1
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Nguyen GT, Schelling MA, Raju A, Buscher KA, Sritharan A, Sashital DG. CRISPR-Cas12a exhibits metal-dependent specificity switching. Nucleic Acids Res 2024; 52:9343-9359. [PMID: 39019776 PMCID: PMC11381342 DOI: 10.1093/nar/gkae613] [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: 02/21/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.
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Affiliation(s)
- Giang T Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Michael A Schelling
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Akshara Raju
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Kathryn A Buscher
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Aneisha Sritharan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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2
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Aguirre Rivera J, Mao G, Sabantsev A, Panfilov M, Hou Q, Lindell M, Chanez C, Ritort F, Jinek M, Deindl S. Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips. Science 2024; 385:892-898. [PMID: 39172826 DOI: 10.1126/science.adn5371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/12/2024] [Indexed: 08/24/2024]
Abstract
Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.
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Affiliation(s)
- J Aguirre Rivera
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - G Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - A Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Q Hou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Lindell
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - C Chanez
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - M Jinek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - S Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
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3
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Severins I, Bastiaanssen C, Kim SH, Simons RB, van Noort J, Joo C. Single-molecule structural and kinetic studies across sequence space. Science 2024; 385:898-904. [PMID: 39172834 DOI: 10.1126/science.adn5968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/01/2024] [Indexed: 08/24/2024]
Abstract
At the core of molecular biology lies the intricate interplay between sequence, structure, and function. Single-molecule techniques provide in-depth dynamic insights into structure and function, but laborious assays impede functional screening of large sequence libraries. We introduce high-throughput Single-molecule Parallel Analysis for Rapid eXploration of Sequence space (SPARXS), integrating single-molecule fluorescence with next-generation sequencing. We applied SPARXS to study the sequence-dependent kinetics of the Holliday junction, a critical intermediate in homologous recombination. By examining the dynamics of millions of Holliday junctions, covering thousands of distinct sequences, we demonstrated the ability of SPARXS to uncover sequence patterns, evaluate sequence motifs, and construct thermodynamic models. SPARXS emerges as a versatile tool for untangling the mechanisms that underlie sequence-specific processes at the molecular scale.
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Affiliation(s)
- Ivo Severins
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, Netherlands
| | - Carolien Bastiaanssen
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Sung Hyun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Roy B Simons
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
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4
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Hu T, Ji Q, Ke X, Zhou H, Zhang S, Ma S, Yu C, Ju W, Lu M, Lin Y, Ou Y, Zhou Y, Xiao Y, Xu C, Hu C. Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV). Commun Biol 2024; 7:858. [PMID: 39003402 PMCID: PMC11246428 DOI: 10.1038/s42003-024-06537-3] [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: 10/12/2023] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
R-loop-triggered collateral single-stranded DNA (ssDNA) nuclease activity within Class 1 Type I CRISPR-Cas systems holds immense potential for nucleic acid detection. However, the hyperactive ssDNase activity of Cas3 introduces unwanted noise and false-positive results. In this study, we identified a novel Type I-A Cas3 variant derived from Thermococcus siculi, which remains in an auto-inhibited state until it is triggered by Cascade complex and R-loop formation. This Type I-A CRISPR-Cas3 system not only exhibits an expanded protospacer adjacent motif (PAM) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. Furthermore, it exhibits dual activation modes-responding to both DNA and RNA targets. The culmination of our research efforts has led to the development of the Hyper-Active-Verification Establishment (HAVE, ). This innovation enables swift and precise human papillomavirus (HPV) diagnosis in clinical samples, providing a robust molecular diagnostic tool based on the Type I-A CRISPR-Cas3 system. Our findings contribute to understanding type I-A CRISPR-Cas3 system regulation and facilitate the creation of advanced diagnostic solutions with broad clinical applicability.
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Affiliation(s)
- Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, Zhejiang, 310052, China
| | - Quanquan Ji
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, Zhejiang, 310052, China
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Senfeng Zhang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Shengsheng Ma
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Chenlin Yu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjun Ju
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yu Lin
- International Peace Maternity & Child Health Hospital, Shanghai Municipal Key Clinical Specialty, Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yangjing Ou
- International Peace Maternity & Child Health Hospital, Shanghai Municipal Key Clinical Specialty, Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yingsi Zhou
- HuidaGene Therapeutics Inc., Shanghai, China.
| | - Yibei Xiao
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
| | - Chunlong Xu
- Lingang Laboratory, Shanghai, China.
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China.
| | - Chunyi Hu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Precision Medicine Translational Research Programme (TRP), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
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5
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Kuo YA, Chen YI, Wang Y, Korkmaz Z, Yonas S, He Y, Nguyen TD, Hong S, Nguyen AT, Kim S, Seifi S, Fan PH, Wu Y, Yang Z, Liu HW, Lu Y, Ren P, Yeh HC. Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602435. [PMID: 39026723 PMCID: PMC11257435 DOI: 10.1101/2024.07.07.602435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
F luorogenic ap tamers (FAPs) have become an increasingly important tool in cellular sensing and pathogen diagnostics. However, fine-tuning FAPs for enhanced performance remains challenging even with the structural details provided by X-ray crystallography. Here we present a novel approach to optimize a DNA-based FAP (D-FAP), Lettuce, on repurposed Illumina next-generation sequencing (NGS) chips. When substituting its cognate chromophore, DFHBI-1T, with TO1-biotin, Lettuce not only shows a red-shifted emission peak by 53 nm (from 505 to 558 nm), but also a 4-fold bulk fluorescence enhancement. After screening 8,821 Lettuce variants complexed with TO1-biotin, the C14T mutation is found to exhibit an improved apparent dissociated constant ( vs. 0.82 µM), an increased quantum yield (QY: 0.62 vs. 0.59) and an elongated fluorescence lifetime (τ: 6.00 vs. 5.77 ns), giving 45% more ensemble fluorescence than the canonical Lettuce/TO1-biotin complex. Molecular dynamic simulations further indicate that the π-π stacking interaction is key to determining the coordination structure of TO1-biotin in Lettuce. Our screening-and-simulation pipeline can effectively optimize FAPs without any prior structural knowledge of the canonical FAP/chromophore complexes, providing not only improved molecular probes for fluorescence sensing but also insights into aptamer-chromophore interactions.
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6
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Nguyen GT, Schelling MA, Buscher KA, Sritharan A, Sashital DG. CRISPR-Cas12a exhibits metal-dependent specificity switching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.29.569287. [PMID: 38076861 PMCID: PMC10705449 DOI: 10.1101/2023.11.29.569287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.
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Affiliation(s)
- Giang T. Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Equal contribution
| | - Michael A. Schelling
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Equal contribution
| | - Kathryn A. Buscher
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Current address: Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aneisha Sritharan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Current address: Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dipali G. Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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7
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Kuo HC, Prupes J, Chou CW, Finkelstein IJ. Massively parallel profiling of RNA-targeting CRISPR-Cas13d. Nat Commun 2024; 15:498. [PMID: 38216559 PMCID: PMC10786891 DOI: 10.1038/s41467-024-44738-w] [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: 04/13/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
CRISPR-Cas13d cleaves RNA and is used in vivo and for diagnostics. However, a systematic understanding of its RNA binding and cleavage specificity is lacking. Here, we describe an RNA Chip-Hybridized Association-Mapping Platform (RNA-CHAMP) for measuring the binding affinity for > 10,000 RNAs containing structural perturbations and other alterations relative to the CRISPR RNA (crRNA). Deep profiling of Cas13d reveals that it does not require a protospacer flanking sequence but is exquisitely sensitive to secondary structure within the target RNA. Cas13d binding is penalized by mismatches in the distal crRNA-target RNA region, while alterations in the proximal region inhibit nuclease activity. A biophysical model built from these data reveals that target recognition initiates in the distal end of the target RNA. Using this model, we design crRNAs that can differentiate between SARS-CoV-2 variants by modulating nuclease activation. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme.
