy.
FRONTIERS IN BIOENGINEERING AND 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)
Article
Biochemical Research Methods
Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin
Summary: The effectiveness of CRISPR/Cas9-mediated genome editing experiments relies on the careful selection of guide RNA (gRNA) for target recognition and cleavage activation. This study presents a user-friendly webserver that incorporates both on- and off-target prediction tools, CRISPRon and CRISPRoff, to facilitate gRNA selection.
Article
Biochemistry & Molecular Biology
Zhixin Lei, Haowei Meng, Yuan Zhuang, Qingguo Zhu, Chengqi Yi
Summary: This article outlines the off-target effects observed for various genome editing tools and discusses the methods for detecting and evaluating off-target editing, along with their advantages and limitations. Additionally, it summarizes current RNA editing tools for RNA therapy and medicine that can potentially serve as alternative approaches to genome editing tools in research and clinical applications.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Wei-Xin Hu, Yu Rong, Yan Guo, Feng Jiang, Wen Tian, Hao Chen, Shan-Shan Dong, Tie-Lin Yang
Summary: Research shows that designing sgRNAs with on-target mismatches can improve binding activity and reduce off-target effects. A web tool named ExsgRNA is provided for optimizing sgRNA design.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
William T. Garrood, Nace Kranjc, Karl Petri, Daniel Y. Kim, Jimmy A. Guo, Andrew M. Hammond, Ioanna Morianou, Vikram Pattanayak, J. Keith Joung, Andrea Crisanti, Alekos Simoni
Summary: The study shows that off-target mutations induced by CRISPR-Cas9 in mosquitoes can be reduced to undetectable levels, with judicious design of the guide RNA and strict temporal control of Cas9 expression in the germline being key factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Jeonghun Kwon, Minyoung Kim, Seungmin Bae, Anna Jo, Youngho Kim, Jungjoon K. Lee
Summary: Prime editors (PEs) are powerful tools for genome editing, and this study presents a cell-based assay called TAPE-seq that can be used to predict genome-wide off-target candidates for PEs. TAPE-seq shows higher accuracy and reliability compared to other prediction methods.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Florian Stoertz, Peter Minary
Summary: With the advancement of CRISPR/Cas programmable nuclease system, in vivo therapeutic gene editing applications are becoming more feasible. However, concerns over non-negligible off-target effects remain prominent. crisprSQL is an interactive collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching cleavage profiling, gene editing safety analysis, and transcriptomics.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Yongxian Fan, Haibo Xu
Summary: The study compared three encoding methods based on One-Hot and combined four CRISPR/Cas9 off-target prediction tools with gene sequences to build an ensemble model with XGBoost. Experimental results showed that the XGBCRISPR model outperformed existing tools, but further improvement in model accuracy is needed as many off-target scores still appear.
CURRENT BIOINFORMATICS
(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
Biochemistry & Molecular Biology
Martin Pacesa, Chun-Han Lin, Antoine Clery, Aakash Saha, Pablo R. Arantes, Katja Bargsten, Matthew J. Irby, Frederic H. -T. Allain, Giulia Palermo, Peter Cameron, Paul D. Donohoue, Martin Jinek
Summary: The crystallographic structures of Cas9 bound to off-target substrates reveal that noncanonical base-pairing interactions within the guide:off-target heteroduplex enable off-target binding. Single-nucleotide deletions in off-target substrates are accommodated by base skipping or multiple noncanonical base pairs. PAM-distal mismatches result in duplex unpairing and induce a conformational change in the Cas9 REC lobe. These insights contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
Article
Biochemistry & Molecular Biology
Muhammad Naeem, Omer S. Alkhnbashi
Summary: The CRISPR-Cas system is an advanced technology that has revolutionized the field of biology through precise gene manipulation. CRISPR/Cas9 nuclease has become a revolutionary method for editing genes in any species with desired outcomes. Bioinformaticians have developed a comprehensive set of tools to assist researchers in efficient guide RNA design, target site selection, and experimental validation, with the goal of reducing off-target effects. This article reviews various computational tools available for assessing off-target effects and quantifying nuclease activity and specificity, and discusses future directions in precision genome editing and its applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Behrouz Eslami-Mossallam, Misha Klein, Constantijn V. D. Smagt, Koen V. D. Sanden, Stephen K. Jones, John A. Hawkins, Ilya J. Finkelstein, Martin Depken
Summary: The authors present a quantitative kinetic model that characterizes the kinetics of SpCas9 in terms of free energy, allowing for the prediction of off-target activity in various experiments. The model is trained and validated on high-throughput bulk-biochemical data and can predict binding and cleavage activity as a function of time, target, and experimental conditions. It outperforms existing classification schemes in predicting off-target activity.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Seung-Hun Kang, Wi-jae Lee, Ju-Hyun An, Jong-Hee Lee, Young-Hyun Kim, Hanseop Kim, Yeounsun Oh, Young-Ho Park, Yeung Bae Jin, Bong-Hyun Jun, Junho K. Hur, Sun-Uk Kim, Seung Hwan Lee
