51
|
Clow PA, Du M, Jillette N, Taghbalout A, Zhu JJ, Cheng AW. CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus. Nat Commun 2022; 13:1871. [PMID: 35387989 PMCID: PMC8987088 DOI: 10.1038/s41467-022-29343-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
Three-dimensional (3D) structures of the genome are dynamic, heterogeneous and functionally important. Live cell imaging has become the leading method for chromatin dynamics tracking. However, existing CRISPR- and TALE-based genomic labeling techniques have been hampered by laborious protocols and are ineffective in labeling non-repetitive sequences. Here, we report a versatile CRISPR/Casilio-based imaging method that allows for a nonrepetitive genomic locus to be labeled using one guide RNA. We construct Casilio dual-color probes to visualize the dynamic interactions of DNA elements in single live cells in the presence or absence of the cohesin subunit RAD21. Using a three-color palette, we track the dynamic 3D locations of multiple reference points along a chromatin loop. Casilio imaging reveals intercellular heterogeneity and interallelic asynchrony in chromatin interaction dynamics, underscoring the importance of studying genome structures in 4D.
Collapse
Affiliation(s)
- Patricia A Clow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Menghan Du
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | | | - Aziz Taghbalout
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Jacqueline J Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA.
| | - Albert W Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA.
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, 04609, USA.
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
| |
Collapse
|
52
|
Bustamante-Jaramillo LF, Fingal J, Blondot ML, Rydell GE, Kann M. Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges. Viruses 2022; 14:v14030557. [PMID: 35336964 PMCID: PMC8950347 DOI: 10.3390/v14030557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/30/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus infections are the main reason for hepatocellular carcinoma development. Current treatment reduces the viral load but rarely leads to virus elimination. Despite its medical importance, little is known about infection dynamics on the cellular level not at least due to technical obstacles. Regardless of infections leading to extreme viral loads, which may reach 1010 virions per mL serum, hepatitis B viruses are of low abundance and productivity in individual cells. Imaging of the infections in cells is thus a particular challenge especially for cccDNA that exists only in a few copies. The review describes the significance of microscopical approaches on genome and transcript detection for understanding hepatitis B virus infections, implications for understanding treatment outcomes, and recent microscopical approaches, which have not been applied in HBV research.
Collapse
Affiliation(s)
- Luisa F. Bustamante-Jaramillo
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Joshua Fingal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Marie-Lise Blondot
- Microbiologie Fondamentale et Pathogénicité (MFP), CNRS UMR 5234, University of Bordeaux, 33076 Bordeaux, France;
| | - Gustaf E. Rydell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Michael Kann
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
- Region Västra Götaland, Department of Clinical Microbiology, Sahlgrenska University Hospital, 405 30 Gothenburg, Sweden
- Correspondence:
| |
Collapse
|
53
|
Safdar S, Driesen S, Leirs K, De Sutter D, Eyckerman S, Lammertyn J, Spasic D. Engineered tracrRNA for enabling versatile CRISPR-dCas9-based biosensing concepts. Biosens Bioelectron 2022; 206:114140. [PMID: 35247858 DOI: 10.1016/j.bios.2022.114140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 12/26/2022]
Abstract
In recent years, CRISPR-Cas (stands for: clustered regularly interspaced short palindromic repeats - CRISPR associated protein) based technologies have gained increasing attention in the biosensing field. Thanks to excellent sequence specificity, their use is of particular interest for detecting nucleic acid (NA) targets. In this context, signal generation and amplification can be realized by employing the cis-cleavage activity of the Cas9 protein, although other options involving the catalytically inactive dead Cas9 (dCas9) are increasingly explored. The latter are however mostly based on complex protein engineering processes and often lack efficient signal amplification. Here we showed for the first time that flexible signal generation and amplification properties can be integrated into the CRISPR-dCas9 complex based on a straightforward incorporation of a DNA sequence into the trans-activating CRISPR RNA (tracrRNA). The intrinsic nuclease activity of the engineered complex remained conserved, while the incorporated DNA stretch enabled two modes of amplified fluorescent signal generation: (1) as an RNA-cleaving DNA-based enzyme (DNAzyme) or (2) as hybridization site for biotinylated DNA probes, allowing subsequent enzyme labeling. Both signal generation strategies were demonstrated in solution as well as while coupled to a solid surface. Finally, in a proof of concept bioassay, we demonstrated the successful detection of single stranded DNA on magnetic microbeads using the engineered CRISPR-dCas9 complex. Thanks to the flexibility of incorporating different NA-based signal generation and amplification strategies, this novel NA engineering approach holds enormous promise for many new CRISPR-based biosensing applications.