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Affiliation(s)
- Hung-Che Kuo
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Joshua Prupes
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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8
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Kauert DJ, Madariaga-Marcos J, Rutkauskas M, Wulfken A, Songailiene I, Sinkunas T, Siksnys V, Seidel R. The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex. Nat Struct Mol Biol 2023:10.1038/s41594-023-01019-2. [PMID: 37415009 DOI: 10.1038/s41594-023-01019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have revolutionized gene editing with their ability to target specific genomic loci using CRISPR RNA (crRNA) complementarity. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base pairing between crRNA and the DNA target strand, forming an R-loop structure. Full R-loop extension is a prerequisite for subsequent DNA cleavage. However, the recognition of unintended sequences with multiple mismatches has limited therapeutic applications and is still poorly understood on a mechanistic level. Here we set up ultrafast DNA unwinding experiments on the basis of plasmonic DNA origami nanorotors to study R-loop formation by the Cascade effector complex in real time, close to base-pair resolution. We resolve a weak global downhill bias of the forming R-loop, followed by a steep uphill bias for the final base pairs. We also show that the energy landscape is modulated by base flips and mismatches. These findings suggest that Cascade-mediated R-loop formation occurs on short timescales in submillisecond single base-pair steps, but on longer timescales in six base-pair intermediate steps, in agreement with the structural periodicity of the crRNA-DNA hybrid.
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Affiliation(s)
- Dominik J Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | | | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Alexander Wulfken
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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9
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Kuo HC, Prupes J, Chou CW, Finkelstein IJ. Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534188. [PMID: 37034598 PMCID: PMC10081190 DOI: 10.1101/2023.03.27.534188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Type VI CRISPR enzymes cleave target RNAs and are widely used for gene regulation, RNA tracking, and diagnostics. However, a systematic understanding of their RNA binding specificity and cleavage activation is lacking. Here, we describe RNA chip-hybridized association-mapping platform (RNA-CHAMP), a massively parallel platform that repurposes next-generation DNA sequencing chips to measure the binding affinity for over 10,000 RNA targets containing structural perturbations, mismatches, insertions, and deletions relative to the CRISPR RNA (crRNA). Deep profiling of Cas13d, a compact and widely used RNA nuclease, reveals that it does not require a protospacer flanking sequence (PFS) but is exquisitely sensitive to secondary structure within the target RNA. Cas13d binding is strongly penalized by mismatches, insertions, and deletions in the distal crRNA-target RNA regions, while alterations in the proximal region inhibit nuclease activity without affecting binding. A biophysical model built from these data reveals that target recognition begins at the distal end of unstructured target RNAs and proceeds to the proximal end. Using this model, we designed a series of partially mismatched guide RNAs that modulate nuclease activity to detect single nucleotide polymorphisms (SNPs) in circulating SARS-CoV-2 variants. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme to improve CRISPR diagnostics and in vivo RNA editing. More broadly, RNA-CHAMP provides a quantitative platform for systematically measuring protein-RNA interactions.
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Affiliation(s)
- Hung-Che Kuo
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Joshua Prupes
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
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10
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Wu D, Feagin T, Mage P, Rangel A, Wan L, Kong D, Li A, Coller J, Eisenstein M, Soh H. Flow-Cell-Based Technology for Massively Parallel Characterization of Base-Modified DNA Aptamers. Anal Chem 2023; 95:2645-2652. [PMID: 36693249 DOI: 10.1021/acs.analchem.1c04777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aptamers incorporating chemically modified bases can achieve superior affinity and specificity compared to natural aptamers, but their characterization remains a labor-intensive, low-throughput task. Here, we describe the "non-natural aptamer array" (N2A2) system, in which a minimally modified Illumina MiSeq instrument is used for the high-throughput generation and characterization of large libraries of base-modified DNA aptamer candidates based on both target binding and specificity. We first demonstrate the capability to screen multiple different base modifications to identify the optimal chemistry for high-affinity target binding. We next use N2A2 to generate aptamers that can maintain excellent specificity even in complex samples, with equally strong target affinity in both buffer and diluted human serum. For both aptamers, affinity was formally calculated with gold-standard binding assays. Given that N2A2 requires only minor mechanical modifications to the MiSeq, we believe that N2A2 offers a broadly accessible tool for generating high-quality affinity reagents for diverse applications.
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Affiliation(s)
- Diana Wu
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Trevor Feagin
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Peter Mage
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Alexandra Rangel
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Leighton Wan
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Dehui Kong
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Anping Li
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - John Coller
- Stanford Functional Genomics Facility, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, California 94305, United States.,Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hyongsok Soh
- Department of Radiology, Stanford University, Stanford, California 94305, United States.,Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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11
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Marklund E, Ke Y, Greenleaf WJ. High-throughput biochemistry in RNA sequence space: predicting structure and function. Nat Rev Genet 2023; 24:401-414. [PMID: 36635406 DOI: 10.1038/s41576-022-00567-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 01/14/2023]
Abstract
RNAs are central to fundamental biological processes in all known organisms. The set of possible intramolecular interactions of RNA nucleotides defines the range of alternative structural conformations of a specific RNA that can coexist, and these structures enable functional catalytic properties of RNAs and/or their productive intermolecular interactions with other RNAs or proteins. However, the immense combinatorial space of potential RNA sequences has precluded predictive mapping between RNA sequence and molecular structure and function. Recent advances in high-throughput approaches in vitro have enabled quantitative thermodynamic and kinetic measurements of RNA-RNA and RNA-protein interactions, across hundreds of thousands of sequence variations. In this Review, we explore these techniques, how they can be used to understand RNA function and how they might form the foundations of an accurate model to predict the structure and function of an RNA directly from its nucleotide sequence. The experimental techniques and modelling frameworks discussed here are also highly relevant for the sampling of sequence-structure-function space of DNAs and proteins.
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Affiliation(s)
- Emil Marklund
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuxi Ke
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Huang TP, Heins ZJ, Miller SM, Wong BG, Balivada PA, Wang T, Khalil AS, Liu DR. High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs. Nat Biotechnol 2023; 41:96-107. [PMID: 36076084 PMCID: PMC9849140 DOI: 10.1038/s41587-022-01410-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/30/2022] [Indexed: 01/25/2023]
Abstract
Despite the availability of Cas9 variants with varied protospacer-adjacent motif (PAM) compatibilities, some genomic loci-especially those with pyrimidine-rich PAM sequences-remain inaccessible by high-activity Cas9 proteins. Moreover, broadening PAM sequence compatibility through engineering can increase off-target activity. With directed evolution, we generated four Cas9 variants that together enable targeting of most pyrimidine-rich PAM sequences in the human genome. Using phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution, we evolved Nme2Cas9, a compact Cas9 variant, into variants that recognize single-nucleotide pyrimidine-PAM sequences. We developed a general selection strategy that requires functional editing with fully specified target protospacers and PAMs. We applied this selection to evolve high-activity variants eNme2-T.1, eNme2-T.2, eNme2-C and eNme2-C.NR. Variants eNme2-T.1 and eNme2-T.2 offer access to N4TN PAM sequences with comparable editing efficiencies as existing variants, while eNme2-C and eNme2-C.NR offer less restrictive PAM requirements, comparable or higher activity in a variety of human cell types and lower off-target activity at N4CN PAM sequences.
