1
|
Chauhan VP, Sharp PA, Langer R. Engineered prime editors with minimal genomic errors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606370. [PMID: 39211228 PMCID: PMC11361031 DOI: 10.1101/2024.08.02.606370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Prime editors make programmed genome modifications by writing new sequences into extensions of nicked DNA 3' ends. These edited 3' new strands must displace competing 5' strands to install edits, yet a bias toward retaining the competing 5' strands hinders efficiency and can cause indel errors. Using rational design of the constituent Cas9-nickase to reposition prime editor nicks, we discovered that competing 5' strands are destabilized to favor the edited 3' new strands. We exploit this mechanism to engineer efficient prime editors with strikingly low indel errors. Combining this error-suppressing strategy with the latest efficiency-boosting architecture, we design a next- generation prime editor (vPE). Compared with previous editors, vPE features comparable efficiency yet up to 60-fold lower indel errors, enabling edit:indel ratios as high as 465:1. One Sentence Summary Prime editors designed with repositioned DNA breaks nearly eliminate undesired genome editing errors.
Collapse
|
2
|
Ferreira da Silva J, Tou CJ, King EM, Eller ML, Rufino-Ramos D, Ma L, Cromwell CR, Metovic J, Benning FMC, Chao LH, Eichler FS, Kleinstiver BP. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. Nat Biotechnol 2024:10.1038/s41587-024-02324-x. [PMID: 39039307 DOI: 10.1038/s41587-024-02324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 06/24/2024] [Indexed: 07/24/2024]
Abstract
Genome editing technologies based on DNA-dependent polymerases (DDPs) could offer several benefits compared with other types of editors to install diverse edits. Here, we develop click editing, a genome writing platform that couples the advantageous properties of DDPs with RNA-programmable nickases to permit the installation of a range of edits, including substitutions, insertions and deletions. Click editors (CEs) leverage the 'click'-like bioconjugation ability of HUH endonucleases with single-stranded DNA substrates to covalently tether 'click DNA' (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs and their clkDNAs, we demonstrate the ability to install precise genome edits with minimal indels in diverse immortalized human cell types and primary fibroblasts with precise editing efficiencies of up to ~30%. Editing efficiency can be improved by rapidly screening clkDNA oligonucleotides with various modifications, including repair-evading substitutions. Click editing is a precise and versatile genome editing approach for diverse biological applications.
Collapse
Affiliation(s)
- Joana Ferreira da Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Connor J Tou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily M King
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Madeline L Eller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Christopher R Cromwell
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jasna Metovic
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Friederike M C Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Florian S Eichler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Vialetto E, Miele S, Goren MG, Yu J, Yu Y, Collias D, Beamud B, Osbelt L, Lourenço M, Strowig T, Brisse S, Barquist L, Qimron U, Bikard D, Beisel C. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity. Nucleic Acids Res 2024; 52:6079-6091. [PMID: 38661215 PMCID: PMC11162776 DOI: 10.1093/nar/gkae281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.
Collapse
Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Solange Miele
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Moran G Goren
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Beatriz Beamud
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Lisa Osbelt
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
| | - Udi Qimron
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - David Bikard
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
| |
Collapse
|
4
|
Zhang W, Petri K, Ma J, Lee H, Tsai CL, Joung JK, Yeh JRJ. Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions. eLife 2024; 12:RP90948. [PMID: 38847802 PMCID: PMC11161173 DOI: 10.7554/elife.90948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Abstract
CRISPR prime editing (PE) requires a Cas9 nickase-reverse transcriptase fusion protein (known as PE2) and a prime editing guide RNA (pegRNA), an extended version of a standard guide RNA (gRNA) that both specifies the intended target genomic sequence and encodes the desired genetic edit. Here, we show that sequence complementarity between the 5' and the 3' regions of a pegRNA can negatively impact its ability to complex with Cas9, thereby potentially reducing PE efficiency. We demonstrate this limitation can be overcome by a simple pegRNA refolding procedure, which improved ribonucleoprotein-mediated PE efficiencies in zebrafish embryos by up to nearly 25-fold. Further gains in PE efficiencies of as much as sixfold could also be achieved by introducing point mutations designed to disrupt internal interactions within the pegRNA. Our work defines simple strategies that can be implemented to improve the efficiency of PE.
Collapse
Affiliation(s)
- Weiting Zhang
- Cardiovascular Research Center, Massachusetts General HospitalCharlestownUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| | - Karl Petri
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General HospitalCharlestownUnited States
- Department of Pathology, Harvard Medical SchoolCharlestownUnited States
| | - Junyan Ma
- Cardiovascular Research Center, Massachusetts General HospitalCharlestownUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Medical College, Dalian UniversityDalianChina
| | - Hyunho Lee
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General HospitalCharlestownUnited States
- Department of Pathology, Harvard Medical SchoolCharlestownUnited States
| | - Chia-Lun Tsai
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | - J Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General HospitalCharlestownUnited States
- Department of Pathology, Harvard Medical SchoolCharlestownUnited States
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General HospitalCharlestownUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
5
|
Feng X, Xu R, Liao J, Zhao J, Zhang B, Xu X, Zhao P, Wang X, Yao J, Wang P, Wang X, Han W, She Q. Flexible TAM requirement of TnpB enables efficient single-nucleotide editing with expanded targeting scope. Nat Commun 2024; 15:3464. [PMID: 38658536 PMCID: PMC11043419 DOI: 10.1038/s41467-024-47697-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
TnpBs encoded by the IS200/IS605 family transposon are among the most abundant prokaryotic proteins from which type V CRISPR-Cas nucleases may have evolved. Since bacterial TnpBs can be programmed for RNA-guided dsDNA cleavage in the presence of a transposon-adjacent motif (TAM), these nucleases hold immense promise for genome editing. However, the activity and targeting specificity of TnpB in homology-directed gene editing remain unknown. Here we report that a thermophilic archaeal TnpB enables efficient gene editing in the natural host. Interestingly, the TnpB has different TAM requirements for eliciting cell death and for facilitating gene editing. By systematically characterizing TAM variants, we reveal that the TnpB recognizes a broad range of TAM sequences for gene editing including those that do not elicit apparent cell death. Importantly, TnpB shows a very high targeting specificity on targets flanked by a weak TAM. Taking advantage of this feature, we successfully leverage TnpB for efficient single-nucleotide editing with templated repair. The use of different weak TAM sequences not only facilitates more flexible gene editing with increased cell survival, but also greatly expands targeting scopes, and this strategy is probably applicable to diverse CRISPR-Cas systems.
Collapse
Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jianglan Liao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jingyu Zhao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Baochang Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoxiao Xu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Pengpeng Zhao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoning Wang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
6
|
Boob AG, Zhu Z, Intasian P, Jain M, Petrov V, Lane ST, Tan SI, Xun G, Zhao H. CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration. Nucleic Acids Res 2024; 52:e30. [PMID: 38346683 PMCID: PMC11014336 DOI: 10.1093/nar/gkae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 04/14/2024] Open
Abstract
The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.
Collapse
Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhixin Zhu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pattarawan Intasian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan Valley, Rayong 21210, Thailand
| | - Manan Jain
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vassily Andrew Petrov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Guanhua Xun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
7
|
Liang Y, Gao S, Qi X, Valentovich LN, An Y. Progress in Gene Editing and Metabolic Regulation of Saccharomyces cerevisiae with CRISPR/Cas9 Tools. ACS Synth Biol 2024; 13:428-448. [PMID: 38326929 DOI: 10.1021/acssynbio.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The CRISPR/Cas9 systems have been developed as tools for genetic engineering and metabolic engineering in various organisms. In this review, various aspects of CRISPR/Cas9 in Saccharomyces cerevisiae, from basic principles to practical applications, have been summarized. First, a comprehensive review has been conducted on the history of CRISPR/Cas9, successful cases of gene disruptions, and efficiencies of multiple DNA fragment insertions. Such advanced systems have accelerated the development of microbial engineering by reducing time and labor, and have enhanced the understanding of molecular genetics. Furthermore, the research progress of the CRISPR/Cas9-based systems in the production of high-value-added chemicals and the improvement of stress tolerance in S. cerevisiae have been summarized, which should have an important reference value for genetic and synthetic biology studies based on S. cerevisiae.
Collapse
Affiliation(s)
- Yaokun Liang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, Guangdong 511370, China
| | - Leonid N Valentovich
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| |
Collapse
|
8
|
Yang DD, Rusch LM, Widney KA, Morgenthaler AB, Copley SD. Synonymous edits in the Escherichia coli genome have substantial and condition-dependent effects on fitness. Proc Natl Acad Sci U S A 2024; 121:e2316834121. [PMID: 38252823 PMCID: PMC10835057 DOI: 10.1073/pnas.2316834121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
CRISPR-Cas-based genome editing is widely used in bacteria at scales ranging from construction of individual mutants to massively parallel libraries. This procedure relies on guide RNA-directed cleavage of the genome followed by repair with a template that introduces a desired mutation along with synonymous "immunizing" mutations to prevent re-cleavage of the genome after editing. Because the immunizing mutations do not change the protein sequence, they are often assumed to be neutral. However, synonymous mutations can change mRNA structures in ways that alter levels of the encoded proteins. We have tested the assumption that immunizing mutations are neutral by constructing a library of over 50,000 edits that consist of only synonymous mutations in Escherichia coli. Thousands of edits had substantial effects on fitness during growth of E. coli on acetate, a poor carbon source that is toxic at high concentrations. The percentage of high-impact edits varied considerably between genes and at different positions within genes. We reconstructed clones with high-impact edits and found that 69% indeed had significant effects on growth in acetate. Interestingly, fewer edits affected fitness during growth in glucose, a preferred carbon source, suggesting that changes in protein expression caused by synonymous mutations may be most important when an organism encounters challenging conditions. Finally, we showed that synonymous edits can have widespread effects; a synonymous edit at the 5' end of ptsI altered expression of hundreds of genes. Our results suggest that the synonymous immunizing edits introduced during CRISPR-Cas-based genome editing should not be assumed to be innocuous.