Collapse
Affiliation(s)
- Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Seppe Driesen
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Karen Leirs
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, UGent Department of Biomolecular Medicine, Technologiepark 75, Zwijnaarde, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, UGent Department of Biomolecular Medicine, Technologiepark 75, Zwijnaarde, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| |
Collapse
|
54
|
Qiao H, Wu J, Zhang X, Luo J, Wang H, Ming D. The Advance of CRISPR-Cas9-Based and NIR/CRISPR-Cas9-Based Imaging System. Front Chem 2021; 9:786354. [PMID: 34976954 PMCID: PMC8716450 DOI: 10.3389/fchem.2021.786354] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
The study of different genes, chromosomes and the spatiotemporal relationship between them is of great significance in the field of biomedicine. CRISPR-Cas9 has become the most widely used gene editing tool due to its excellent targeting ability. In recent years, a series of advanced imaging technologies based on Cas9 have been reported, providing fast and convenient tools for studying the sites location of genome, RNA, and chromatin. At the same time, a variety of CRISPR-Cas9-based imaging systems have been developed, which are widely used in real-time multi-site imaging in vivo. In this review, we summarized the component and mechanism of CRISPR-Cas9 system, overviewed the NIR imaging and the application of NIR fluorophores in the delivery of CRISPR-Cas9, and highlighted advances of the CRISPR-Cas9-based imaging system. In addition, we also discussed the challenges and potential solutions of CRISPR-Cas9-based imaging methods, and looked forward to the development trend of the field.
Collapse
Affiliation(s)
- Huanhuan Qiao
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Jieting Wu
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xiaodong Zhang
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Jian Luo
- Palo Alto Veterans Institute for Research, VA Palo Alto Health Care System, Palo Alto, CA, United States
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, Stanford, CA, United States
| | - Hao Wang
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Hao Wang, ; Dong Ming,
| | - Dong Ming
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Hao Wang, ; Dong Ming,
| |
Collapse
|
55
|
Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
Collapse
Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
56
|
Abstract
CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a trans-activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances.
Collapse
Affiliation(s)
- Chunyu Liao
- 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
| |
Collapse
|
57
|
Chaudhary N, Im JK, Nho SH, Kim H. Visualizing Live Chromatin Dynamics through CRISPR-Based Imaging Techniques. Mol Cells 2021; 44:627-636. [PMID: 34588320 PMCID: PMC8490199 DOI: 10.14348/molcells.2021.2254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/27/2022] Open
Abstract
The three-dimensional organization of chromatin and its time-dependent changes greatly affect virtually every cellular function, especially DNA replication, genome maintenance, transcription regulation, and cell differentiation. Sequencing-based techniques such as ChIP-seq, ATAC-seq, and Hi-C provide abundant information on how genomic elements are coupled with regulatory proteins and functionally organized into hierarchical domains through their interactions. However, visualizing the time-dependent changes of such organization in individual cells remains challenging. Recent developments of CRISPR systems for site-specific fluorescent labeling of genomic loci have provided promising strategies for visualizing chromatin dynamics in live cells. However, there are several limiting factors, including background signals, off-target binding of CRISPR, and rapid photobleaching of the fluorophores, requiring a large number of target-bound CRISPR complexes to reliably distinguish the target-specific foci from the background. Various modifications have been engineered into the CRISPR system to enhance the signal-to-background ratio and signal longevity to detect target foci more reliably and efficiently, and to reduce the required target size. In this review, we comprehensively compare the performances of recently developed CRISPR designs for improved visualization of genomic loci in terms of the reliability of target detection, the ability to detect small repeat loci, and the allowed time of live tracking. Longer observation of genomic loci allows the detailed identification of the dynamic characteristics of chromatin. The diffusion properties of chromatin found in recent studies are reviewed, which provide suggestions for the underlying biological processes.