Summary: A correction to the paper has been published to address the error.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Keunsub Lee, Yingxiao Zhang, Benjamin P. Kleinstiver, Jimmy A. Guo, Martin J. Aryee, Jonah Miller, Aimee Malzahn, Scott Zarecor, Carolyn J. Lawrence-Dill, J. Keith Joung, Yiping Qi, Kan Wang
PLANT BIOTECHNOLOGY JOURNAL
(2019)
Article
Plant Sciences
Kyoung Tak Cho, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Carolyn J. Lawrence-Dill, Iddo Friedberg, Carson M. Andorf
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Biochemistry & Molecular Biology
Steffen Knauer, Marie Javelle, Lin Li, Xianran Li, Xiaoli Ma, Kokulapalan Wimalanathan, Sunita Kumari, Robyn Johnston, Samuel Leiboff, Robert Meeley, Patrick S. Schnable, Doreen Ware, Carolyn Lawrence-Dill, Jianming Yu, Gary J. Muehlbauer, Michael J. Scanlon, Marja C. P. Timmermans
Article
Biochemical Research Methods
Yin Bao, Scott Zarecor, Dylan Shah, Taylor Tuel, Darwin A. Campbell, Antony V. E. Chapman, David Imberti, Daniel Kiekhaefer, Henry Imberti, Thomas Luebberstedt, Yanhai Yin, Dan Nettleton, Carolyn J. Lawrence-Dill, Steven A. Whitham, Lie Tang, Stephen H. Howell
Article
Biotechnology & Applied Microbiology
Nancy Manchanda, John L. Portwood, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf, Matthew B. Hufford
Article
Agronomy
Celeste M. Falcon, Shawn M. Kaeppler, Edgar P. Spalding, Nathan D. Miller, Nicholas Haase, Naser AlKhalifah, Martin Bohn, Edward S. Buckler, Darwin A. Campbell, Ignacio Ciampitti, Lisa Coffey, Jode Edwards, David Ertl, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice N. Hirsch, James B. Holland, Diego Jarquin, Joseph Knoll, Nick Lauter, Carolyn J. Lawrence-Dill, Elizabeth C. Lee, Aaron Lorenz, Jonathan P. Lynch, Seth C. Murray, Rebecca Nelson, M. Cinta Romay, Torbert Rocheford, Patrick S. Schnable, Brian Scully, Margaret Smith, Nathan Springer, Mitchell R. Tuinstra, Renee Walton, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu, Natalia de Leon
Article
Plant Sciences
Ian R. Braun, Carolyn J. Lawrence-Dill
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Agronomy
Ian R. Braun, Colleen F. Yanarella, Carolyn J. Lawrence-Dill
Editorial Material
Plant Sciences
Cyril Pommier, Trevor Garnett, Carolyn J. Lawrence-Dill, Tony Pridmore, Michelle Watt, Roland Pieruschka, Kioumars Ghamkhar
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Genetics & Heredity
Diego Jarquin, Natalia de Leon, Cinta Romay, Martin Bohn, Edward S. Buckler, Ignacio Ciampitti, Jode Edwards, David Ertl, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice N. Hirsch, James B. Holland, David Hooker, Shawn M. Kaeppler, Joseph Knoll, Elizabeth C. Lee, Carolyn J. Lawrence-Dill, Jonathan P. Lynch, Stephen P. Moose, Seth C. Murray, Rebecca Nelson, Torbert Rocheford, James C. Schnable, Patrick S. Schnable, Margaret Smith, Nathan Springer, Peter Thomison, Mitch Tuinstra, Randall J. Wisser, Wenwei Xu, Jianming Yu, Aaron Lorenz
Summary: Genomic prediction is an efficient method for developing improved cultivars, with new methods continuously being developed to integrate various data types. The use of modern automated weather systems can enhance predictive ability by capturing continuous data on environmental parameters, but further research is needed to link observed weather conditions with important physiological aspects in plant development for improved predictive ability.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Kokulapalan Wimalanathan, Carolyn J. Lawrence-Dill
Summary: The GOMAP pipeline is a high-throughput genome-scale GO annotation tool optimized for plants, with containerization increasing portability and reproducibility. Testing on multiple maize genomes showed that GOMAP expands the number of annotated genes and improves the quality of annotations per gene.
Article
Biochemical Research Methods
Carolyn J. Lawrence-Dill, Robyn L. Allscheid, Albert Boaitey, Todd Bauman, Edward S. Buckler, Jennifer L. Clarke, Christopher Cullis, Jack Dekkers, Cassandra J. Dorius, Shawn F. Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M. Reecy, Patrick S. Schnable, Nicole M. Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K. Tuggle, Alison Van Eenennaam, Rachael Voas
PLOS COMPUTATIONAL BIOLOGY
(2022)
Correction
Agronomy
Celeste M. Falcon, Shawn M. Kaeppler, Edgar P. Spalding, Nathan D. Miller, Nicholas Haase, Naser AlKhalifah, Martin Bohn, Edward S. Buckler, Darwin A. Campbell, Ignacio Ciampitti, Lisa Coffey, Jode Edwards, David Ertl, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice N. Hirsch, James B. Holland, Diego Jarquin, Joseph Knoll, Nick Lauter, Carolyn J. Lawrence-Dill, Elizabeth C. Lee, Aaron Lorenz, Jonathan P. Lynch, Seth C. Murray, Rebecca Nelson, M. Cinta Romay, Torbert Rocheford, Patrick S. Schnable, Brian Scully, Margaret Smith, Nathan Springer, Mitchell R. Tuinstra, Renee Walton, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu, Natalia de Leon
Article
Biology
Leila Fattel, Dennis Psaroudakis, Colleen F. Yanarella, Kevin O. Chiteri, Haley A. Dostalik, Parnal Joshi, Dollye C. Starr, Ha Vu, Kokulapalan Wimalanathan, Carolyn J. Lawrence-Dill
Summary: Genome-wide functional annotations are crucial for studying gene function and traits in plants. By comparing functional annotation data from different species, similarities and differences can be identified, leading to the generation of novel hypotheses about gene function and evolutionary relationships.
Article
Agronomy
Carolyn J. Lawrence-Dill, Patrick S. Schnable, Nathan M. Springer