Collapse
Affiliation(s)
- Dong-Dong Yang
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Leo M. Rusch
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Karl A. Widney
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Andrew B. Morgenthaler
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
- Amyris, Inc., Emeryville, CA94608
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| |
Collapse
|
9
|
Nagorska A, Zaucker A, Lambert F, Inman A, Toral-Perez S, Gorodkin J, Wan Y, Smutny M, Sampath K. Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function. Development 2023; 150:dev201657. [PMID: 38032088 PMCID: PMC10730018 DOI: 10.1242/dev.201657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Heart development is a complex process that requires asymmetric positioning of the heart, cardiac growth and valve morphogenesis. The mechanisms controlling heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA functions in heart development across vertebrates. How FurinA activity is regulated during heart development is unknown. Through computational analysis of the zebrafish transcriptome, we identified an RNA motif in a variant FurinA transcript harbouring a long 3' untranslated region (3'UTR). The alternative 3'UTR furina isoform is expressed prior to organ positioning. Somatic deletions in the furina 3'UTR lead to embryonic left-right patterning defects. Reporter localisation and RNA-binding assays show that the furina 3'UTR forms complexes with the conserved RNA-binding translational repressor, Ybx1. Conditional ybx1 mutant embryos show premature and increased Furin reporter expression, abnormal cardiac morphogenesis and looping defects. Mutant ybx1 hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and retrograde blood flow from the ventricle to the atrium. This is similar to observations in humans with heart valve regurgitation. Thus, the furina 3'UTR element/Ybx1 regulon is important for translational repression of FurinA and regulation of heart development.
Collapse
Affiliation(s)
- Agnieszka Nagorska
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andreas Zaucker
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Finnlay Lambert
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Angus Inman
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Sara Toral-Perez
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jan Gorodkin
- Center for non-coding RNAs in Technology and Health, Department of Veterinary and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Grønnega °rdsvej 3, 1870 Frederiksberg C, Denmark
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Michael Smutny
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Karuna Sampath
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Early Life, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| |
Collapse
|
10
|
Sagarbarria MGS, Caraan JAM, Layos AJG. Usefulness of current sgRNA design guidelines and in vitro cleavage assays for plant CRISPR/Cas genome editing: a case targeting the polyphenol oxidase gene family in eggplant (Solanum melongena L.). Transgenic Res 2023; 32:561-573. [PMID: 37874448 DOI: 10.1007/s11248-023-00371-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
The advent of genome editing platforms such as the CRISPR/Cas9 system ushers an unprecedented speed in the development of new crop varieties that can withstand the agricultural challenges of the 21st century. The CRISPR/Cas9 system depends on the specificity of engineered single guide RNAs (sgRNAs). However, sgRNA design in plants can be challenging due to the multitude of design tools to choose from, many of which use guidelines that are based on animal experiments yet allow the use of plant genomes. Upon choosing sgRNAs, it is also unclear whether an in vitro assay is needed to validate the targeting efficiency of a particular sgRNA before in vivo delivery of the CRISPR/Cas9 system. Here, we demonstrate the in vitro and in vivo activity of four different sgRNAs that we selected based on their ability to target multiple members of the eggplant polyphenol oxidase gene family. Some sgRNAs that have high in vitro cleavage activity did not produce edits in vivo, suggesting that an in vitro assay may not be a reliable basis to predict sgRNAs with highly efficient in vivo cleavage activity. Further analysis of our sgRNAs using other design algorithms suggest that plant-validated criteria such as the presence of necessary secondary structures and appropriate base-pairing may be the reason for the discrepancy between our observed in vitro and in vivo cleavage efficiencies. However, recent reports and our data suggests that there is no guaranteed way to ensure the in vivo cleavage of chosen sgRNAs.
Collapse
Affiliation(s)
- Mark Gabriel S Sagarbarria
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines.
| | - John Albert M Caraan
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Angelo John G Layos
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| |
Collapse
|
11
|
Motoche-Monar C, Ordoñez JE, Chang O, Gonzales-Zubiate FA. gRNA Design: How Its Evolution Impacted on CRISPR/Cas9 Systems Refinement. Biomolecules 2023; 13:1698. [PMID: 38136570 PMCID: PMC10741458 DOI: 10.3390/biom13121698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 12/24/2023] Open
Abstract
Over the past decade, genetic engineering has witnessed a revolution with the emergence of a relatively new genetic editing tool based on RNA-guided nucleases: the CRISPR/Cas9 system. Since the first report in 1987 and characterization in 2007 as a bacterial defense mechanism, this system has garnered immense interest and research attention. CRISPR systems provide immunity to bacteria against invading genetic material; however, with specific modifications in sequence and structure, it becomes a precise editing system capable of modifying the genomes of a wide range of organisms. The refinement of these modifications encompasses diverse approaches, including the development of more accurate nucleases, understanding of the cellular context and epigenetic conditions, and the re-designing guide RNAs (gRNAs). Considering the critical importance of the correct performance of CRISPR/Cas9 systems, our scope will emphasize the latter approach. Hence, we present an overview of the past and the most recent guide RNA web-based design tools, highlighting the evolution of their computational architecture and gRNA characteristics over the years. Our study explains computational approaches that use machine learning techniques, neural networks, and gRNA/target interactions data to enable predictions and classifications. This review could open the door to a dynamic community that uses up-to-date algorithms to optimize and create promising gRNAs, suitable for modern CRISPR/Cas9 engineering.
Collapse
Affiliation(s)
- Cristofer Motoche-Monar
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Julián E. Ordoñez
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Oscar Chang
- Departamento de Electrónica, Universidad Simon Bolivar, Caracas 1080, Venezuela
- MIND Research Group, Model Intelligent Networks Development, Urcuquí 100119, Ecuador
| | - Fernando A. Gonzales-Zubiate
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
- MIND Research Group, Model Intelligent Networks Development, Urcuquí 100119, Ecuador
| |
Collapse
|
12
|
Mendoza CS, Findlay A, Judelson HS. A Variant of LbCas12a and Elevated Incubation Temperatures Enhance the Rate of Gene Editing in the Oomycete Phytophthora infestans. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:677-681. [PMID: 37470431 DOI: 10.1094/mpmi-05-23-0072-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
CRISPR-Cas editing systems have proved to be powerful tools for functional genomics research, but their effectiveness in many non-model species remains limited. In the potato and tomato pathogen Phytophthora infestans, an editing system was previously developed that expresses the Lachnospiracae bacterium Cas12a endonuclease (LbCas12a) and guide RNA from a DNA vector. However, the method works at low efficiency. Based on a hypothesis that editing is constrained by a mismatch between the optimal temperatures for P. infestans growth and endonuclease catalysis, we tested two strategies that increased the frequency of editing of two target genes by about 10-fold. First, we found that editing was boosted by a mutation in LbCas12a (D156R) that had been reported to expand its catalytic activity over a broader temperature range. Second, we observed that editing was enhanced by transiently incubating transformed tissue at a higher temperature. These modifications should make CRISPR-Cas12a more useful for interrogating gene and protein function in P. infestans and its relatives, especially species that grow optimally at lower temperatures. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Carl S Mendoza
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Annika Findlay
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| |
Collapse
|
13
|
da Silva JF, Tou CJ, King EM, Eller ML, Ma L, Rufino-Ramos D, Kleinstiver BP. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557440. [PMID: 37745481 PMCID: PMC10515857 DOI: 10.1101/2023.09.12.557440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Genome editing technologies that install diverse edits can widely enable genetic studies and new therapeutics. Here we develop click editing, a genome writing platform that couples the advantageous properties of DNA-dependent DNA polymerases with RNA-programmable nickases (e.g. CRISPR-Cas) to permit the installation of a range of edits including substitutions, insertions, and deletions. Click editors (CEs) leverage the "click"-like bioconjugation ability of HUH endonucleases (HUHes) with single stranded DNA substrates to covalently tether "click DNA" (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs (DNA polymerase and HUHe orthologs, architectural modifications, etc.) and their clkDNAs (template configurations, repair evading substitutions, etc.), we demonstrate the ability to install precise genome edits with minimal indels and no unwanted byproduct insertions. Since clkDNAs can be ordered as simple DNA oligonucleotides for cents per base, it is possible to screen many different clkDNA parameters rapidly and inexpensively to maximize edit efficiency. Together, click editing is a precise and highly versatile platform for modifying genomes with a simple workflow and broad utility across diverse biological applications.
Collapse
Affiliation(s)
- Joana Ferreira da Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Connor J. Tou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emily M. King
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, 02115, USA
| | - Madeline L. Eller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
14
|
Bush K, Corsi GI, Yan AC, Haynes K, Layzer JM, Zhou JH, Llanga T, Gorodkin J, Sullenger BA. Utilizing directed evolution to interrogate and optimize CRISPR/Cas guide RNA scaffolds. Cell Chem Biol 2023; 30:879-892.e5. [PMID: 37390831 PMCID: PMC10529641 DOI: 10.1016/j.chembiol.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/09/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
CRISPR-based editing has revolutionized genome engineering despite the observation that many DNA sequences remain challenging to target. Unproductive interactions formed between the single guide RNA's (sgRNA) Cas9-binding scaffold domain and DNA-binding antisense domain are often responsible for such limited editing resolution. To bypass this limitation, we develop a functional SELEX (systematic evolution of ligands by exponential enrichment) approach, termed BLADE (binding and ligand activated directed evolution), to identify numerous, diverse sgRNA variants that bind Streptococcus pyogenes Cas9 and support DNA cleavage. These variants demonstrate surprising malleability in sgRNA sequence. We also observe that particular variants partner more effectively with specific DNA-binding antisense domains, yielding combinations with enhanced editing efficiencies at various target sites. Using molecular evolution, CRISPR-based systems could be created to efficiently edit even challenging DNA sequences making the genome more tractable to engineering. This selection approach will be valuable for generating sgRNAs with a range of useful activities.