Collapse
Affiliation(s)
- Narendra Chaudhary
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jae-Kyeong Im
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Si-Hyeong Nho
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Hajin Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| |
Collapse
|
58
|
Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, Ito Y, Tokunaga M, Stasevich TJ, Kimura H. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. Genes Cells 2021; 26:905-926. [PMID: 34465007 PMCID: PMC8893316 DOI: 10.1111/gtc.12893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022]
Abstract
In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here, we demonstrate a new method to see endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps: First, we develop an anti-FLAG frankenbody that can bind FLAG-tagged proteins in diverse live-cell environments. The anti-FLAG frankenbody complements the anti-HA frankenbody, enabling two-color signal amplification from FLAG- and HA-tagged proteins. Second, we develop a pair of cell-permeable ZF probes that specifically bind two endogenous chromatin loci predicted to be involved in chromatin looping. By coupling our anti-FLAG and anti-HA frankenbodies with FLAG- and HA-tagged ZF probes, we simultaneously see the dynamics of the two loci in single living cells. This shows a close association between the two loci in the majority of cells, but the loci markedly separate from the triggered degradation of the cohesin subunit RAD21. Our ability to image two endogenous genomic loci simultaneously in single living cells provides a proof of principle that ZF probes coupled with frankenbodies are useful new tools for exploring genome dynamics in multiple colors.
Collapse
Affiliation(s)
- Yang Liu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, SOKENDAI, Mishima, Japan
| | - Yotaro Yamamoto
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yoshifusa Sadamura
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
59
|
Lingam S, Liu Z, Yang B, Wong W, Parikh BH, Ong JY, Goh D, Wong DSL, Tan QSW, Tan GSW, Holder GE, Regha K, Barathi VA, Hunziker W, Lingam G, Zeng X, Su X. cGMP-grade human iPSC-derived retinal photoreceptor precursor cells rescue cone photoreceptor damage in non-human primates. Stem Cell Res Ther 2021; 12:464. [PMID: 34412697 PMCID: PMC8375124 DOI: 10.1186/s13287-021-02539-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022] Open
Abstract
Background Retinal regenerative therapies hold great promise for the treatment of inherited retinal degenerations (IRDs). Studies in preclinical lower mammal models of IRDs have suggested visual improvement following retinal photoreceptor precursors transplantation, but there is limited evidence on the ability of these transplants to rescue retinal damage in higher mammals. The purpose of this study was to evaluate the therapeutic potential of photoreceptor precursors derived from clinically compliant induced pluripotent stem cells (iPSCs). Methods Photoreceptor precursors were sub-retinally transplanted into non-human primates (Macaca fascicularis). The cells were transplanted both in naïve and cobalt chloride-induced retinal degeneration models who had been receiving systemic immunosuppression for one week prior to the procedure. Optical coherence tomography, fundus autofluorescence imaging, electroretinography, ex vivo histology and immunofluorescence staining were used to evaluate retinal structure, function and survival of transplanted cells. Results There were no adverse effects of iPSC-derived photoreceptor precursors on retinal structure or function in naïve NHP models, indicating good biocompatibility. In addition, photoreceptor precursors injected into cobalt chloride-induced retinal degeneration NHP models demonstrated an ability both to survive and to mature into cone photoreceptors at 3 months post-transplant. Optical coherence tomography showed restoration of retinal ellipsoid zone post-transplantation. Conclusions These findings demonstrate the safety and therapeutic potential of clinically compliant iPSC-derived photoreceptor precursors as a cell replacement source for future clinical trials. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02539-8.
Collapse
Affiliation(s)
- Swathi Lingam
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Zengping Liu
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.,Singapore Eye Research Institute (SERI), Singapore, 169856, Singapore
| | - Binxia Yang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Wendy Wong
- Department of Ophthalmology, National University Hospital, Singapore, 119074, Singapore
| | - Bhav Harshad Parikh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jun Yi Ong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Debbie Goh
- Department of Ophthalmology, National University Hospital, Singapore, 119074, Singapore
| | - Daniel Soo Lin Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Queenie Shu Woon Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Gavin S W Tan
- Singapore Eye Research Institute (SERI), Singapore, 169856, Singapore.,Academic Clinical Program in Ophthalmology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Graham E Holder
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.,Department of Ophthalmology, National University Hospital, Singapore, 119074, Singapore.,UCL Institute of Ophthalmology, London, WC1E 6BT, UK
| | - Kakkad Regha
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Veluchamy Amutha Barathi
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.,Singapore Eye Research Institute (SERI), Singapore, 169856, Singapore.,Academic Clinical Program in Ophthalmology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Walter Hunziker
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Gopal Lingam
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.,Singapore Eye Research Institute (SERI), Singapore, 169856, Singapore.,Department of Ophthalmology, National University Hospital, Singapore, 119074, Singapore
| | - Xianmin Zeng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.,RxCell Inc, Novato, CA, 94949, USA
| | - Xinyi Su
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore. .,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore. .,Singapore Eye Research Institute (SERI), Singapore, 169856, Singapore. .,Department of Ophthalmology, National University Hospital, Singapore, 119074, Singapore.