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Affiliation(s)
- Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zachary J Heins
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Brandon G Wong
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Pallavi A Balivada
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Tina Wang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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13
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A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex. Nat Commun 2022; 13:7460. [PMID: 36460652 PMCID: PMC9718816 DOI: 10.1038/s41467-022-35116-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.
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14
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Patterson A, White A, Waymire E, Fleck S, Golden S, Wilkinson RA, Wiedenheft B, Bothner B. Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex. Nucleic Acids Res 2022; 50:11243-11254. [PMID: 36215034 DOI: 10.1093/nar/gkac841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR RNA-guided detection and degradation of foreign DNA is a dynamic process. Viruses can interfere with this cellular defense by expressing small proteins called anti-CRISPRs. While structural models of anti-CRISPRs bound to their target complex provide static snapshots that inform mechanism, the dynamics and thermodynamics of these interactions are often overlooked. Here, we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) and differential scanning fluorimetry (DSF) experiments to determine how anti-CRISPR binding impacts the conformational landscape of the type IF CRISPR RNA guided surveillance complex (Csy) upon binding of two different anti-CRISPR proteins (AcrIF9 and AcrIF2). The results demonstrate that AcrIF2 binding relies on enthalpic stabilization, whereas AcrIF9 uses an entropy driven reaction to bind the CRISPR RNA-guided surveillance complex. Collectively, this work reveals the thermodynamic basis and mechanistic versatility of anti-CRISPR-mediated immune suppression. More broadly, this work presents a striking example of how allosteric effectors are employed to regulate nucleoprotein complexes.
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Affiliation(s)
- Angela Patterson
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Aidan White
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Elizabeth Waymire
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Sophie Fleck
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Sarah Golden
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Royce A Wilkinson
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Brian Bothner
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
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15
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Kuo YA, Jung C, Chen YA, Kuo HC, Zhao OS, Nguyen TD, Rybarski JR, Hong S, Chen YI, Wylie DC, Hawkins JA, Walker JN, Shields SWJ, Brodbelt JS, Petty JT, Finkelstein IJ, Yeh HC. Massively Parallel Selection of NanoCluster Beacons. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204957. [PMID: 35945159 PMCID: PMC9588665 DOI: 10.1002/adma.202204957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/18/2022] [Indexed: 06/15/2023]
Abstract
NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here, a high-throughput selection method is reported that takes advantage of repurposed next-generation-sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs, respectively. Based on these findings, a "zipper-bag" model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high-throughput screening with machine-learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.
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Affiliation(s)
- Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Yu-An Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Oliver S Zhao
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Trung D Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Dennis C Wylie
- Computational Biology and Bioinformatics, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, 78712, USA
| | - John A Hawkins
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Samuel W J Shields
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, SC, 29617, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, 78712, USA
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16
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Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernández IS, Sternberg SH. Selective TnsC recruitment enhances the fidelity of RNA-guided transposition. Nature 2022; 609:384-393. [PMID: 36002573 PMCID: PMC10583602 DOI: 10.1038/s41586-022-05059-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 06/29/2022] [Indexed: 01/25/2023]
Abstract
Bacterial transposons are pervasive mobile genetic elements that use distinct DNA-binding proteins for horizontal transmission. For example, Escherichia coli Tn7 homes to a specific attachment site using TnsD1, whereas CRISPR-associated transposons use type I or type V Cas effectors to insert downstream of target sites specified by guide RNAs2,3. Despite this targeting diversity, transposition invariably requires TnsB, a DDE-family transposase that catalyses DNA excision and insertion, and TnsC, a AAA+ ATPase that is thought to communicate between transposase and targeting proteins4. How TnsC mediates this communication and thereby regulates transposition fidelity has remained unclear. Here we use chromatin immunoprecipitation with sequencing to monitor in vivo formation of the type I-F RNA-guided transpososome, enabling us to resolve distinct protein recruitment events before integration. DNA targeting by the TniQ-Cascade complex is surprisingly promiscuous-hundreds of genomic off-target sites are sampled, but only a subset of those sites is licensed for TnsC and TnsB recruitment, revealing a crucial proofreading checkpoint. To advance the mechanistic understanding of interactions responsible for transpososome assembly, we determined structures of TnsC using cryogenic electron microscopy and found that ATP binding drives the formation of heptameric rings that thread DNA through the central pore, thereby positioning the substrate for downstream integration. Collectively, our results highlight the molecular specificity imparted by consecutive factor binding to genomic target sites during RNA-guided transposition, and provide a structural roadmap to guide future engineering efforts.
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Affiliation(s)
- Florian T Hoffmann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Minjoo Kim
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, NY, USA
| | - Leslie Y Beh
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Illumina Singapore Pte, Ltd., Singapore, Singapore
| | - Jing Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Diego R Gelsinger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jerrin Thomas George
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Christopher Acree
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jason T Mohabir
- Department of Computer Science, Columbia University, New York, NY, USA
- Genomic Center for Infectious Diseases, Broad Institute, Cambridge, MA, USA
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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17
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Santiago-Frangos A, Nemudryi A, Nemudraia A, Wiegand T, Nichols JE, Krishna P, Scherffius AM, Zahl TR, Wilkinson RA, Wiedenheft B. CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics. Methods 2022; 205:1-10. [PMID: 35690249 PMCID: PMC9181078 DOI: 10.1016/j.ymeth.2022.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/06/2022] [Accepted: 06/04/2022] [Indexed: 01/04/2023] Open
Abstract
Polymerase Chain Reaction (PCR) is the reigning gold standard for molecular diagnostics. However, the SARS-CoV-2 pandemic reveals an urgent need for new diagnostics that provide users with immediate results without complex procedures or sophisticated equipment. These new demands have stimulated a tsunami of innovations that improve turnaround times without compromising the specificity and sensitivity that has established PCR as the paragon of diagnostics. Here we briefly introduce the origins of PCR and isothermal amplification, before turning to the emergence of CRISPR-Cas and Argonaute proteins, which are being coupled to fluorimeters, spectrometers, microfluidic devices, field-effect transistors, and amperometric biosensors, for a new generation of nucleic acid-based diagnostics.
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Affiliation(s)
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Anna Nemudraia
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Joseph E Nichols
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Pushya Krishna
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Andrew M Scherffius
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Trevor R Zahl
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Royce A Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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18
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Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
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19
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Chen H, Mayer A, Balasubramanian V. A scaling law in CRISPR repertoire sizes arises from the avoidance of autoimmunity. Curr Biol 2022; 32:2897-2907.e5. [PMID: 35659862 DOI: 10.1016/j.cub.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/13/2022] [Accepted: 05/09/2022] [Indexed: 12/28/2022]
Abstract
Some prokaryotes possess CRISPR-Cas systems that use DNA segments called spacers, which are acquired from invading phages, to guide immune defense. Here, we propose that cross-reactive CRISPR targeting can, however, lead to "heterologous autoimmunity," whereby foreign spacers guide self-targeting in a spacer-length-dependent fashion. Balancing antiviral defense against autoimmunity predicts a scaling relation between spacer length and CRISPR repertoire size. We find evidence for this scaling through a comparative analysis of sequenced prokaryotic genomes and show that this association also holds at the level of CRISPR types. By contrast, the scaling is absent in strains with nonfunctional CRISPR loci. Finally, we demonstrate that stochastic spacer loss can explain variations around the scaling relation, even between strains of the same species. Our results suggest that heterologous autoimmunity is a selective factor shaping the evolution of CRISPR-Cas systems, analogous to the trade-offs between immune specificity, breadth, and autoimmunity that constrain the diversity of adaptive immune systems in vertebrates.