Collapse
Affiliation(s)
- Korie Bush
- Department of Surgery, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA; Moderna Genomics, Cambridge, MA 02139, USA
| | - Giulia I Corsi
- Center for non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; Tessera Therapeutics, Somerville, MA 02143, USA
| | - Amy C Yan
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Keith Haynes
- Department of Information Technology, Midlands Technical College, Columbia, SC 29202, USA
| | | | - Jonathan H Zhou
- Department of Surgery, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Telmo Llanga
- Department of Surgery, Duke University, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Jan Gorodkin
- Center for non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Bruce A Sullenger
- Department of Surgery, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA.
| |
Collapse
|
15
|
Zhang W, Petri K, Ma J, Lee H, Tsai CL, Joung JK, Yeh JRJ. Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553324. [PMID: 37645936 PMCID: PMC10462064 DOI: 10.1101/2023.08.14.553324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
CRISPR prime editing (PE) requires a Cas9 nickase-reverse transcriptase fusion protein (known as PE2) and a prime editing guide RNA (pegRNA), an extended version of a standard guide RNA (gRNA) that both specifies the intended target genomic sequence and encodes the desired genetic edit. Here we show that sequence complementarity between the 5' and the 3' regions of a pegRNA can negatively impact its ability to complex with Cas9, thereby potentially reducing PE efficiency. We demonstrate this limitation can be overcome by a simple pegRNA refolding procedure, which improved ribonucleoprotein-mediated PE efficiencies in zebrafish embryos by up to nearly 25-fold. Further gains in PE efficiencies of as much as 6-fold could also be achieved by introducing point mutations designed to disrupt internal interactions within the pegRNA. Our work defines simple strategies that can be implemented to improve the efficiency of PE.
Collapse
Affiliation(s)
- Weiting Zhang
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Karl Petri
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Junyan Ma
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Medical College, Dalian University, Dalian 116622, China
| | - Hyunho Lee
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Chia-Lun Tsai
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - J. Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
16
|
Sinan S, Appleby NM, Russell R. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550589. [PMID: 37546762 PMCID: PMC10402064 DOI: 10.1101/2023.07.25.550589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (Kd = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the affinities of both the precursor and mature forms of the crRNA, while deletion of an upstream sequence had no significant effect on affinity of the pre-crRNA. After processing, the mature crRNA remains very tightly bound to Cas12a, with a half-life of ~1 day and a Kd value of 60 pM. Addition of a 5'-phosphoryl group, which is normally lost during the processing reaction as the scissile phosphate, tightens binding of the mature crRNA by ~10-fold by accelerating binding and slowing dissociation. Using a direct competition assay, we found that pre-crRNA binding specificity is robust to other changes in RNA sequence, including tested changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. Together our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in some genome editing applications.
Collapse
Affiliation(s)
- Selma Sinan
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Nathan M. Appleby
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| |
Collapse
|
17
|
Huszár K, Welker Z, Györgypál Z, Tóth E, Ligeti Z, Kulcsár P, Dancsó J, Tálas A, Krausz S, Varga É, Welker E. Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs. Nucleic Acids Res 2023; 51:5847-5863. [PMID: 37140059 PMCID: PMC10287927 DOI: 10.1093/nar/gkad323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 04/04/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) nuclease exhibits considerable position-dependent sequence preferences. The reason behind these preferences is not well understood and is difficult to rationalise, since the protein establishes interactions with the target-spacer duplex in a sequence-independent manner. We revealed here that intramolecular interactions within the single guide RNA (sgRNA), between the spacer and the scaffold, cause most of these preferences. By using in cellulo and in vitro SpCas9 activity assays with systematically designed spacer and scaffold sequences and by analysing activity data from a large SpCas9 sequence library, we show that some long (>8 nucleotides) spacer motifs, that are complementary to the RAR unit of the scaffold, interfere with sgRNA loading, and that some motifs of more than 4 nucleotides, that are complementary to the SL1 unit, inhibit DNA binding and cleavage. Furthermore, we show that intramolecular interactions are present in the majority of the inactive sgRNA sequences of the library, suggesting that they are the most important intrinsic determinants of the activity of the SpCas9 ribonucleoprotein complex. We also found that in pegRNAs, sequences at the 3' extension of the sgRNA that are complementary to the SL2 unit are also inhibitory to prime editing, but not to the nuclease activity of SpCas9.
Collapse
Affiliation(s)
- Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Genetics, Doctoral School of Biology, Faculty of Science, Eötvös Loránd University, Budapest, H-1117, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Zsombor Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
| | - Zoltán Györgypál
- Biospiral-2006 Ltd, Szeged, Hungary
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - János Dancsó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| |
Collapse
|
18
|
Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
Collapse
Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| |
Collapse
|
19
|
Chenouard V, Leray I, Tesson L, Remy S, Allan A, Archer D, Caulder A, Fortun A, Bernardeau K, Cherifi Y, Teboul L, David L, Anegon I. Excess of guide RNA reduces knockin efficiency and drastically increases on-target large deletions. iScience 2023; 26:106399. [PMID: 37034986 PMCID: PMC10074149 DOI: 10.1016/j.isci.2023.106399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
CRISPR-Cas9 cleavage efficacy and accuracy are the main challenges gene editing faces, and they are particularly affected by the optimal formation of the ribonucleoprotein (RNP) complex. We used nano differential scanning fluorimetry, a label and immobilization-free assay, to demonstrate that an equimolar ratio of Cas9 and guide RNA (gRNA) is optimal for RNP complex formation. We almost achieved 50% of green fluorescent protein (GFP) to blue fluorescent protein (BFP) conversion using a biallelic homozygous GFP human induced pluripotent stem cell line, when 0.4 μM of Cas9, equimolar Cas9/gRNA ratio and 2 μM of single-stranded oligonucleotide, were used and showed that increasing Cas9/gRNA ratio did not further improve KI efficiency. Additionally, excess gRNA decreased point mutation KI efficiency in rat embryos and drastically increased the occurrence of on-target large deletions. These findings highlight the importance of CRISPR/Cas9 stoichiometric optimization to ensure efficient and accurate KI generation, which will be applicable to other in vitro as well as in vivo models.
Collapse
Affiliation(s)
- Vanessa Chenouard
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
- genOway, Lyon 69007, France
| | - Isabelle Leray
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Laurent Tesson
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| | - Severine Remy
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| | - Alasdair Allan
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Daniel Archer
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Adam Caulder
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Agnès Fortun
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, Plateforme P2R, SFR Bonamy, F-44000 Nantes, France
- Cibles et Médicaments des Infections et du Cancer, IICiMed, Nantes Université, UR 1155, F-44000 Nantes, France
| | - Karine Bernardeau
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, Plateforme P2R, SFR Bonamy, F-44000 Nantes, France
| | | | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Laurent David
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Ignacio Anegon
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| |
Collapse
|
20
|
Xu J, Bai X, Zhang X, Yuan B, Lin L, Guo Y, Cui Y, Liu J, Cui H, Ren X, Wang J, Yuan Y. Development and application of DETECTR-based rapid detection for pathogenic Bacillusanthracis. Anal Chim Acta 2023; 1247:340891. [PMID: 36781250 DOI: 10.1016/j.aca.2023.340891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/02/2023]
Abstract
Bacillus anthracis (B. anthracis) is a gram-positive bacterium responsible for the acute disease anthrax. Rapid and reliable identification of pathogenic B. anthracis is important in the detection of natural infectious disease cases or bio-threats. Herein, a DNA endonuclease targeted CRISPR trans reporter (DETECTR) detection platform based on recombinase polymerase amplification (RPA) was studied. The DETECTR system targeted three sequences from B. anthracis (the BA_5345 chromosomal specific marker, the protective antigen gene pag A from pXO1 plasmid and the capsule-biosynthesis-related gene cap A from pXO2 plasmid). We developed a rapid (<40 min), easy-to-implement and accurate identification method for of B. anthracis nucleic acid with near two-copies sensitivity. The combination of tripartite primer sets is effective for the reliable identification of B. anthracis but also for fast screening of pathogenic strains. More importantly, DETECTR correctly detected simulated clinical blood samples and firstly detected positive samples collected from the location of world War-II site, preserved at north-east China (45°36'55.940″ N, 126°38'33.738″ E) with high sensitivity and specificity. Our study provides insight into the DETECTR-based detection of B. anthracis. We present a novel screening and diagnostic option for pathogenic B. anthracis that can be performed on a user-friendly portable device. Based on its proven reliability, sensitivity, specificity and simplicity, our proposed method can be readily adapted to detect pathogenic B. anthracis, anthrax and biothreats.
Collapse
Affiliation(s)
- Jianhao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xinru Bai
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Lei Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Jinxiong Liu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Hongyu Cui
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Xiangang Ren
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
| |
Collapse
|
21
|
Christie KA, Guo JA, Silverstein RA, Doll RM, Mabuchi M, Stutzman HE, Lin J, Ma L, Walton RT, Pinello L, Robb GB, Kleinstiver BP. Precise DNA cleavage using CRISPR-SpRYgests. Nat Biotechnol 2023; 41:409-416. [PMID: 36203014 PMCID: PMC10023266 DOI: 10.1038/s41587-022-01492-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Methods for in vitro DNA cleavage and molecular cloning remain unable to precisely cleave DNA directly adjacent to bases of interest. Restriction enzymes (REs) must bind specific motifs, whereas wild-type CRISPR-Cas9 or CRISPR-Cas12 nucleases require protospacer adjacent motifs (PAMs). Here we explore the utility of our previously reported near-PAMless SpCas9 variant, named SpRY, to serve as a universal DNA cleavage tool for various cloning applications. By performing SpRY DNA digests (SpRYgests) using more than 130 guide RNAs (gRNAs) sampling a wide diversity of PAMs, we discovered that SpRY is PAMless in vitro and can cleave DNA at practically any sequence, including sites refractory to cleavage with wild-type SpCas9. We illustrate the versatility and effectiveness of SpRYgests to improve the precision of several cloning workflows, including those not possible with REs or canonical CRISPR nucleases. We also optimize a rapid and simple one-pot gRNA synthesis protocol to streamline SpRYgest implementation. Together, SpRYgests can improve various DNA engineering applications that benefit from precise DNA breaks.