| |
Collapse
|
60
|
Abstract
The imaging of chromatin, genomic loci, RNAs, and proteins is very important to study their localization, interaction, and coordinated regulation. Recently, several clustered regularly interspaced short palindromic repeats (CRISPR) based imaging methods have been established. The refurbished tool kits utilizing deactivated Cas9 (dCas9) and dCas13 have been established to develop applications of CRISPR-Cas technology beyond genome editing. Here, we review recent advancements in CRISPR-based methods that enable efficient imaging and visualization of chromatin, genomic loci, RNAs, and proteins. RNA aptamers, Pumilio, SuperNova tagging system, molecular beacons, halotag, bimolecular fluorescence complementation, RNA-guided endonuclease in situ labeling, and oligonucleotide-based imaging methods utilizing fluorescent proteins, organic dyes, or quantum dots have been developed to achieve improved fluorescence and signal-to-noise ratio for the imaging of chromatin or genomic loci. RNA-guided RNA targeting CRISPR systems (CRISPR/dCas13) and gene knock-in strategies based on CRISPR/Cas9 mediated site-specific cleavage and DNA repair mechanisms have been employed for efficient RNA and protein imaging, respectively. A few CRISPR-Cas-based methods to investigate the coordinated regulation of DNA-protein, DNA-RNA, or RNA-protein interactions for understanding chromatin dynamics, transcription, and protein function are also available. Overall, the CRISPR-based methods offer a significant improvement in elucidating chromatin organization and dynamics, RNA visualization, and protein imaging. The current and future advancements in CRISPR-based imaging techniques can revolutionize genome biology research for various applications.
Collapse
Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
61
|
Pederson T. The epistemological wheel turns: AI's tipping point is here. FASEB J 2021; 35:e21632. [PMID: 34029420 DOI: 10.1096/fj.202100640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
62
|
de Voogt WS, Tanenbaum ME, Vader P. Illuminating RNA trafficking and functional delivery by extracellular vesicles. Adv Drug Deliv Rev 2021; 174:250-264. [PMID: 33894328 DOI: 10.1016/j.addr.2021.04.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/07/2021] [Accepted: 04/17/2021] [Indexed: 12/12/2022]
Abstract
RNA-based therapeutics are highly promising for the treatment of numerous diseases, by their ability to tackle the genetic origin in multiple possible ways. RNA molecules are, however, incapable of crossing cell membranes, hence a safe and efficient delivery vehicle is pivotal. Extracellular vesicles (EVs) are endogenously derived nano-sized particles and possess several characteristics which make them excellent candidates as therapeutic RNA delivery agent. This includes the inherent capability to functionally transfer RNAs in a selective manner and an enhanced safety profile compared to synthetic particles. Nonetheless, the fundamental mechanisms underlying this selective inter- and intracellular trafficking and functional transfer of RNAs by EVs are poorly understood. Improving our understanding of these systems is a key element of working towards an EV-based or EV-mimicking system for the functional delivery of therapeutic RNA. In this review, state-of-the-art approaches to detect and visualize RNA in situ and in live cells are discussed, as well as strategies to assess functional RNA transfer, highlighting their potential in studying EV-RNA trafficking mechanisms.
Collapse
Affiliation(s)
- Willemijn S de Voogt
- CDL Research, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center, Uppsalalaan 8, 3584 CT Utrecht, Utrecht, the Netherlands.