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Affiliation(s)
- Hanrong Chen
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA; Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore 138672, Singapore.
| | - Andreas Mayer
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Vijay Balasubramanian
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA; Theoretische Natuurkunde, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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20
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Severins I, Joo C, van Noort J. Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics. Mol Cell 2022; 82:1788-1805. [PMID: 35561688 DOI: 10.1016/j.molcel.2022.04.024] [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: 02/01/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
Abstract
Next-generation sequencing techniques have led to a new quantitative dimension in the biological sciences. In particular, integrating sequencing techniques with biophysical tools allows sequence-dependent mechanistic studies. Using the millions of DNA clusters that are generated during sequencing to perform high-throughput binding affinity and kinetics measurements enabled the construction of energy landscapes in sequence space, uncovering relationships between sequence, structure, and function. Here, we review the approaches to perform ensemble fluorescence experiments on next-generation sequencing chips for variations of DNA, RNA, and protein sequences. As the next step, we anticipate that these fluorescence experiments will be pushed to the single-molecule level, which can directly uncover kinetics and molecular heterogeneity in an unprecedented high-throughput fashion. Molecular biophysics in sequence space, both at the ensemble and single-molecule level, leads to new mechanistic insights. The wide spectrum of applications in biology and medicine ranges from the fundamental understanding of evolutionary pathways to the development of new therapeutics.
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Affiliation(s)
- Ivo Severins
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands; Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands.
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21
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McKenzie RE, Keizer EM, Vink JNA, van Lopik J, Büke F, Kalkman V, Fleck C, Tans SJ, Brouns SJJ. Single cell variability of CRISPR-Cas interference and adaptation. Mol Syst Biol 2022; 18:e10680. [PMID: 35467080 PMCID: PMC10561596 DOI: 10.15252/msb.202110680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/26/2022] Open
Abstract
While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell-to-cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.
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Affiliation(s)
- Rebecca E McKenzie
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Emma M Keizer
- Biometris, Department of Mathematical and Statistical MethodsWageningen UniversityWageningenThe Netherlands
| | - Jochem N A Vink
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Jasper van Lopik
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Ferhat Büke
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Vera Kalkman
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM)Spatial Systems Biology GroupUniversity of FreiburgFreiburgGermany
| | - Sander J Tans
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Stan J J Brouns
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
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22
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Eslami-Mossallam B, Klein M, Smagt CVD, Sanden KVD, Jones SK, Hawkins JA, Finkelstein IJ, Depken M. A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity. Nat Commun 2022; 13:1367. [PMID: 35292641 PMCID: PMC8924176 DOI: 10.1038/s41467-022-28994-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/11/2022] [Indexed: 12/26/2022] Open
Abstract
The S. pyogenes (Sp) Cas9 endonuclease is an important gene-editing tool. SpCas9 is directed to target sites based on complementarity to a complexed single-guide RNA (sgRNA). However, SpCas9-sgRNA also binds and cleaves genomic off-targets with only partial complementarity. To date, we lack the ability to predict cleavage and binding activity quantitatively, and rely on binary classification schemes to identify strong off-targets. We report a quantitative kinetic model that captures the SpCas9-mediated strand-replacement reaction in free-energy terms. The model predicts binding and cleavage activity as a function of time, target, and experimental conditions. Trained and validated on high-throughput bulk-biochemical data, our model predicts the intermediate R-loop state recently observed in single-molecule experiments, as well as the associated conversion rates. Finally, we show that our quantitative activity predictor can be reduced to a binary off-target classifier that outperforms the established state-of-the-art. Our approach is extensible, and can characterize any CRISPR-Cas nuclease - benchmarking natural and future high-fidelity variants against SpCas9; elucidating determinants of CRISPR fidelity; and revealing pathways to increased specificity and efficiency in engineered systems.
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Affiliation(s)
- Behrouz Eslami-Mossallam
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
- Dept. Building Physics and Systems, TNO Building and Construction Research, Leeghwaterstraat 44, Delft, The Netherlands
| | - Misha Klein
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands
| | - Constantijn V D Smagt
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands
| | - Koen V D Sanden
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
| | - Stephen K Jones
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - John A Hawkins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, TX, 78712, USA
- European Molecular Biology Laboratory, Genome Biology Department, Heidelberg, Germany
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Martin Depken
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands.
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23
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Wu D, Gordon CKL, Shin JH, Eisenstein M, Soh HT. Directed Evolution of Aptamer Discovery Technologies. Acc Chem Res 2022; 55:685-695. [PMID: 35130439 DOI: 10.1021/acs.accounts.1c00724] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although antibodies are a powerful tool for molecular biology and clinical diagnostics, there are many emerging applications for which nucleic acid-based aptamers can be advantageous. However, generating high-quality aptamers with sufficient affinity and specificity for biomedical applications is a challenging feat for most research laboratories. In this Account, we describe four techniques developed in our laboratory to accelerate the discovery of high-quality aptamer reagents that can achieve robust binding even for challenging molecular targets. The first method is particle display, in which we convert solution-phase aptamers into aptamer particles that can be screened via fluorescence-activated cell sorting (FACS) to quantitatively isolate individual aptamer particles based on their affinity. This enables the efficient isolation of high-affinity aptamers in fewer selection rounds than conventional methods, thereby minimizing selection biases and reducing the emergence of artifacts in the final aptamer pool. We subsequently developed the multiparametric particle display (MPPD) method, which employs two-color FACS to isolate aptamer particles based on both affinity and specificity, yielding aptamers that exhibit excellent target binding even in complex matrixes such as serum. The third method is an alkyne-azide chemistry ("click chemistry")-based particle display (click-PD) that enables the generation and screening of "non-natural" aptamers with a wide range of base modifications. We have shown that these base-modified aptamers can achieve robust affinity and specificity for targets that have proven challenging or inaccessible with natural nucleotide-based aptamer libraries. Finally, we describe the non-natural aptamer array (N2A2) platform in which a modified benchtop sequencing instrument is used to characterize base-modified aptamers in high throughput, enabling the efficient identification of molecules with excellent affinity and specificity for their targets. This system first generates aptamer clusters on the flow-cell surface that incorporate alkyne-modified nucleobases and then performs a click reaction to couple those nucleobases to an azide-modified chemical moiety. This yields a sequence-defined array of tens of millions of base-modified sequences, which can then be characterized for affinity and specificity in a high-throughput fashion. Collectively, we believe that these advancements are helping to make aptamer technology more accessible, efficient, and robust, thereby enabling the use of these affinity reagents for a wider range of molecular recognition and detection-based applications.