Collapse
Affiliation(s)
- Kathleen A Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jimmy A Guo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Roman M Doll
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Biosciences/Cancer Biology Program, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Jiecong Lin
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital Charlestown, Boston, MA, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Russell T Walton
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luca Pinello
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital Charlestown, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
22
|
Okafor I, Ha T. Single Molecule FRET Analysis of CRISPR Cas9 Single Guide RNA Folding Dynamics. J Phys Chem B 2022; 127:45-51. [PMID: 36563314 PMCID: PMC9841515 DOI: 10.1021/acs.jpcb.2c05428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CRISPR Cas9 is an RNA guided endonuclease that is part of a bacterial adaptive immune system. Single guide RNA (sgRNA) can be designed to target genomic DNA, making Cas9 a programmable DNA binding/cutting enzyme and allowing applications such as epigenome editing, controlling transcription, and targeted DNA insertion. Some of the main hurdles against an even wider adoption are off-target effects and variability in Cas9 editing outcomes. Most studies that aim to understand the mechanisms that underlie these two areas have focused on Cas9 DNA binding, DNA unwinding, and target cleavage. The assembly of Cas9 RNA ribonucleoprotein complex (RNP) precedes all these steps and includes sgRNA folding and Cas9 binding to sgRNA. We know from the crystal structure of the Cas9 RNP what the final sgRNA conformation is. However, the assembly dynamics has not been studied in detail and a better understanding of RNP assembly could lead to better-designed sgRNAs and better editing outcomes. To study this process, we developed a single molecule FRET assay to monitor the conformation of the sgRNA and the binding of Cas9 to sgRNA. We labeled the sgRNA with a donor fluorophore and an acceptor fluorophore such that when the sgRNA folds, there are changes in FRET efficiency. We measured sgRNA folding dynamics under different ion conditions, under various methods of folding (refolding vs vectorial), and with or without Cas9. sgRNA that closely mimics the sgRNA construct used for high resolution structural analysis of the Cas9-gRNA complex showed two main FRET states without Cas9, and Cas9 addition shifted the distribution toward the higher FRET state attributed to the properly assembled complex. Even in the absence of Cas9, folding the sgRNA vectorially using a superhelicase-dependent release of the sgRNA in the direction of transcription resulted in almost exclusively high FRET state. An addition of Cas9 during vectorial folding greatly reduced a slow-folding fraction. Our studies shed light on the heterogeneous folding dynamics of sgRNA and the impact of co-transcriptional folding and Cas9 binding in sgRNA folding. Further studies of sequence dependence may inform rational design of sgRNAs for optimal function.
Collapse
Affiliation(s)
- Ikenna
C. Okafor
- Department
of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Taekjip Ha
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States,Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States,Department
of Biomedical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States,Howard
Hughes Medical Institute, Baltimore, Maryland 21205, United States,
| |
Collapse
|
23
|
Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun 2022; 13:6568. [PMID: 36323688 PMCID: PMC9630310 DOI: 10.1038/s41467-022-34320-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crisprVerse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe) and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a user-friendly and unified interface to add off-target annotations, rich gene and SNP annotations, and on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. The crisprVerse ecosystem is open-source and deployed through the Bioconductor project ( https://github.com/crisprVerse ).
Collapse
Affiliation(s)
- Luke Hoberecht
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Aaron Lun
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jean-Philippe Fortin
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| |
Collapse
|
24
|
Costigan R, Stoakes E, Floto RA, Parkhill J, Grant AJ. Development and validation of a CRISPR interference system for gene regulation in Campylobacter jejuni. BMC Microbiol 2022; 22:238. [PMID: 36199015 PMCID: PMC9533551 DOI: 10.1186/s12866-022-02645-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campylobacter spp. are the leading cause of bacterial food-borne illness in humans worldwide, with Campylobacter jejuni responsible for 80% of these infections. There is an urgent need to understand fundamental C. jejuni biology for the development of new strategies to prevent and treat infections. The range of molecular tools available to regulate gene expression in C. jejuni is limited, which in turn constrains our ability to interrogate the function of essential and conditionally essential genes. We have addressed this by developing and utilising a CRISPR-based interference system known as CRISPRi in C. jejuni to control gene expression. To achieve this, a catalytically inactive ("dead") cas9 and sgRNA backbone from the Streptococcus pyogenes CRISPRi system was combined with C. jejuni-derived promoters of predetermined expression activities to develop a CRISPRi-based repression tool in C. jejuni strains M1Cam and 81-176. RESULTS The CRISPRi tool was validated through successful repression of the arylsulphatase-encoding gene astA using a range of sgRNA target sequences spanning the astA gene. The tool was also applied to target astA in an M1Cam CRISPR-Cas9 deletion strain, which showed that the presence of an endogenous CRISPR-Cas9 system did not affect the activity of the CRISPRi-based repression tool. The tool was further validated against the hippicurase-encoding gene hipO. Following this, the flagella genes flgR, flaA, flaB and both flaA and flaB were targeted for CRISPRi-based repression, which resulted in varying levels of motility reduction and flagella phenotypes as determined by phenotypical assays and transmission electron microscopy (TEM). CONCLUSIONS This is the first report of a CRISPRi-based tool in C. jejuni, which will provide a valuable resource to the Campylobacter community.
Collapse
Affiliation(s)
- Ruby Costigan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Emily Stoakes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Department of Medicine, MRC-Laboratory of Molecular Biology, Molecular Immunity Unit, University of Cambridge, Cambridge, UK
- University of Cambridge, Centre for AI in Medicine, Cambridge, UK
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| |
Collapse
|
25
|
Asadbeigi A, Norouzi M, Vafaei Sadi MS, Saffari M, Bakhtiarizadeh MR. CaSilico: A versatile CRISPR package for in silico CRISPR RNA designing for Cas12, Cas13, and Cas14. Front Bioeng Biotechnol 2022; 10:957131. [PMID: 36017348 PMCID: PMC9395711 DOI: 10.3389/fbioe.2022.957131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/04/2022] [Indexed: 12/13/2022] Open
Abstract
The efficiency of the CRISPR-Cas system is highly dependent on well-designed CRISPR RNA (crRNA). To facilitate the use of various types of CRISPR-Cas systems, there is a need for the development of computational tools to design crRNAs which cover different CRISPR-Cas systems with off-target analysis capability. Numerous crRNA design tools have been developed, but nearly all of them are dedicated to design crRNA for genome editing. Hence, we developed a tool matching the needs of both beginners and experts, named CaSilico, which was inspired by the limitations of the current crRNA design tools for designing crRNAs for Cas12, Cas13, and Cas14 CRISPR-Cas systems. This tool considers a comprehensive list of the principal rules that are not yet well described to design crRNA for these types. Using a list of important features such as mismatch tolerance rules, self-complementarity, GC content, frequency of cleaving base around the target site, target accessibility, and PFS (protospacer flanking site) or PAM (protospacer adjacent motif) requirement, CaSilico searches all potential crRNAs in a user-input sequence. Considering these features help users to rank all crRNAs for a sequence and make an informed decision about whether a crRNA is suited for an experiment or not. Our tool is sufficiently flexible to tune some key parameters governing the design of crRNA and identification of off-targets, which can lead to an increase in the chances of successful CRISPR-Cas experiments. CaSilico outperforms previous crRNA design tools in the following aspects: 1) supporting any reference genome/gene/transcriptome for which an FASTA file is available; 2) designing crRNAs that simultaneously target multiple sequences through conserved region detection among a set of sequences; 3) considering new CRISPR-Cas subtypes; and 4) reporting a list of different features for each candidate crRNA, which can help the user to select the best one. Given these capabilities, CaSilico addresses end-user concerns arising from the use of sophisticated bioinformatics algorithms and has a wide range of potential research applications in different areas, especially in the design of crRNA for pathogen diagnosis. CaSilico was successfully applied to design crRNAs for different genes in the SARS-CoV-2 genome, as some of the crRNAs have been experimentally tested in the previous studies.
Collapse
Affiliation(s)
- Adnan Asadbeigi
- Department of Medical Genetics, Cancer Institute, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Milad Norouzi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Mojtaba Saffari
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mohammad Reza Bakhtiarizadeh
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
- *Correspondence: Mohammad Reza Bakhtiarizadeh,
| |
Collapse
|
26
|
Lou J, Wang B, Li J, Ni P, Jin Y, Chen S, Xi Y, Zhang R, Duan G. The CRISPR-Cas system as a tool for diagnosing and treating infectious diseases. Mol Biol Rep 2022; 49:11301-11311. [PMID: 35857175 PMCID: PMC9297709 DOI: 10.1007/s11033-022-07752-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/12/2022] [Accepted: 06/28/2022] [Indexed: 10/26/2022]
Abstract
Emerging and relapsing infectious diseases pose a huge health threat to human health and a new challenge to global public health. Rapid, sensitive and simple diagnostic tools are keys to successful management of infectious patients and containment of disease transmission. In recent years, international research on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-related proteins (Cas) has revolutionized our understanding of biology. The CRISPR-Cas system has the advantages of high specificity, high sensitivity, simple, rapid, low cost, and has begun to be used for molecular diagnosis and treatment of infectious diseases. In this paper, we described the biological principles, application fields and prospects of CRISPR-Cas system in the molecular diagnosis and treatment of infectious diseases, and compared it with existing molecular diagnosis methods, the advantages and disadvantages were summarized.
Collapse
Affiliation(s)
- Juan Lou
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Junwei Li
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yuanlin Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Rongguang Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China. .,International School of Public Health and One Health, The First Affiliated Hospital, Hainan Medical University, Haikou, China.
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
27
|
Metsky HC, Welch NL, Pillai PP, Haradhvala NJ, Rumker L, Mantena S, Zhang YB, Yang DK, Ackerman CM, Weller J, Blainey PC, Myhrvold C, Mitzenmacher M, Sabeti PC. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol 2022; 40:1123-1131. [PMID: 35241837 PMCID: PMC9287178 DOI: 10.1038/s41587-022-01213-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022]
Abstract
Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.