| | - Pieter Vader
- CDL Research, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Experimental Cardiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
| |
Collapse
|
63
|
Pan C, Wu X, Markel K, Malzahn AA, Kundagrami N, Sretenovic S, Zhang Y, Cheng Y, Shih PM, Qi Y. CRISPR-Act3.0 for highly efficient multiplexed gene activation in plants. NATURE PLANTS 2021; 7:942-953. [PMID: 34168320 DOI: 10.1038/s41477-021-00953-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 05/27/2021] [Indexed: 05/22/2023]
Abstract
RNA-guided CRISPR activation (CRISPRa) systems have been developed in plants. However, the simultaneous activation of multiple genes remains challenging. Here, we develop a highly robust CRISPRa system working in rice, Arabidopsis and tomato, CRISPR-Act3.0, through systematically exploring different effector recruitment strategies and various transcription activators based on deactivated Streptococcus pyogenes Cas9 (dSpCas9). The CRISPR-Act3.0 system results in fourfold to sixfold higher activation than the state-of-the-art CRISPRa systems. We further develop a tRNA-gR2.0 (single guide RNA 2.0) expression system enabling CRISPR-Act3.0-based robust activation of up to seven genes for metabolic engineering in rice. In addition, CRISPR-Act3.0 allows the simultaneous modification of multiple traits in Arabidopsis, which are stably transmitted to the T3 generations. On the basis of CRISPR-Act3.0, we elucidate guide RNA targeting rules for effective transcriptional activation. To target T-rich protospacer adjacent motifs (PAMs), we transfer this activation strategy to CRISPR-dCas12b and further improve the dAaCas12b-based CRISPRa system. Moreover, we develop a potent near-PAM-less CRISPR-Act3.0 system on the basis of the SpRY dCas9 variant, which outperforms the dCas9-NG system in both activation potency and targeting scope. Altogether, our study has substantially improved the CRISPRa technology in plants and provided plant researchers a powerful toolbox for efficient gene activation in foundational and translational research.
Collapse
Affiliation(s)
- Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Xincheng Wu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Neil Kundagrami
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| |
Collapse
|
64
|
Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Mol Syst Biol 2021; 17:e9653. [PMID: 34232558 PMCID: PMC8262488 DOI: 10.15252/msb.20209653] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.
Collapse
Affiliation(s)
- Liangqi Xie
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| | - Zhe Liu
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| |
Collapse
|
65
|
Rajpurkar AR, Mateo LJ, Murphy SE, Boettiger AN. Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. Nat Commun 2021; 12:3423. [PMID: 34103507 PMCID: PMC8187657 DOI: 10.1038/s41467-021-23831-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/19/2021] [Indexed: 11/27/2022] Open
Abstract
Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these complex data sets with a computationally unbiased method has been challenging. Here, we present a deep learning-based approach to better understand to what degree chromatin structure relates to transcriptional state of individual cells. Furthermore, we explore methods to "unpack the black box" to determine in an unbiased manner which structural features of chromatin regulation are most important for gene expression state. We apply this approach to an Optical Reconstruction of Chromatin Architecture dataset of the Bithorax gene cluster in Drosophila and show it outperforms previous contact-focused methods in predicting expression state from 3D structure. We find the structural information is distributed across the domain, overlapping and extending beyond domains identified by prior genetic analyses. Individual enhancer-promoter interactions are a minor contributor to predictions of activity.
Collapse
Affiliation(s)
- Aparna R Rajpurkar
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Leslie J Mateo
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Sedona E Murphy
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | | |
Collapse
|
66
|
Damiati LA, El-Messeiry S. An Overview of RNA-Based Scaffolds for Osteogenesis. Front Mol Biosci 2021; 8:682581. [PMID: 34169095 PMCID: PMC8217814 DOI: 10.3389/fmolb.2021.682581] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
Tissue engineering provides new hope for the combination of cells, scaffolds, and bifactors for bone osteogenesis. This is achieved by mimicking the bone's natural behavior in recruiting the cell's molecular machinery for our use. Many researchers have focused on developing an ideal scaffold with specific features, such as good cellular adhesion, cell proliferation, differentiation, host integration, and load bearing. Various types of coating materials (organic and non-organic) have been used to enhance bone osteogenesis. In the last few years, RNA-mediated gene therapy has captured attention as a new tool for bone regeneration. In this review, we discuss the use of RNA molecules in coating and delivery, including messenger RNA (mRNA), RNA interference (RNAi), and long non-coding RNA (lncRNA) on different types of scaffolds (such as polymers, ceramics, and metals) in osteogenesis research. In addition, the effect of using gene-editing tools-particularly CRISPR systems-to guide RNA scaffolds in bone regeneration is also discussed. Given existing knowledge about various RNAs coating/expression may help to understand the process of bone formation on the scaffolds during osseointegration.