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24
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Wimmer F, Mougiakos I, Englert F, Beisel CL. Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Mol Cell 2022; 82:1210-1224.e6. [PMID: 35216669 DOI: 10.1016/j.molcel.2022.01.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/30/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
CRISPR-Cas biology and technologies have been largely shaped to date by the characterization and use of single-effector nucleases. By contrast, multi-subunit effectors dominate natural systems, represent emerging technologies, and were recently associated with RNA-guided DNA transposition. This disconnect stems from the challenge of working with multiple protein subunits in vitro and in vivo. Here, we apply cell-free transcription-translation (TXTL) systems to radically accelerate the characterization of multi-subunit CRISPR effectors and transposons. Numerous DNA constructs can be combined in one TXTL reaction, yielding defined biomolecular readouts in hours. Using TXTL, we mined phylogenetically diverse I-E effectors, interrogated extensively self-targeting I-C and I-F systems, and elucidated targeting rules for I-B and I-F CRISPR transposons using only DNA-binding components. We further recapitulated DNA transposition in TXTL, which helped reveal a distinct branch of I-B CRISPR transposons. These capabilities will facilitate the study and exploitation of the broad yet underexplored diversity of CRISPR-Cas systems and transposons.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Ioannis Mougiakos
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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25
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Hou Z, Hu C, Ke A, Zhang Y. Introducing Large Genomic Deletions in Human Pluripotent Stem Cells Using CRISPR-Cas3. Curr Protoc 2022; 2:e361. [PMID: 35129865 PMCID: PMC8843033 DOI: 10.1002/cpz1.361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CRISPR-Cas systems provide researchers with eukaryotic genome editing tools and therapeutic platforms that make it possible to target disease mutations in somatic organs. Most of these tools employ Type II (e.g., Cas9) or Type V (e.g., Cas12a) CRISPR enzymes to create RNA-guided precise double-strand breaks in the genome. However, such technologies are limited in their capacity to make targeted large deletions. Recently, the Type I CRISPR system, which is prevalent in microbes and displays unique enzymatic features, has been harnessed to effectively create large chromosomal deletions in human cells. Type I CRISPR first uses a multisubunit ribonucleoprotein (RNP) complex called Cascade to find its guide-complementary target site, and then recruits a helicase-nuclease enzyme, Cas3, to travel along and shred the target DNA over a long distance with high processivity. When introduced into human cells as purified RNPs, the CRISPR-Cas3 complex can efficiently induce large genomic deletions of varying lengths (1-100 kb) from the CRISPR-targeted site. Because of this unique editing outcome, CRISPR-Cas3 holds great promise for tasks such as the removal of integrated viral genomes and the interrogation of structural variants affecting gene function and human disease. Here, we provide detailed protocols for introducing large deletions using CRISPR-Cas3. We describe step-by-step procedures for purifying the Type I-E CRISPR proteins Cascade and Cas3 from Thermobifida fusca, electroporating RNPs into human cells, and characterizing DNA deletions using PCR and sequencing. We focus here on human pluripotent stem cells due to their clinical potential, but these protocols will be broadly useful for other cell lines and model organisms for applications including large genomic deletion, full-gene or -chromosome removal, and CRISPR screening for noncoding elements, among others. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Expression and purification of Tfu Cascade RNP Support Protocol 1: Expression and purification of TfuCas3 protein Support Protocol 2: Culture of human pluripotent stem cells Basic Protocol 2: Introduction of Tfu Cascade RNP and Cas3 protein into hPSCs via electroporation Basic Protocol 3: Characterization of genomic DNA lesions using long-range PCR, TOPO cloning, and Sanger sequencing Alternate Protocol: Comprehensive analysis of genomic lesions by Tn5-based next-generation sequencing Support Protocol 3: Single-cell clonal isolation.
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Affiliation(s)
- Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.,These authors contributed equally to the work
| | - Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.,These authors contributed equally to the work
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA., Correspondence: (A.K.), (Y.Z.)
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA., Correspondence: (A.K.), (Y.Z.)
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26
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Drees A, Fischer M. High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers. Int J Mol Sci 2021; 22:9202. [PMID: 34502110 PMCID: PMC8431662 DOI: 10.3390/ijms22179202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. 'High-throughput sequencing fluorescent ligand interaction profiling' (HiTS-FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS-FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS-FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.
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Affiliation(s)
- Alissa Drees
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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27
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Osakabe K, Wada N, Murakami E, Miyashita N, Osakabe Y. Genome editing in mammalian cells using the CRISPR type I-D nuclease. Nucleic Acids Res 2021; 49:6347-6363. [PMID: 34076237 PMCID: PMC8216271 DOI: 10.1093/nar/gkab348] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 04/15/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
Adoption of CRISPR-Cas systems, such as CRISPR-Cas9 and CRISPR-Cas12a, has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I-the most abundant CRISPR system in bacteria-remains less developed. Type I systems, such as type I-E, and I-F, comprise the CRISPR-associated complex for antiviral defense ('Cascade': Cas5, Cas6, Cas7, Cas8 and the small subunit) and Cas3, which degrades the target DNA; in contrast, for the sub-type CRISPR-Cas type I-D, which lacks a typical Cas3 nuclease in its CRISPR locus, the mechanism of target DNA degradation remains unknown. Here, we found that Cas10d is a functional nuclease in the type I-D system, performing the role played by Cas3 in other CRISPR-Cas type I systems. The type I-D system can be used for targeted mutagenesis of genomic DNA in human cells, directing both bi-directional long-range deletions and short insertions/deletions. Our findings suggest the CRISPR-Cas type I-D system as a unique effector pathway in CRISPR that can be repurposed for genome engineering in eukaryotic cells.
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Affiliation(s)
- Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Emi Murakami
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Naoyuki Miyashita
- Department of Computational Systems Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Yuriko Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8502, Japan
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28
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Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T, Wimmer F, Yu Y, Barquist L, Schoen C, Kurzai O, Sharma CM, Beisel CL. Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science 2021; 372:941-948. [PMID: 33906967 PMCID: PMC8224270 DOI: 10.1126/science.abe7106] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/09/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas systems recognize foreign genetic material using CRISPR RNAs (crRNAs). In type II systems, a trans-activating crRNA (tracrRNA) hybridizes to crRNAs to drive their processing and utilization by Cas9. While analyzing Cas9-RNA complexes from Campylobacter jejuni, we discovered tracrRNA hybridizing to cellular RNAs, leading to formation of "noncanonical" crRNAs capable of guiding DNA targeting by Cas9. Our discovery inspired the engineering of reprogrammed tracrRNAs that link the presence of any RNA of interest to DNA targeting with different Cas9 orthologs. This capability became the basis for a multiplexable diagnostic platform termed LEOPARD (leveraging engineered tracrRNAs and on-target DNAs for parallel RNA detection). LEOPARD allowed simultaneous detection of RNAs from different viruses in one test and distinguished severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its D614G (Asp614→Gly) variant with single-base resolution in patient samples.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sahil Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg. 97080 Würzburg, Germany
| | - Gaurav Dugar
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg. 97080 Würzburg, Germany
| | - Natalia L Peeck
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Franziska Wimmer
- 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
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Christoph Schoen
- Institute for Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, 07745 Germany
| | - Cynthia M Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg. 97080 Würzburg, Germany.
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany.
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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29
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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.
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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
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30
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Veenstra TD. Omics in Systems Biology: Current Progress and Future Outlook. Proteomics 2021; 21:e2000235. [PMID: 33320441 DOI: 10.1002/pmic.202000235] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Biological research has undergone tremendous changes over the past three decades. Research used to almost exclusively focus on a single aspect of a single molecule per experiment. Modern technologies have enabled thousands of molecules to be simultaneously analyzed and the way that these molecules influence each other to be discerned. The change is so dramatic that it has given rise to a whole new descriptive suffix (i.e., omics) to describe these fields of study. While genomics was arguably the initial driver of this new trend, it quickly spread to other biological entities resulting in the creation of transcriptomics, proteomics, metabolomics, etc. The development of these "big four omics" created a wave of other omic fields, such as epigenomics, glycomics, lipidomics, microbiomics, and even foodomics; all with the purpose of comprehensively studying all the molecular entities or processes within their respective domain. The large number of omic fields that are invented even led to the term "panomics" as a way to classify them all under one category. Ultimately, all of these omic fields are setting the foundation for developing systems biology; in which the focus will be on determining the complex interactions that occur within biological systems.