Collapse
Affiliation(s)
- Hayden C Metsky
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
| | - Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Virology Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biophysics Program, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | | | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Mitzenmacher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
28
|
SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish. Nat Commun 2022; 13:3421. [PMID: 35701400 PMCID: PMC9198057 DOI: 10.1038/s41467-022-31034-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 05/31/2022] [Indexed: 11/27/2022] Open
Abstract
Precise genetic modifications in model organisms are essential for biomedical research. The recent development of PAM-less base editors makes it possible to assess the functional impact and pathogenicity of nucleotide mutations in animals. Here we first optimize SpG and SpRY systems in zebrafish by purifying protein combined with synthetically modified gRNA. SpG shows high editing efficiency at NGN PAM sites, whereas SpRY efficiently edit PAM-less sites in the zebrafish genome. Then, we generate the SpRY-mediated cytosine base editor SpRY-CBE4max and SpRY-mediated adenine base editor zSpRY-ABE8e. Both target relaxed PAM with up to 96% editing efficiency and high product purity. With these tools, some previously inaccessible disease-relevant genetic variants are generated in zebrafish, supporting the utility of high-resolution targeting across genome-editing applications. Our study significantly improves CRISPR-Cas targeting in the genomic landscape of zebrafish, promoting the application of this model organism in revealing gene function, physiological mechanisms, and disease pathogenesis.
Collapse
|
29
|
Corsi GI, Qu K, Alkan F, Pan X, Luo Y, Gorodkin J. CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context. Nat Commun 2022; 13:3006. [PMID: 35637227 PMCID: PMC9151727 DOI: 10.1038/s41467-022-30515-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
A major challenge of CRISPR/Cas9-mediated genome engineering is that not all guide RNAs (gRNAs) cleave the DNA efficiently. Although the heterogeneity of gRNA activity is well recognized, the current understanding of how CRISPR/Cas9 activity is regulated remains incomplete. Here, we identify a sweet spot range of binding free energy change for optimal efficiency which largely explains why gRNAs display changes in efficiency at on- and off-target sites, including why gRNAs can cleave an off-target with higher efficiency than the on-target. Using an energy-based model, we show that local gRNA-DNA interactions resulting from Cas9 "sliding" on overlapping protospacer adjacent motifs (PAMs) profoundly impact gRNA activities. Combining the effects of local sliding for a given PAM context with global off-targets allows us to better identify highly specific, and thus efficient, gRNAs. We validate the effects of local sliding on gRNA efficiency using both public data and in-house data generated by measuring SpCas9 cleavage efficiency at 1024 sites designed to cover all possible combinations of 4-nt PAM and context sequences of 4 gRNAs. Our results provide insights into the mechanisms of Cas9-PAM compatibility and cleavage activation, underlining the importance of accounting for local sliding in gRNA design.
Collapse
Affiliation(s)
- Giulia I Corsi
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Thorvaldsensvej 57, 1871, Frederiksberg, Denmark
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ferhat Alkan
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Thorvaldsensvej 57, 1871, Frederiksberg, Denmark
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark.
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark.
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Thorvaldsensvej 57, 1871, Frederiksberg, Denmark.
| |
Collapse
|
30
|
Paul B, Chaubet L, Verver DE, Montoya G. Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA. Nucleic Acids Res 2022; 50:5208-5225. [PMID: 34951457 PMCID: PMC9122593 DOI: 10.1093/nar/gkab1272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here, we selected a target site on bacteriophage λ-DNA and used optical tweezers combined with fluorescence to provide mechanistic insight into wild type Cas12a and three engineered variants, where the specific dsDNA and the unspecific ssDNA cleavage are dissociated (M1 and M2) and a third one which nicks the target DNA (M3). At low forces wtCas12a and the variants display two main off-target binding sites, while on stretched dsDNA at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. The multiple binding events onto dsDNA at high tension do not lead to cleavage, which is observed on the target site at low forces when the DNA is flexible. In addition, activity assays also show that the preferential off-target sites for this crRNA are not cleaved by wtCas12a, indicating that λ-DNA is only severed at the target site. Our single molecule data indicate that the Cas12a scaffold presents singular mechanical properties, which could be used to generate new endonucleases with biomedical and biotechnological applications.
Collapse
Affiliation(s)
- Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Loïc Chaubet
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | | | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| |
Collapse
|
31
|
Konstantakos V, Nentidis A, Krithara A, Paliouras G. CRISPR-Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning. Nucleic Acids Res 2022; 50:3616-3637. [PMID: 35349718 PMCID: PMC9023298 DOI: 10.1093/nar/gkac192] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become a successful and promising technology for gene-editing. To facilitate its effective application, various computational tools have been developed. These tools can assist researchers in the guide RNA (gRNA) design process by predicting cleavage efficiency and specificity and excluding undesirable targets. However, while many tools are available, assessment of their application scenarios and performance benchmarks are limited. Moreover, new deep learning tools have been explored lately for gRNA efficiency prediction, but have not been systematically evaluated. Here, we discuss the approaches that pertain to the on-target activity problem, focusing mainly on the features and computational methods they utilize. Furthermore, we evaluate these tools on independent datasets and give some suggestions for their usage. We conclude with some challenges and perspectives about future directions for CRISPR-Cas9 guide design.
Collapse
Affiliation(s)
- Vasileios Konstantakos
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
| | - Anastasios Nentidis
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
- School of Informatics, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia Krithara
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
| | - Georgios Paliouras
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
| |
Collapse
|
32
|
Okada K, Aoki K, Tabei T, Sugio K, Imai K, Bonkohara Y, Kamachi Y. Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9. Nucleic Acids Res 2022; 50:2854-2871. [PMID: 35166844 PMCID: PMC8934663 DOI: 10.1093/nar/gkac100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
Abstract
Specific sequence features of the protospacer and protospacer-adjacent motif (PAM) are critical for efficient cleavage by CRISPR-Cas9, but current knowledge is largely derived from single-guide RNA (sgRNA) systems assessed in cultured cells. In this study, we sought to determine gRNA sequence features of a more native CRISPR-Cas9 ribonucleoprotein (RNP) complex with dual-guide RNAs (dgRNAs) composed of crRNA and tracrRNA, which has been used increasingly in recent CRISPR-Cas9 applications, particularly in zebrafish. Using both wild-type and HiFi SpCas9, we determined on-target cleavage efficiencies of 51 crRNAs in zebrafish embryos by assessing indel occurrence. Statistical analysis of these data identified novel position-specific mononucleotide features relevant to cleavage efficiencies throughout the protospacer sequence that may be unique to CRISPR-Cas9 RNPs pre-assembled with perfectly matched gRNAs. Overall features for wild-type Cas9 resembled those for HiFi Cas9, but specific differences were also observed. Mutational analysis of mononucleotide features confirmed their relevance to cleavage efficiencies. Moreover, the mononucleotide feature-based score, CRISPR-kp, correlated well with efficiencies of gRNAs reported in previous zebrafish RNP injection experiments, as well as independently tested crRNAs only in RNP format, but not with Cas9 mRNA co-injection. These findings will facilitate design of gRNA/crRNAs in genome editing applications, especially when using pre-assembled RNPs.
Collapse
Affiliation(s)
- Keita Okada
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Kanae Aoki
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Teruyuki Tabei
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Kota Sugio
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Katsunori Imai
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Yuki Bonkohara
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Yusuke Kamachi
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| |
Collapse
|
33
|
Riesenberg S, Helmbrecht N, Kanis P, Maricic T, Pääbo S. Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage. Nat Commun 2022; 13:489. [PMID: 35078986 PMCID: PMC8789806 DOI: 10.1038/s41467-022-28137-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 01/07/2022] [Indexed: 12/26/2022] Open
Abstract
The first step in CRISPR-Cas9-mediated genome editing is the cleavage of target DNA sequences that are complementary to so-called spacer sequences in CRISPR guide RNAs (gRNAs). However, some DNA sequences are refractory to CRISPR-Cas9 cleavage, which is at least in part due to gRNA misfolding. To overcome this problem, we have engineered gRNAs with highly stable hairpins in their constant parts and further enhanced their stability by chemical modifications. The 'Genome-editing Optimized Locked Design' (GOLD)-gRNA increases genome editing efficiency up to around 1000-fold (from 0.08 to 80.5%) with a mean increase across different other targets of 7.4-fold. We anticipate that this improved gRNA will allow efficient editing regardless of spacer sequence composition and will be especially useful if a desired genomic site is difficult to edit.
Collapse
Affiliation(s)
| | - Nelly Helmbrecht
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Kanis
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Okinawa Institute of Science and Technology, Onna-son, Japan
| |
Collapse
|
34
|
Shelake RM, Pramanik D, Kim JY. In Vivo Rapid Investigation of CRISPR-Based Base Editing Components in Escherichia coli (IRI-CCE): A Platform for Evaluating Base Editing Tools and Their Components. Int J Mol Sci 2022; 23:ijms23031145. [PMID: 35163069 PMCID: PMC8834901 DOI: 10.3390/ijms23031145] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid assessment of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing (GE) tools and their components is a critical aspect for successful GE applications in different organisms. In many bacteria, double-strand breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient nonhomologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide (nt) editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs, cytidine base editor (CBE) and adenine base editor (ABE), capable of converting C to T and A to G, respectively, have been recently developed but yet to be tested for editing characteristics in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising a combination of promoters and terminators enabling the expression of nCas9-based BE and sgRNA to nontoxic levels, eventually leading to successful base editing. We demonstrate the use of IRI-CCE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e) for bacteria, exhibiting that each independent BE has its specific editing pattern for a given target site depending on protospacer length. In summary, CRISPR-BE components expressed without lethal effects on cell survival in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and sgRNAs.
Collapse
Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Correspondence: (R.M.S.); (J.-Y.K.)