Collapse
Affiliation(s)
- Laila A. Damiati
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Sarah El-Messeiry
- Department of Genetics, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| |
Collapse
|
67
|
Balderston S, Clouse G, Ripoll JJ, Pratt GK, Gasiunas G, Bock JO, Bennett EP, Aran K. Diversification of the CRISPR Toolbox: Applications of CRISPR-Cas Systems Beyond Genome Editing. CRISPR J 2021; 4:400-415. [PMID: 34152221 PMCID: PMC8418451 DOI: 10.1089/crispr.2020.0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The discovery of CRISPR has revolutionized the field of genome engineering, but the potential of this technology is far from reaching its limits. In this review, we explore the broad range of applications of CRISPR technology to highlight the rapid expansion of the field beyond gene editing alone. It has been demonstrated that CRISPR technology can control gene expression, spatiotemporally image the genome in vivo, and detect specific nucleic acid sequences for diagnostics. In addition, new technologies are under development to improve CRISPR quality controls for gene editing, thereby improving the reliability of these technologies for therapeutics and beyond. These are just some of the many CRISPR tools that have been developed in recent years, and the toolbox continues to diversify.
Collapse
Affiliation(s)
- Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabrielle Clouse
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juan-José Ripoll
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Grace K. Pratt
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giedrius Gasiunas
- Novo Nordisk A/S, Biopharm Research, Gene Therapy Department, Måløv, Denmark; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- CasZyme, Vilnius, Lithuania; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens-Ole Bock
- Cobo Technologies ApS, Maaloev, Denmark; and Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric Paul Bennett
- Novo Nordisk A/S, Biopharm Research, Gene Therapy Department, Måløv, Denmark; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
68
|
Wang Y, Cottle WT, Wang H, Feng XA, Mallon J, Gavrilov M, Bailey S, Ha T. Genome oligopaint via local denaturation fluorescence in situ hybridization. Mol Cell 2021; 81:1566-1577.e8. [PMID: 33657402 PMCID: PMC8026568 DOI: 10.1016/j.molcel.2021.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/22/2020] [Accepted: 02/04/2021] [Indexed: 12/26/2022]
Abstract
Cas9 in complex with a programmable guide RNA targets specific double-stranded DNA for cleavage. By harnessing Cas9 as a programmable loader of superhelicase to genomic DNA, we report a physiological-temperature DNA fluorescence in situ hybridization (FISH) method termed genome oligopaint via local denaturation (GOLD) FISH. Instead of global denaturation as in conventional DNA FISH, loading a superhelicase at a Cas9-generated nick allows for local DNA denaturation, reducing nonspecific binding of probes and avoiding harsh treatments such as heat denaturation. GOLD FISH relies on Cas9 cleaving target DNA sequences and avoids the high nuclear background associated with other genome labeling methods that rely on Cas9 binding. The excellent signal brightness and specificity enable us to image nonrepetitive genomic DNA loci and analyze the conformational differences between active and inactive X chromosomes. Finally, GOLD FISH could be used for rapid identification of HER2 gene amplification in patient tissue.
Collapse
Affiliation(s)
- Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinyu Ashlee Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John Mallon
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Momcilo Gavrilov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| |
Collapse
|
69
|
Iaffaldano B, Reiser J. Full-Spectrum Targeted Mutagenesis in Plant and Animal Cells. Int J Mol Sci 2021; 22:ijms22020857. [PMID: 33467049 PMCID: PMC7830027 DOI: 10.3390/ijms22020857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022] Open
Abstract
Directed evolution is a powerful approach for protein engineering and functional studies. However, directed evolution outputs from bacterial and yeast systems do not always translate to higher organisms. In situ directed evolution in plant and animal cells has previously been limited by an inability to introduce targeted DNA sequence diversity. New hypermutation tools have emerged that can generate targeted mutations in plant and animal cells, by recruiting mutagenic proteins to defined DNA loci. Progress in this field, such as the development of CRISPR-derived hypermutators, now allows for all DNA nucleotides within user-defined regions to be altered through the recruitment of error-prone DNA polymerases or highly active DNA deaminases. The further engineering of these mutagenesis systems will potentially allow for all transition and transversion substitutions to be generated within user-defined genomic windows. Such targeted full-spectrum mutagenesis tools would provide a powerful platform for evolving antibodies, enzymes, structural proteins and RNAs with specific desired properties in relevant cellular contexts. These tools are expected to benefit many aspects of biological research and, ultimately, clinical applications.