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31
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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.
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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.
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32
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Zhang L, Rube HT, Vakulskas CA, Behlke MA, Bussemaker HJ, Pufall MA. Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes. Nucleic Acids Res 2020; 48:5037-5053. [PMID: 32315032 PMCID: PMC7229833 DOI: 10.1093/nar/gkaa231] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/06/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR RNA-guided endonucleases (RGEs) cut or direct activities to specific genomic loci, yet each has off-target activities that are often unpredictable. We developed a pair of simple in vitro assays to systematically measure the DNA-binding specificity (Spec-seq), catalytic activity specificity (SEAM-seq) and cleavage efficiency of RGEs. By separately quantifying binding and cleavage specificity, Spec/SEAM-seq provides detailed mechanistic insight into off-target activity. Feature-based models generated from Spec/SEAM-seq data for SpCas9 were consistent with previous reports of its in vitro and in vivo specificity, validating the approach. Spec/SEAM-seq is also useful for profiling less-well characterized RGEs. Application to an engineered SpCas9, HiFi-SpCas9, indicated that its enhanced target discrimination can be attributed to cleavage rather than binding specificity. The ortholog ScCas9, on the other hand, derives specificity from binding to an extended PAM. The decreased off-target activity of AsCas12a (Cpf1) appears to be primarily driven by DNA-binding specificity. Finally, we performed the first characterization of CasX specificity, revealing an all-or-nothing mechanism where mismatches can be bound, but not cleaved. Together, these applications establish Spec/SEAM-seq as an accessible method to rapidly and reliably evaluate the specificity of RGEs, Cas::gRNA pairs, and gain insight into the mechanism and thermodynamics of target discrimination.
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Affiliation(s)
- Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Coralville, IA 52241, USA.,Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - H Tomas Rube
- Department of Bioengineering, University of California, Merced, New York, NY 10027, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Coralville, IA 52241, USA
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33
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Li Z, Wang X, Xu D, Zhang D, Wang D, Dai X, Wang Q, Li Z, Gu Y, Ouyang W, Zhao S, Huang B, Gong J, Zhao J, Chen A, Shen Y, Dong Y, Zhang W, Xu X, Xu C, Jiang Y. DNB-based on-chip motif finding: A high-throughput method to profile different types of protein-DNA interactions. SCIENCE ADVANCES 2020; 6:eabb3350. [PMID: 32789179 PMCID: PMC7399529 DOI: 10.1126/sciadv.abb3350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Here, we report a sensitive DocMF system that uses next-generation sequencing chips to profile protein-DNA interactions. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer adjacent motif (PAM) sequences of different CRISPR systems. DocMF can simultaneously screen both 5' and 3' PAMs with high coverage. For SpCas9, we found noncanonical 5'-NAG-3' (~5%) and 5'-NGA-3' (~1.6%), in addition to its common PAMs, 5'-NGG-3' (~89.9%). More relaxed PAM sequences of two uncharacterized Cas endonucleases, VeCas9 and BvCas12a, were extensively characterized using DocMF. Moreover, we observed that dCas9, a DNA binding protein lacking endonuclease activity, preferably bound to the previously reported 5'-NGG-3' sequence. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA binding proteins.
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Affiliation(s)
| | - Xiaojue Wang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | | | - Dengwei Zhang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Dan Wang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Xuechen Dai
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Qi Wang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Zhou Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Shuchang Zhao
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266000, China
| | - Baoqian Huang
- BGI-Shenzhen, Shenzhen 518083, China
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Jian Gong
- Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, CA 95134, USA
| | - Jing Zhao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ao Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Shen
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-ShenzhenShenzhen 518083, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Chongjun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Yuan Jiang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
- Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, CA 95134, USA
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Tuminauskaite D, Norkunaite D, Fiodorovaite M, Tumas S, Songailiene I, Tamulaitiene G, Sinkunas T. DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system. BMC Biol 2020; 18:65. [PMID: 32539804 PMCID: PMC7296934 DOI: 10.1186/s12915-020-00799-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND CRISPR-Cas systems, which provide adaptive immunity against foreign nucleic acids in prokaryotes, can serve as useful molecular tools for multiple applications in genome engineering. Diverse CRISPR-Cas systems originating from distinct prokaryotes function through a common mechanism involving the assembly of small crRNA molecules and Cas proteins into a ribonucleoprotein (RNP) effector complex, and formation of an R-loop structure upon binding to the target DNA. Extensive research on the I-E subtype established the prototypical mechanism of DNA interference in type I systems, where the coordinated action of a ribonucleoprotein Cascade complex and Cas3 protein destroys foreign DNA. However, diverse protein composition between type I subtypes suggests differences in the mechanism of DNA interference that could be exploited for novel practical applications that call for further exploration of these systems. RESULTS Here we examined the mechanism of DNA interference provided by the type I-F1 system from Aggregatibacter actinomycetemcomitans D7S-1 (Aa). We show that functional Aa-Cascade complexes can be assembled not only with WT spacer of 32 nt but also with shorter or longer (14-176 nt) spacers. All complexes guided by the spacer bind to the target DNA sequence (protospacer) forming an R-loop when a C or CT protospacer adjacent motif (PAM) is present immediately upstream the protospacer (at -1 or -2,-1 position, respectively). The range of spacer and protospacer complementarity predetermine the length of the R-loop; however, only R-loops of WT length or longer trigger the nuclease/helicase Cas2/3, which initiates ATP-dependent unidirectional degradation at the PAM-distal end of the WT R-loop. Meanwhile, truncation of the WT R-loop at the PAM-distal end abolishes Cas2/3 cleavage. CONCLUSIONS We provide a comprehensive characterisation of the DNA interference mechanism in the type I-F1 CRISPR-Cas system, which is different from the type I-E in a few aspects. First, DNA cleavage initiation, which usually happens at the PAM-proximal end in type I-E, is shifted to the PAM-distal end of WT R-loop in the type I-F1. Second, the R-loop length controls on/off switch of DNA interference in the type I-F1, while cleavage initiation is less restricted in the type I-E. These results indicate that DNA interference in type I-F1 systems is governed through a checkpoint provided by the Cascade complex, which verifies the appropriate length for the R-loop.
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Affiliation(s)
- Donata Tuminauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Danguole Norkunaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Marija Fiodorovaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Sarunas Tumas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania.,Pressent Address: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania.
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Abstract
CRISPR-Cas systems have been engineered as powerful tools to control gene expression in bacteria. The most common strategy relies on the use of Cas effectors modified to bind target DNA without introducing DNA breaks. These effectors can either block the RNA polymerase or recruit it through activation domains. Here, we discuss the mechanistic details of how Cas effectors can modulate gene expression by blocking transcription initiation or acting as transcription roadblocks. CRISPR-Cas tools can be further engineered to obtain fine-tuned control of gene expression or target multiple genes simultaneously. Several caveats in using these tools have also been revealed, including off-target effects and toxicity, making it important to understand the design rules of engineered CRISPR-Cas effectors in bacteria. Alternatively, some types of CRISPR-Cas systems target RNA and could be used to block gene expression at the posttranscriptional level. Finally, we review applications of these tools in high-throughput screens and the progress and challenges in introducing CRISPR knockdown to other species, including nonmodel bacteria with industrial or clinical relevance. A deep understanding of how CRISPR-Cas systems can be harnessed to control gene expression in bacteria and build powerful tools will certainly open novel research directions.