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
- Correspondence: (R.M.S.); (J.-Y.K.)
| |
Collapse
|
35
|
Lewis IC, Yan Y, Finnigan GC. Analysis of a Cas12a-based gene-drive system in budding yeast. Access Microbiol 2022; 3:000301. [PMID: 35024561 PMCID: PMC8749140 DOI: 10.1099/acmi.0.000301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
The discovery and adaptation of CRISPR/Cas systems within molecular biology has provided advances across biological research, agriculture and human health. Genomic manipulation through use of a CRISPR nuclease and programmed guide RNAs has become a common and widely accessible practice. The identification and introduction of new engineered variants and orthologues of Cas9 as well as alternative CRISPR systems such as the type V group have provided additional molecular options for editing. These include distinct PAM requirements, staggered DNA double-strand break formation, and the ability to multiplex guide RNAs from a single expression construct. Use of CRISPR/Cas has allowed for the construction and testing of a powerful genetic architecture known as a gene drive within eukaryotic model systems. Our previous work developed a drive within budding yeast using Streptococcus pyogenes Cas9. Here, we installed the type V Francisella novicida Cas12a (Cpf1) nuclease gene and its corresponding guide RNA to power a highly efficient artificial gene drive in diploid yeast. We examined the consequence of altering guide length or introduction of individual mutational substitutions to the crRNA sequence. Cas12a-dependent gene-drive function required a guide RNA of at least 18 bp and could not tolerate most changes within the 5' end of the crRNA.
Collapse
Affiliation(s)
- Isabel C Lewis
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.,Present address: School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yao Yan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
36
|
Takasugi PR, Wang S, Truong KT, Drage EP, Kanishka SN, Higbee MA, Bamidele N, Ojelabi O, Sontheimer EJ, Gagnon JA. Orthogonal CRISPR-Cas tools for genome editing, inhibition, and CRISPR recording in zebrafish embryos. Genetics 2022; 220:iyab196. [PMID: 34735006 PMCID: PMC8733422 DOI: 10.1093/genetics/iyab196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 10/26/2021] [Indexed: 11/15/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas universe continues to expand. The type II CRISPR-Cas system from Streptococcus pyogenes (SpyCas9) is the most widely used for genome editing due to its high efficiency in cells and organisms. However, concentrating on a single CRISPR-Cas system imposes limits on target selection and multiplexed genome engineering. We hypothesized that CRISPR-Cas systems originating from different bacterial species could operate simultaneously and independently due to their distinct single-guide RNAs (sgRNAs) or CRISPR-RNAs (crRNAs), and protospacer adjacent motifs (PAMs). Additionally, we hypothesized that CRISPR-Cas activity in zebrafish could be regulated through the expression of inhibitory anti-CRISPR (Acr) proteins. Here, we use a simple mutagenesis approach to demonstrate that CRISPR-Cas systems from S. pyogenes (SpyCas9), Streptococcus aureus (SauCas9), Lachnospiraceae bacterium (LbaCas12a, previously known as LbCpf1) are orthogonal systems capable of operating simultaneously in zebrafish. CRISPR systems from Acidaminococcus sp. (AspCas12a, previously known as AsCpf1) and Neisseria meningitidis (Nme2Cas9) were also active in embryos. We implemented multichannel CRISPR recording using three CRISPR systems and show that LbaCas12a may provide superior information density compared with previous methods. We also demonstrate that type II Acrs (anti-CRISPRs) are effective inhibitors of SpyCas9 in zebrafish. Our results indicate that at least five CRISPR-Cas systems and two anti-CRISPR proteins are functional in zebrafish embryos. These orthogonal CRISPR-Cas systems and Acr proteins will enable combinatorial and intersectional strategies for spatiotemporal control of genome editing and genetic recording in animals.
Collapse
Affiliation(s)
- Paige R Takasugi
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Shengzhou Wang
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kimberly T Truong
- Department of Mathematics, University of Utah, Salt Lake City, UT 84112, USA
| | - Evan P Drage
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sahar N Kanishka
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Marissa A Higbee
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nathan Bamidele
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ogooluwa Ojelabi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James A Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
37
|
Yeap WC, Norkhairunnisa Che Mohd Khan, Norfadzilah Jamalludin, Muad MR, Appleton DR, Harikrishna Kulaveerasingam. An Efficient Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-Associated Protein 9 Mutagenesis System for Oil Palm ( Elaeis guineensis). FRONTIERS IN PLANT SCIENCE 2021; 12:773656. [PMID: 34880893 PMCID: PMC8647858 DOI: 10.3389/fpls.2021.773656] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/18/2021] [Indexed: 07/27/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has emerged as a powerful tool for the precise editing of plant genomes for crop improvement. Rapid in vitro methods for the determination of guide RNA (gRNA) cleavage efficiency and an efficient DNA delivery system is essential for gene editing. However, we lack an efficient gene-editing system for palm species. In this study, we described the development of a transient oil palm protoplast assay to rapidly evaluate the cleavage efficiency of CRISPR/Cas9 mutagenesis and the generation of stable transformed oil palms using biolistic particle bombardment in immature embryos. Using the phytoene desaturase (EgPDS) gene, we found cleavage frequency of up to 25.49% in electro-transfected protoplast, which enables the production of transgenic oil palm shoots exhibiting chimeric albino phenotypes as a result of DNA insertions, deletions (InDels), and nucleotide substitutions, with a mutation efficiency of 62.5-83.33%. We further validated the mutagenesis efficiency and specificity of the CRISPR/Cas9 system in oil palm by targeting the brassinosteroid-insensitive 1 (EgBRI1) gene, which resulted in nucleotide substitutions in EgBRI1 with premature necrosis phenotype in oil palm transgenic shoots and stunted phenotype resulting from DNA InDels. Taken together, our results showed that effective and efficient editing of genes using the CRISPR/Cas9 system can be achieved in oil palm by optimizing the selection of efficient gRNA and DNA delivery methods. This newly designed strategy will enable new routes for the genetic improvement in oil palm and related species.
Collapse
Affiliation(s)
- Wan-Chin Yeap
- Sime Darby Plantation Technology Centre Sdn. Bhd., Serdang, Malaysia
| | | | | | | | | | | |
Collapse
|
38
|
Shojaei Baghini S, Gardanova ZR, Zekiy AO, Shomali N, Tosan F, Jarahian M. Optimizing sgRNA to Improve CRISPR/Cas9 Knockout Efficiency: Special Focus on Human and Animal Cell. Front Bioeng Biotechnol 2021; 9:775309. [PMID: 34869290 PMCID: PMC8640246 DOI: 10.3389/fbioe.2021.775309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
During recent years, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technologies have been noticed as a rapidly evolving tool to deliver a possibility for modifying target sequence expression and function. The CRISPR/Cas9 tool is currently being used to treat a myriad of human disorders, ranging from genetic diseases and infections to cancers. Preliminary reports have shown that CRISPR technology could result in valued consequences for the treatment of Duchenne muscular dystrophy (DMD), cystic fibrosis (CF), β-thalassemia, Huntington's diseases (HD), etc. Nonetheless, high rates of off-target effects may hinder its application in clinics. Thereby, recent studies have focused on the finding of the novel strategies to ameliorate these off-target effects and thereby lead to a high rate of fidelity and accuracy in human, animals, prokaryotes, and also plants. Meanwhile, there is clear evidence indicating that the design of the specific sgRNA with high efficiency is of paramount importance. Correspondingly, elucidation of the principal parameters that contributed to determining the sgRNA efficiencies is a prerequisite. Herein, we will deliver an overview regarding the therapeutic application of CRISPR technology to treat human disorders. More importantly, we will discuss the potent influential parameters (e.g., sgRNA structure and feature) implicated in affecting the sgRNA efficacy in CRISPR/Cas9 technology, with special concentration on human and animal studies.
Collapse
Affiliation(s)
- Sadegh Shojaei Baghini
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Zhanna R. Gardanova
- Department of Psychotherapy, Pirogov Russian National Research Medical University, Moscow, Russia
- Medical Faculty, Russian State Social University, Moscow, Russia
| | - Angelina Olegovna Zekiy
- Department of Prosthetic Dentistry, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Navid Shomali
- Immunology Research Center (IRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Foad Tosan
- Student Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Mostafa Jarahian
- German Cancer Research Center, Toxicology and Chemotherapy Unit (G401), Heidelberg, Germany
| |
Collapse
|
39
|
Uthayakumar D, Sharma J, Wensing L, Shapiro RS. CRISPR-Based Genetic Manipulation of Candida Species: Historical Perspectives and Current Approaches. Front Genome Ed 2021; 2:606281. [PMID: 34713231 PMCID: PMC8525362 DOI: 10.3389/fgeed.2020.606281] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022] Open
Abstract
The Candida genus encompasses a diverse group of ascomycete fungi that have captured the attention of the scientific community, due to both their role in pathogenesis and emerging applications in biotechnology; the development of gene editing tools such as CRISPR, to analyze fungal genetics and perform functional genomic studies in these organisms, is essential to fully understand and exploit this genus, to further advance antifungal drug discovery and industrial value. However, genetic manipulation of Candida species has been met with several distinctive barriers to progress, such as unconventional codon usage in some species, as well as the absence of a complete sexual cycle in its diploid members. Despite these challenges, the last few decades have witnessed an expansion of the Candida genetic toolbox, allowing for diverse genome editing applications that range from introducing a single point mutation to generating large-scale mutant libraries for functional genomic studies. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is among the most recent of these advancements, bringing unparalleled versatility and precision to genetic manipulation of Candida species. Since its initial applications in Candida albicans, CRISPR-Cas9 platforms are rapidly evolving to permit efficient gene editing in other members of the genus. The technology has proven useful in elucidating the pathogenesis and host-pathogen interactions of medically relevant Candida species, and has led to novel insights on antifungal drug susceptibility and resistance, as well as innovative treatment strategies. CRISPR-Cas9 tools have also been exploited to uncover potential applications of Candida species in industrial contexts. This review is intended to provide a historical overview of genetic approaches used to study the Candida genus and to discuss the state of the art of CRISPR-based genetic manipulation of Candida species, highlighting its contributions to deciphering the biology of this genus, as well as providing perspectives for the future of Candida genetics.