Collapse
|
70
|
Shechner DM. Targeting Noncoding RNA Domains to Genomic Loci with CRISPR-Display: Guidelines for Designing, Building, and Testing sgRNA-ncRNA Expression Constructs. Methods Mol Biol 2021; 2162:115-152. [PMID: 32926381 DOI: 10.1007/978-1-0716-0687-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
CRISPR-Display uses the S. pyogenes Cas9 protein to posttranscriptionally localize noncoding RNA (ncRNA) domains to any genomic site, by directly fusing these domains to the Cas9 sgRNA cofactor. This versatile technology enables numerous applications for interrogating natural chromatin-regulatory ncRNAs, or for utilizing artificial ncRNA and ribonucleoprotein (RNP) devices at individual chromatin loci. To achieve these, a successful CRISPR-Display experiment requires that chimeric sgRNA-ncRNA fusions are stably expressed and incorporated into Cas9 complexes, and that they retain their ncRNA "cargo" domains at the targeted genomic sites. Here, I describe a workflow for designing, building, and testing such chimeric sgRNA-ncRNA expression constructs. I detail strategies for choosing expression systems and sgRNA insertion topologies, for assaying the incorporation of sgRNA-ncRNA fusions into functional Cas9 complexes, and for surveying the activities of ncRNA domains at targeted genomic loci. This establishes an initial set of "best practices" for the design and implementation of CRISPR-Display experiments.
Collapse
Affiliation(s)
- David M Shechner
- Department of Pharmacology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
71
|
Bizhanova A, Kaufman PD. Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194666. [PMID: 33307247 PMCID: PMC7855492 DOI: 10.1016/j.bbagrm.2020.194666] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Chromatin is a dynamic structure composed of DNA, RNA, and proteins, regulating storage and expression of the genetic material in the nucleus. Heterochromatin plays a crucial role in driving the three-dimensional arrangement of the interphase genome, and in preserving genome stability by maintaining a subset of the genome in a silent state. Spatial genome organization contributes to normal patterns of gene function and expression, and is therefore of broad interest. Mammalian heterochromatin, the focus of this review, mainly localizes at the nuclear periphery, forming Lamina-associated domains (LADs), and at the nucleolar periphery, forming Nucleolus-associated domains (NADs). Together, these regions comprise approximately one-half of mammalian genomes, and most but not all loci within these domains are stochastically placed at either of these two locations after exit from mitosis at each cell cycle. Excitement about the role of these heterochromatic domains in early development has recently been heightened by the discovery that LADs appear at some loci in the preimplantation mouse embryo prior to other chromosomal features like compartmental identity and topologically-associated domains (TADs). While LADs have been extensively studied and mapped during cellular differentiation and early embryonic development, NADs have been less thoroughly studied. Here, we summarize pioneering studies of NADs and LADs, more recent advances in our understanding of cis/trans-acting factors that mediate these localizations, and discuss the functional significance of these associations.
Collapse
Affiliation(s)
- Aizhan Bizhanova
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
72
|
Feng Y, Wang Y, Wang X, He X, Yang C, Naseri A, Pederson T, Zheng J, Zhang S, Xiao X, Xie W, Ma H. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Genome Biol 2020; 21:296. [PMID: 33292531 PMCID: PMC7722448 DOI: 10.1186/s13059-020-02201-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cells remains unclear. RESULT Here, we develop EpiGo (Epigenetic perturbation induced Genome organization)-KRAB to introduce H3K9me3 at hundreds of loci spanning megabases on human chromosome 19 and simultaneously track genome organization. EpiGo-KRAB is sufficient to induce genomic clustering and de novo heterochromatin-like domain formation, which requires SETDB1, a methyltransferase of H3K9me3. Unexpectedly, EpiGo-KRAB-induced heterochromatin-like domain does not result in widespread gene repression except a small set of genes with concurrent loss of H3K4me3 and H3K27ac. Ectopic H3K9me3 appears to spread in inactive regions but is largely restricted from transcriptional initiation sites in active regions. Finally, Hi-C analysis showed that EpiGo-KRAB reshapes existing compartments mainly at compartment boundaries. CONCLUSIONS These results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression.