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Affiliation(s)
- Antoine Vigouroux
- Synthetic Biology, Institut Pasteur, Paris, France
- Microbial Morphogenesis and Growth, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology, Institut Pasteur, Paris, France
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36
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Hirakawa M, Krishnakumar R, Timlin J, Carney J, Butler K. Gene editing and CRISPR in the clinic: current and future perspectives. Biosci Rep 2020; 40:BSR20200127. [PMID: 32207531 PMCID: PMC7146048 DOI: 10.1042/bsr20200127] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.
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Affiliation(s)
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, Livermore, CA 94551, U.S.A
| | - Jerilyn A. Timlin
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - James P. Carney
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - Kimberly S. Butler
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
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37
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Smargon AA, Shi YJ, Yeo GW. RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering. Nat Cell Biol 2020; 22:143-150. [PMID: 32015437 PMCID: PMC8008746 DOI: 10.1038/s41556-019-0454-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022]
Abstract
Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, we chart progress in the RNA-targeting CRISPR-Cas (RCas) field and illustrate how continuing evolution in scientific discovery translates into applications for RNA biology and insights into mysteries, obstacles, and alternative technologies that lie ahead.
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Affiliation(s)
- Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yilan J Shi
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.
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38
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Vink JNA, Martens KJA, Vlot M, McKenzie RE, Almendros C, Estrada Bonilla B, Brocken DJW, Hohlbein J, Brouns SJJ. Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism. Mol Cell 2020; 77:39-50.e10. [PMID: 31735642 DOI: 10.1016/j.molcel.2019.10.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/31/2019] [Accepted: 10/11/2019] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here, we visualize individual Cascade complexes in a native type I CRISPR-Cas system. We uncover an exponential relation between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and affect CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.
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Affiliation(s)
- Jochem N A Vink
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Laboratory of Bionanotechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Rebecca E McKenzie
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Cristóbal Almendros
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Boris Estrada Bonilla
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daan J W Brocken
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, the Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Microspectroscopy Research Facility, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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39
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Belushkin A, Yesilkoy F, González-López JJ, Ruiz-Rodríguez JC, Ferrer R, Fàbrega A, Altug H. Rapid and Digital Detection of Inflammatory Biomarkers Enabled by a Novel Portable Nanoplasmonic Imager. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906108. [PMID: 31830370 DOI: 10.1002/smll.201906108] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Indexed: 05/18/2023]
Abstract
New point-of-care diagnostic devices are urgently needed for rapid and accurate diagnosis, particularly in the management of life-threatening infections and sepsis, where immediate treatment is key. Sepsis is a critical condition caused by systemic response to infection, with chances of survival drastically decreasing every hour. A novel portable biosensor based on nanoparticle-enhanced digital plasmonic imaging is reported for rapid and sensitive detection of two sepsis-related inflammatory biomarkers, procalcitonin (PCT) and C-reactive protein (CRP) directly from blood serum. The device achieves outstanding limit of detection of 21.3 pg mL-1 for PCT and 36 pg mL-1 for CRP, and dynamic range of at least three orders of magnitude. The portable device is deployed at Vall d'Hebron University Hospital in Spain and tested with a wide range of patient samples with sepsis, noninfectious systemic inflammatory response syndrome (SIRS), and healthy subjects. The results are validated against ultimate clinical diagnosis and currently used immunoassays, and show that the device provides accurate and robust performance equivalent to gold-standard laboratory tests. Importantly, the plasmonic imager can enable identification of PCT levels typical of sepsis and SIRS patients in less than 15 min. The compact and low-cost device is a promising solution for assisting rapid and accurate on-site sepsis diagnosis.
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Affiliation(s)
- Alexander Belushkin
- Institute of BioEngineering, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Filiz Yesilkoy
- Institute of BioEngineering, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Juan Jose González-López
- Department of Clinical Microbiology, Vall d'Hebron University Hospital, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodríguez
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
| | - Anna Fàbrega
- Department of Clinical Microbiology, Vall d'Hebron University Hospital, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Hatice Altug
- Institute of BioEngineering, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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40
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Morisaka H, Yoshimi K, Okuzaki Y, Gee P, Kunihiro Y, Sonpho E, Xu H, Sasakawa N, Naito Y, Nakada S, Yamamoto T, Sano S, Hotta A, Takeda J, Mashimo T. CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun 2019; 10:5302. [PMID: 31811138 PMCID: PMC6897959 DOI: 10.1038/s41467-019-13226-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022] Open
Abstract
Although single-component Class 2 CRISPR systems, such as type II Cas9 or type V Cas12a (Cpf1), are widely used for genome editing in eukaryotic cells, the application of multi-component Class 1 CRISPR has been less developed. Here we demonstrate that type I-E CRISPR mediates distinct DNA cleavage activity in human cells. Notably, Cas3, which possesses helicase and nuclease activity, predominantly triggered several thousand base pair deletions upstream of the 5'-ARG protospacer adjacent motif (PAM), without prominent off-target activity. This Cas3-mediated directional and broad DNA degradation can be used to introduce functional gene knockouts and knock-ins. As an example of potential therapeutic applications, we show Cas3-mediated exon-skipping of the Duchenne muscular dystrophy (DMD) gene in patient-induced pluripotent stem cells (iPSCs). These findings broaden our understanding of the Class 1 CRISPR system, which may serve as a unique genome editing tool in eukaryotic cells distinct from the Class 2 CRISPR system.
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Affiliation(s)
- Hiroyuki Morisaka
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Kazuto Yoshimi
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yuya Okuzaki
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Peter Gee
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yayoi Kunihiro
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Ekasit Sonpho
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Huaigeng Xu
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Noriko Sasakawa
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yuki Naito
- Database Center for Life Science, Mishima, 411-8540, Japan
- National Institute of Genetics, Mishima, 411-8540, Japan
| | - Shinichiro Nakada
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 565-0871, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Shigetoshi Sano
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan.
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan.
| | - Tomoji Mashimo
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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41
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Mamet N, Harari G, Zamir A, Bachelet I. Simulating the Monty Hall problem in a DNA sequencing machine. Comput Biol Chem 2019; 83:107122. [DOI: 10.1016/j.compbiolchem.2019.107122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 08/04/2019] [Accepted: 09/04/2019] [Indexed: 02/04/2023]
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42
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Cameron P, Coons MM, Klompe SE, Lied AM, Smith SC, Vidal B, Donohoue PD, Rotstein T, Kohrs BW, Nyer DB, Kennedy R, Banh LM, Williams C, Toh MS, Irby MJ, Edwards LS, Lin CH, Owen ALG, Künne T, van der Oost J, Brouns SJJ, Slorach EM, Fuller CK, Gradia S, Kanner SB, May AP, Sternberg SH. Harnessing type I CRISPR-Cas systems for genome engineering in human cells. Nat Biotechnol 2019; 37:1471-1477. [PMID: 31740839 DOI: 10.1038/s41587-019-0310-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/06/2019] [Indexed: 12/26/2022]
Abstract
Type I CRISPR-Cas systems are the most abundant adaptive immune systems in bacteria and archaea1,2. Target interference relies on a multi-subunit, RNA-guided complex called Cascade3,4, which recruits a trans-acting helicase-nuclease, Cas3, for target degradation5-7. Type I systems have rarely been used for eukaryotic genome engineering applications owing to the relative difficulty of heterologous expression of the multicomponent Cascade complex. Here, we fuse Cascade to the dimerization-dependent, non-specific FokI nuclease domain8-11 and achieve RNA-guided gene editing in multiple human cell lines with high specificity and efficiencies of up to ~50%. FokI-Cascade can be reconstituted via an optimized two-component expression system encoding the CRISPR-associated (Cas) proteins on a single polycistronic vector and the guide RNA (gRNA) on a separate plasmid. Expression of the full Cascade-Cas3 complex in human cells resulted in targeted deletions of up to ~200 kb in length. Our work demonstrates that highly abundant, previously untapped type I CRISPR-Cas systems can be harnessed for genome engineering applications in eukaryotic cells.