Collapse
Affiliation(s)
- Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Lauren Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
40
|
O'Keeffe Ahern J, Lara-Sáez I, Zhou D, Murillas R, Bonafont J, Mencía Á, García M, Manzanares D, Lynch J, Foley R, Xu Q, Sigen A, Larcher F, Wang W. Non-viral delivery of CRISPR-Cas9 complexes for targeted gene editing via a polymer delivery system. Gene Ther 2021; 29:157-170. [PMID: 34363036 PMCID: PMC9013665 DOI: 10.1038/s41434-021-00282-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022]
Abstract
Recent advances in molecular biology have led to the CRISPR revolution, but the lack of an efficient and safe delivery system into cells and tissues continues to hinder clinical translation of CRISPR approaches. Polymeric vectors offer an attractive alternative to viruses as delivery vectors due to their large packaging capacity and safety profile. In this paper, we have demonstrated the potential use of a highly branched poly(β-amino ester) polymer, HPAE-EB, to enable genomic editing via CRISPRCas9-targeted genomic excision of exon 80 in the COL7A1 gene, through a dual-guide RNA sequence system. The biophysical properties of HPAE-EB were screened in a human embryonic 293 cell line (HEK293), to elucidate optimal conditions for efficient and cytocompatible delivery of a DNA construct encoding Cas9 along with two RNA guides, obtaining 15–20% target genomic excision. When translated to human recessive dystrophic epidermolysis bullosa (RDEB) keratinocytes, transfection efficiency and targeted genomic excision dropped. However, upon delivery of CRISPR–Cas9 as a ribonucleoprotein complex, targeted genomic deletion of exon 80 was increased to over 40%. Our study provides renewed perspective for the further development of polymer delivery systems for application in the gene editing field in general, and specifically for the treatment of RDEB.
Collapse
Affiliation(s)
| | - Irene Lara-Sáez
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland.
| | - Dezhong Zhou
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland
| | - Rodolfo Murillas
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain.,Fundación Instituto de Investigaciones Sanitarias de la Fundación Jimenez Díaz, Madrid, Spain
| | - Jose Bonafont
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain.,Fundación Instituto de Investigaciones Sanitarias de la Fundación Jimenez Díaz, Madrid, Spain
| | - Ángeles Mencía
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Marta García
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain.,Fundación Instituto de Investigaciones Sanitarias de la Fundación Jimenez Díaz, Madrid, Spain.,Department of Bioengineering Universidad Carlos III de Madrid, Madrid, Spain
| | - Darío Manzanares
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland
| | - Jennifer Lynch
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland
| | - Ruth Foley
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland
| | - Qian Xu
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland
| | - A Sigen
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland
| | - Fernando Larcher
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain.,Fundación Instituto de Investigaciones Sanitarias de la Fundación Jimenez Díaz, Madrid, Spain.,Department of Bioengineering Universidad Carlos III de Madrid, Madrid, Spain
| | - Wenxin Wang
- Charles Institute of Dermatology, University College Dublin, Dublin, Republic of Ireland.
| |
Collapse
|
41
|
Poggi L, Emmenegger L, Descorps-Declère S, Dumas B, Richard GF. Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations. Nucleic Acids Res 2021; 49:8120-8134. [PMID: 34233005 PMCID: PMC8373144 DOI: 10.1093/nar/gkab569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Microsatellite expansions are the cause of >20 neurological or developmental human disorders. Shortening expanded repeats using specific DNA endonucleases may be envisioned as a gene editing approach. Here, we measured the efficacy of several CRISPR-Cas nucleases to induce recombination within disease-related microsatellites, in Saccharomyces cerevisiae. Broad variations in nuclease performances were detected on all repeat tracts. Wild-type Streptococcus pyogenes Cas9 (SpCas9) was more efficient than Staphylococcus aureus Cas9 on all repeats tested, except (CAG)33. Cas12a (Cpf1) was the most efficient on GAA trinucleotide repeats, whereas GC-rich repeats were more efficiently cut by SpCas9. The main genetic factor underlying Cas efficacy was the propensity of the recognition part of the sgRNA to form a stable secondary structure, independently of its structural part. This suggests that such structures form in vivo and interfere with sgRNA metabolism. The yeast genome contains 221 natural CAG/CTG and GAA/CTT trinucleotide repeats. Deep sequencing after nuclease induction identified three of them as carrying statistically significant low frequency mutations, corresponding to SpCas9 off-target double-strand breaks.
Collapse
Affiliation(s)
- Lucie Poggi
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France.,Sorbonne Université, Collège Doctoral, 4 Place Jussieu, F-75005 Paris, France.,Biologics Research, Sanofi R&D, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Lisa Emmenegger
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France
| | - Stéphane Descorps-Declère
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France.,Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR3756 CNRS, F-75015 Paris, France
| | - Bruno Dumas
- Biologics Research, Sanofi R&D, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Guy-Franck Richard
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France.,Sorbonne Université, Collège Doctoral, 4 Place Jussieu, F-75005 Paris, France
| |
Collapse
|
42
|
Malik A, Gul A, Munir F, Amir R, Alipour H, Babar MM, Bakhtiar SM, Paracha RZ, Khalid Z, Hayat MQ. Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome. PeerJ 2021; 9:e11409. [PMID: 34055482 PMCID: PMC8142926 DOI: 10.7717/peerj.11409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas9 system has recently evolved as a powerful mutagenic tool for targeted genome editing. The impeccable functioning of the system depends on the optimal design of single guide RNAs (sgRNAs) that mainly involves sgRNA specificity and on-target cleavage efficacy. Several research groups have designed algorithms and models, trained on mammalian genomes, for predicting sgRNAs cleavage efficacy. These models are also implemented in most plant sgRNA design tools due to the lack of on-target cleavage efficacy studies in plants. However, one of the major drawbacks is that almost all of these models are biased for considering only coding regions of the DNA while excluding ineffective regions, which are of immense importance in functional genomics studies especially for plants, thus making prediction less reliable. In the present study, we evaluate the on-target cleavage efficacy of experimentally validated sgRNAs designed against diverse ineffective regions of Arabidopsis thaliana genome using various statistical tests. We show that nucleotide preference in protospacer adjacent motif (PAM) proximal region, GC content in the PAM proximal seed region, intact RAR and 3rd stem loop structures, and free accessibility of nucleotides in seed and tracrRNA regions of sgRNAs are important determinants associated with their high on-target cleavage efficacy. Thus, our study describes the features important for plant sgRNAs high on-target cleavage efficacy against ineffective genomic regions previously shown to give rise to ineffective sgRNAs. Moreover, it suggests the need of developing an elaborative plant-specific sgRNA design model considering the entire genomic landscape including ineffective regions for enabling highly efficient genome editing without wasting time and experimental resources.
Collapse
Affiliation(s)
- Afsheen Malik
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
| | - Mustafeez Mujtaba Babar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Zoya Khalid
- Computational Biology Research Lab, Department of Computer Science, National University of Computer and Emerging Sciences-FAST, Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| |
Collapse
|
43
|
Thavarajah W, Hertz LM, Bushhouse DZ, Archuleta CM, Lucks JB. RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics. Annu Rev Chem Biomol Eng 2021; 12:263-286. [PMID: 33900805 PMCID: PMC9714562 DOI: 10.1146/annurev-chembioeng-101420-014055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA is essential for cellular function: From sensing intra- and extracellular signals to controlling gene expression, RNA mediates a diverse and expansive list of molecular processes. A long-standing goal of synthetic biology has been to develop RNA engineering principles that can be used to harness and reprogram these RNA-mediated processes to engineer biological systems to solve pressing global challenges. Recent advances in the field of RNA engineering are bringing this to fruition, enabling the creation of RNA-based tools to combat some of the most urgent public health crises. Specifically, new diagnostics using engineered RNAs are able to detect both pathogens and chemicals while generating an easily detectable fluorescent signal as an indicator. New classes of vaccines and therapeutics are also using engineered RNAs to target a wide range of genetic and pathogenic diseases. Here, we discuss the recent breakthroughs in RNA engineering enabling these innovations and examine how advances in RNA design promise to accelerate the impact of engineered RNA systems.
Collapse
Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laura M Hertz
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - David Z Bushhouse
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Chloé M Archuleta
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA.,Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
| |
Collapse
|
44
|
Beniwal A, Saini P, De S, Vij S. Harnessing the nutritional potential of concentrated whey for enhanced galactose flux in fermentative yeast. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
45
|
Rahman MM, Tollefsbol TO. Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects. Methods 2021; 187:77-91. [PMID: 32315755 PMCID: PMC7572534 DOI: 10.1016/j.ymeth.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer therapeutics is an ever-evolving field due to incessant demands for effective and precise treatment options. Over the last few decades, cancer treatment strategies have shifted somewhat from surgery to targeted precision medicine. CRISPR-dCas9 is an emerging version of precision cancer therapy that has been adapted from the prokaryotic CRISPR-Cas system. Once ligated to epigenetic effectors (EE), CRISPR-dCas9 can function as an epigenetic editing tool and CRISPR-dCas9-EE complexes could be exploited to alter cancerous epigenetic features associated with different cancer hallmarks. In this article, we discuss the rationale of epigenetic editing as a therapeutic strategy against cancer. We also outline how sgRNA-dCas9 was derived from the CRISPR-Cas system. In addition, the current status of sgRNA-dCas9 use (in vivo and in vitro) in cancer is updated with a molecular illustration of CRISPR-dCas9-mediated epigenetic and transcriptional modulation. As sgRNA-dCas9 is still at the developmental phase, challenges are inherent to its use. We evaluate major challenges in targeting cancer with sgRNA-dCas9 such as off-target effects, lack of sgRNA designing rubrics, target site selection dilemmas and deficient sgRNA-dCas9 delivery systems. Finally, we appraise the sgRNA-dCas9 as a prospective cancer therapeutic by summarizing ongoing improvements of sgRNA-dCas9 methodology.
Collapse
Affiliation(s)
- Mohammad Mijanur Rahman
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
| |
Collapse
|
46
|
Trivedi D. Using CRISPR-Cas9-based genome engineering tools in Drosophila melanogaster. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:85-121. [PMID: 33934839 DOI: 10.1016/bs.pmbts.2021.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drosophila melanogaster has been used as a model organism for over a century. Mutant-based analyses have been used extensively to understand the genetic basis of different cellular processes, including development, neuronal function and diseases. Most of the earlier genetic mutants and specific tools were generated by random insertions and deletion strategies and then mapped to specific genomic loci. Since all genomic regions are not equally accessible to random mutations and insertions, many genes still remain uncharacterized. Low efficiency of targeted genomic manipulation approaches that rely on homologous recombination, and difficulty in generating resources for sequence-specific endonucleases, such as ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator-Like Effector Nucleases), could not make these gene targeting techniques very popular. However, recently RNA directed DNA endonucleases, such as CRISPR-Cas, have transformed genome engineering owing to their comparative ease, versatility, and low expense. With the added advantage of preexisting genetic tools, CRISPR-Cas-based manipulations are being extensively used in Drosophila melanogaster and simultaneously being fine-tuned for specific experimental requirements. In this chapter, I will discuss various uses of CRISPR-Cas-based genetic engineering and specific design methods in Drosophila melanogaster. I will summarize various already available tools that are being utilized in conjunction with CRISPR-Cas technology to generate specific genetic manipulation and are being optimized to address specific questions. Finally, I will discuss the future directions of Drosophila genetics research and how CRISPR-Cas can be utilized to target specific questions, addressing which has not been possible thus far.
Collapse
Affiliation(s)
- Deepti Trivedi
- National Centre for Biological Sciences-TIFR, Bengaluru, India.
| |
Collapse
|
47
|
Pramanik D, Shelake RM, Park J, Kim MJ, Hwang I, Park Y, Kim JY. CRISPR/Cas9-Mediated Generation of Pathogen-Resistant Tomato against Tomato Yellow Leaf Curl Virus and Powdery Mildew. Int J Mol Sci 2021; 22:1878. [PMID: 33668636 PMCID: PMC7917697 DOI: 10.3390/ijms22041878] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/27/2022] Open
Abstract
Tomato is one of the major vegetable crops consumed worldwide. Tomato yellow leaf curl virus (TYLCV) and fungal Oidium sp. are devastating pathogens causing yellow leaf curl disease and powdery mildew. Such viral and fungal pathogens reduce tomato crop yields and cause substantial economic losses every year. Several commercial tomato varieties include Ty-5 (SlPelo) and Mildew resistance locus o 1 (SlMlo1) locus that carries the susceptibility (S-gene) factors for TYLCV and powdery mildew, respectively. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is a valuable genome editing tool to develop disease-resistant crop varieties. In this regard, targeting susceptibility factors encoded by the host plant genome instead of the viral genome is a promising approach to achieve pathogen resistance without the need for stable inheritance of CRISPR components. In this study, the CRISPR/Cas9 system was employed to target the SlPelo and SlMlo1 for trait introgression in elite tomato cultivar BN-86 to confer host-mediated immunity against pathogens. SlPelo-knockout lines were successfully generated, carrying the biallelic indel mutations. The pathogen resistance assays in SlPelo mutant lines confirmed the suppressed accumulation of TYLCV and restricted the spread to non-inoculated plant parts. Generated knockout lines for the SlMlo1 showed complete resistance to powdery mildew fungus. Overall, our results demonstrate the efficiency of the CRISPR/Cas9 system to introduce targeted mutagenesis for the rapid development of pathogen-resistant varieties in tomato.
Collapse
Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (D.P.); (M.J.K.)
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (D.P.); (M.J.K.)
| | - Jiyeon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (D.P.); (M.J.K.)
| | - Indeok Hwang
- R&D Center, Bunongseed Co., Ltd., Gimje 54324, Korea;
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (D.P.); (M.J.K.)
| |
Collapse
|
48
|
Boyle EA, Becker WR, Bai HB, Chen JS, Doudna JA, Greenleaf WJ. Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement. SCIENCE ADVANCES 2021; 7:7/8/eabe5496. [PMID: 33608277 PMCID: PMC7895440 DOI: 10.1126/sciadv.abe5496] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
The RNA-guided nuclease Cas9 has unlocked powerful methods for perturbing both the genome through targeted DNA cleavage and the regulome through targeted DNA binding, but limited biochemical data have hampered efforts to quantitatively model sequence perturbation of target binding and cleavage across diverse guide sequences. We present scalable, sequencing-based platforms for high-throughput filter binding and cleavage and then perform 62,444 quantitative binding and cleavage assays on 35,047 on- and off-target DNA sequences across 90 Cas9 ribonucleoproteins (RNPs) loaded with distinct guide RNAs. We observe that binding and cleavage efficacy, as well as specificity, vary substantially across RNPs; canonically studied guides often have atypically high specificity; sequence context surrounding the target modulates Cas9 on-rate; and Cas9 RNPs may sequester targets in nonproductive states that contribute to "proofreading" capability. Lastly, we distill our findings into an interpretable biophysical model that predicts changes in binding and cleavage for diverse target sequence perturbations.
Collapse
Affiliation(s)
- Evan A Boyle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Winston R Becker
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Hua B Bai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences (QB3), University of California, Howard Hughes Medical Institute, Department of Chemistry, and the Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences (QB3), University of California, Howard Hughes Medical Institute, Department of Chemistry, and the Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
49
|
Hernandez VA, Carvajal-Moreno J, Papa JL, Shkolnikov N, Li J, Ozer HG, Yalowich JC, Elton TS. CRISPR/Cas9 Genome Editing of the Human Topoisomerase II α Intron 19 5' Splice Site Circumvents Etoposide Resistance in Human Leukemia K562 Cells. Mol Pharmacol 2021; 99:226-241. [PMID: 33446509 DOI: 10.1124/molpharm.120.000173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/28/2020] [Indexed: 01/17/2023] Open
Abstract
An essential function of DNA topoisomerase IIα (TOP2α; 170 kDa, TOP2α/170) is to resolve DNA topologic entanglements during chromosome disjunction by introducing transient DNA double-stranded breaks. TOP2α/170 is an important target for DNA damage-stabilizing anticancer drugs, whose clinical efficacy is compromised by drug resistance often associated with decreased TOP2α/170 expression. We recently demonstrated that an etoposide-resistant K562 clonal subline, K/VP.5, with reduced levels of TOP2α/170, expresses high levels of a novel C-terminal truncated TOP2α isoform (90 kDa, TOP2α/90). TOP2α/90, the translation product of a TOP2α mRNA that retains a processed intron 19 (I19), heterodimerizes with TOP2α/170 and is a resistance determinant through a dominant-negative effect on drug activity. We hypothesized that genome editing to enhance I19 removal would provide a tractable strategy to circumvent acquired TOP2α-mediated drug resistance. To enhance I19 removal in K/VP.5 cells, CRISPR/Cas9 was used to make changes (GAG//GTAA AC →GAG//GTAA GT ) in the TOP2α gene's suboptimal exon 19/intron 19 5' splice site (E19/I19 5' SS). Gene-edited clones were identified by quantitative polymerase chain reaction and verified by sequencing. Characterization of a clone with all TOP2α alleles edited revealed improved I19 removal, decreased TOP2α/90 mRNA/protein, and increased TOP2α/170 mRNA/protein. Sensitivity to etoposide-induced DNA damage (γH2AX, Comet assays) and growth inhibition was restored to levels comparable to those in parental K562 cells. Together, the results indicate that our gene-editing strategy for optimizing the TOP2α E19/I19 5' SS in K/VP.5 cells circumvents resistance to etoposide and other TOP2α-targeted drugs. SIGNIFICANCE STATEMENT: Results presented here indicate that CRISPR/Cas9 gene editing of a suboptimal exon 19/intron 19 5' splice site in the DNA topoisomerase IIα (TOP2α) gene results in circumvention of acquired drug resistance to etoposide and other TOP2α-targeted drugs in a clonal K562 cell line by enhancing removal of intron 19 and thereby decreasing formation of a truncated TOP2α 90 kDa isoform and increasing expression of full-length TOP2α 170 kDa in these resistant cells. Results demonstrate the importance of RNA processing in acquired drug resistance to TOP2α-targeted drugs.
Collapse
Affiliation(s)
- Victor A Hernandez
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Jonathan L Papa
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Nicholas Shkolnikov
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Junan Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Hatice Gulcin Ozer
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| |
Collapse
|
50
|
Jones SK, Hawkins JA, Johnson NV, Jung C, Hu K, Rybarski JR, Chen JS, Doudna JA, Press WH, Finkelstein IJ. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nat Biotechnol 2021; 39:84-93. [PMID: 32895548 PMCID: PMC9665413 DOI: 10.1038/s41587-020-0646-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/14/2020] [Indexed: 12/26/2022]
Abstract
Engineered SpCas9s and AsCas12a cleave fewer off-target genomic sites than wild-type (wt) Cas9. However, understanding their fidelity, mechanisms and cleavage outcomes requires systematic profiling across mispaired target DNAs. Here we describe NucleaSeq-nuclease digestion and deep sequencing-a massively parallel platform that measures the cleavage kinetics and time-resolved cleavage products for over 10,000 targets containing mismatches, insertions and deletions relative to the guide RNA. Combining cleavage rates and binding specificities on the same target libraries, we benchmarked five SpCas9 variants and AsCas12a. A biophysical model built from these data sets revealed mechanistic insights into off-target cleavage. Engineered Cas9s, especially Cas9-HF1, dramatically increased cleavage specificity but not binding specificity compared to wtCas9. Surprisingly, AsCas12a cleavage specificity differed little from that of wtCas9. Initial DNA cleavage sites and end trimming varied by nuclease, guide RNA and the positions of mispaired nucleotides. More broadly, NucleaSeq enables rapid, quantitative and systematic comparisons of specificity and cleavage outcomes across engineered and natural nucleases.
Collapse
Affiliation(s)
- Stephen K Jones
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
| | - John A Hawkins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, TX, USA.
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Cheulhee Jung
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kuang Hu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - James R Rybarski
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, CA, USA
| | - William H Press
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|