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Affiliation(s)
| | | | - Sanne E Klompe
- Caribou Biosciences, Inc., Berkeley, CA, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | | | | | | | - Tomer Rotstein
- Caribou Biosciences, Inc., Berkeley, CA, USA.,Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Rachel Kennedy
- Caribou Biosciences, Inc., Berkeley, CA, USA.,Invitae Corporation, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Tim Künne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands.,Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
| | | | | | | | | | - Andrew P May
- Caribou Biosciences, Inc., Berkeley, CA, USA.,Sana Biotechnology, South San Francisco, CA, USA
| | - Samuel H Sternberg
- Caribou Biosciences, Inc., Berkeley, CA, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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Songailiene I, Rutkauskas M, Sinkunas T, Manakova E, Wittig S, Schmidt C, Siksnys V, Seidel R. Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length. Cell Rep 2019; 28:3157-3166.e4. [PMID: 31533038 PMCID: PMC6859484 DOI: 10.1016/j.celrep.2019.08.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022] Open
Abstract
The multi-subunit type I CRISPR-Cas surveillance complex Cascade uses its crRNA to recognize dsDNA targets. Recognition involves DNA unwinding and base-pairing between the crRNA spacer region and a complementary DNA strand, resulting in formation of an R-loop structure. The modular Cascade architecture allows assembly of complexes containing crRNAs with altered spacer lengths that promise increased target specificity in emerging biotechnological applications. Here we produce type I-E Cascade complexes containing crRNAs with up to 57-nt-long spacers. We show that these complexes form R-loops corresponding to the designed target length, even for the longest spacers tested. Furthermore, the complexes can bind their targets with much higher affinity compared with the wild-type form. However, target recognition and the subsequent Cas3-mediated DNA cleavage do not require extended R-loops but already occur for wild-type-sized R-loops. These findings set important limits for specificity improvements of type I CRISPR-Cas systems.
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Affiliation(s)
- Inga Songailiene
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Marius Rutkauskas
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Tomas Sinkunas
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Sabine Wittig
- HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Carla Schmidt
- HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania.
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany.
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Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R. Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro. Nucleic Acids Res 2019; 46:4087-4098. [PMID: 29596641 PMCID: PMC5934681 DOI: 10.1093/nar/gky219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
In type I CRISPR-Cas systems, primed adaptation of new spacers into CRISPR arrays occurs when the effector Cascade-crRNA complex recognizes imperfectly matched targets that are not subject to efficient CRISPR interference. Thus, primed adaptation allows cells to acquire additional protection against mobile genetic elements that managed to escape interference. Biochemical and biophysical studies suggested that Cascade-crRNA complexes formed on fully matching targets (subject to efficient interference) and on partially mismatched targets that promote primed adaption are structurally different. Here, we probed Escherichia coli Cascade-crRNA complexes bound to matched and mismatched DNA targets using a magnetic tweezers assay. Significant differences in complex stabilities were observed consistent with the presence of at least two distinct conformations. Surprisingly, in vivo analysis demonstrated that all mismatched targets stimulated robust primed adaptation irrespective of conformational states observed in vitro. Our results suggest that primed adaptation is a direct consequence of a reduced interference efficiency and/or rate and is not a consequence of distinct effector complex conformations on target DNA.
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Affiliation(s)
- Andrey Krivoy
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Marius Rutkauskas
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Konstantin Kuznedelov
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Olga Musharova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Christophe Rouillon
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Konstantin Severinov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
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45
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Layton CJ, McMahon PL, Greenleaf WJ. Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip. Mol Cell 2019; 73:1075-1082.e4. [PMID: 30849388 DOI: 10.1016/j.molcel.2019.02.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/18/2019] [Accepted: 02/14/2019] [Indexed: 01/22/2023]
Abstract
High-throughput DNA sequencing techniques have enabled diverse approaches for linking DNA sequence to biochemical function. In contrast, assays of protein function have substantial limitations in terms of throughput, automation, and widespread availability. We have adapted an Illumina high-throughput sequencing chip to display an immense diversity of ribosomally translated proteins and peptides and then carried out fluorescence-based functional assays directly on this flow cell, demonstrating that a single, widely available high-throughput platform can perform both sequencing-by-synthesis and protein assays. We quantified the binding of the M2 anti-FLAG antibody to a library of 1.3 × 104 variant FLAG peptides, exploring non-additive effects of combinations of mutations and discovering a "superFLAG" epitope variant. We also measured the enzymatic activity of 1.56 × 105 molecular variants of full-length human O6-alkylguanine-DNA alkyltransferase (SNAP-tag). This comprehensive corpus of catalytic rates revealed amino acid interaction networks and cooperativity, linked positive cooperativity to structural proximity, and revealed ubiquitous positively cooperative interactions with histidine residues.
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Affiliation(s)
- Curtis J Layton
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter L McMahon
- Department of Applied Physics, Stanford University, Stanford, CA 94305, 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; Chan-Zuckerberg Initiative, Palo Alto, CA 94301, USA.
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46
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Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019; 19:e1800438. [PMID: 30901150 DOI: 10.1002/pmic.201800438] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/24/2019] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
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47
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Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell 2019; 74:936-950.e5. [PMID: 30975459 PMCID: PMC6555677 DOI: 10.1016/j.molcel.2019.03.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.
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Affiliation(s)
- Adam E Dolan
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA; State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Max J Gramelspacher
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jaewon Heo
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Sara E Howden
- Murdoch Children's Research Institute, Flemington Rd., Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.
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48
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Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell 2019. [PMID: 30975459 DOI: 10.1016/j.molcel.2019.03.014.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.
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49
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Kocak DD, Josephs EA, Bhandarkar V, Adkar SS, Kwon JB, Gersbach CA. Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol 2019; 37:657-666. [PMID: 30988504 PMCID: PMC6626619 DOI: 10.1038/s41587-019-0095-1] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 03/11/2019] [Indexed: 12/26/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeat) systems have been broadly adopted for basic science, biotechnology, and gene and cell therapy. In some cases, these bacterial nucleases have demonstrated off-target activity. This creates a potential hazard for therapeutic applications and could confound results in biological research. Therefore, improving the precision of these nucleases is of broad interest. Here we show that engineering a hairpin secondary structure onto the spacer region of single guide RNAs (hp-sgRNAs) can increase specificity by several orders of magnitude when combined with various CRISPR effectors. We first demonstrate that designed hp-sgRNAs can tune the activity of a transactivator based on Cas9 from Streptococcus pyogenes (SpCas9). We then show that hp-sgRNAs increase the specificity of gene editing using five different Cas9 or Cas12a variants. Our results demonstrate that RNA secondary structure is a fundamental parameter that can tune the activity of diverse CRISPR systems.
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Affiliation(s)
- D Dewran Kocak
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Eric A Josephs
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
- Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Vidit Bhandarkar
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Shaunak S Adkar
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Jennifer B Kwon
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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50
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