Collapse
Affiliation(s)
- Ying Feng
- School of Biotechnology, East China University of Science and Technology, Shanghai, China; School of Life Science and Technology, ShanghaiTech University,, Shanghai, China
| | - Yao Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiangnan Wang
- School of Life Science and Technology, ShanghaiTech University,, Beijing, China
| | - Xiaohui He
- School of Life Science and Technology, ShanghaiTech University,, Beijing, China
| | - Chen Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jing Zheng
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiao Xiao
- School of Biotechnology, East China University of Science and Technology,, Shanghai, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University,, Beijing, China.
| |
Collapse
|
73
|
Lu S, Wang D, Hou Y, Guo D, Deng Y, Zhang XE. Illuminating single genomic loci in live cells by reducing nuclear background fluorescence. SCIENCE CHINA-LIFE SCIENCES 2020; 64:667-677. [PMID: 33131028 DOI: 10.1007/s11427-020-1794-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/10/2020] [Indexed: 11/28/2022]
Abstract
The tagging of genomic loci in living cells provides visual evidence for the study of genomic spatial organization and gene interaction. CRISPR/dCas9 (clustered regularly interspaced short palindromic repeats/deactivated Cas9) labeling system labels genes through binding of the dCas9/sgRNA/fluorescent protein complex to repeat sequences in the target genomic loci. However, the existence of numerous fluorescent proteins in the nucleus usually causes a high background fluorescent readout. This study aims to limit the number of fluorescent modules entering the nucleus by redesigning the current CRISPR/dCas9-SunTag labeling system consisting of dCas9-SunTag-NLS (target module) and scFv-sfGFP-NLS (signal module). We removed the nuclear location sequence (NLS) of the signal module and inserted two copies of EGFP into the signal module. The ratio of the fluorescent intensity of the nucleus to that of the cytoplasm (N/C ratio) was decreased by 71%, and the ratio of the signal to the background (S/B ratio) was increased by 1.6 times. The system can stably label randomly selected genomic loci with as few as 9 repeat sequences.
Collapse
Affiliation(s)
- Song Lu
- School of Life Sciences, Beijing Institute of Technology, Beijing, 100081, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dianbing Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongge Guo
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yulin Deng
- School of Life Sciences, Beijing Institute of Technology, Beijing, 100081, China.
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
74
|
Affiliation(s)
- Baohui Chen
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
| | - Yuyu Niu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500 China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006 China
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| |
Collapse
|
75
|
Hu M, Cherkaoui I, Misra S, Rutter GA. Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research. Front Endocrinol (Lausanne) 2020; 11:576632. [PMID: 33162936 PMCID: PMC7580382 DOI: 10.3389/fendo.2020.576632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
The inheritance of variants that lead to coding changes in, or the mis-expression of, genes critical to pancreatic beta cell function can lead to alterations in insulin secretion and increase the risk of both type 1 and type 2 diabetes. Recently developed clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene editing tools provide a powerful means of understanding the impact of identified variants on cell function, growth, and survival and might ultimately provide a means, most likely after the transplantation of genetically "corrected" cells, of treating the disease. Here, we review some of the disease-associated genes and variants whose roles have been probed up to now. Next, we survey recent exciting developments in CRISPR/Cas9 technology and their possible exploitation for β cell functional genomics. Finally, we will provide a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes.
Collapse
Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cherkaoui
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shivani Misra
- Metabolic Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
76
|
Tasan I, Su CJ, Enghiad B, Zhang M, Mishra S, Zhao H. Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. ACS Synth Biol 2020; 9:2502-2514. [PMID: 32822529 DOI: 10.1021/acssynbio.0c00295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tools for live cell imaging of multiple nonrepetitive genomic loci in mammalian cells are necessary to study chromatin dynamics. Here, we report a new system based on two chromosomally integrated orthogonal irregular repeat arrays and particularly a new general strategy to construct irregular repeat arrays. Briefly, we utilized a "bridge oligonucleotide-mediated ligation" protocol to assemble 8-mer repeats de novo which were then combined into a final 96-mer repeat array using Golden Gate cloning. This strategy was used for assembling a new mutant TetO irregular repeat array, which worked orthogonally to the wild type TetO repeat. Single copy integration of the new repeat array did not cause replication deficiencies at the tagged locus. Moreover, the mutant TetO irregular repeat could also be visualized by CRISPR imaging. Our new irregular repeat assembly method demonstrates a generally applicable strategy that can be used for assembling additional orthogonal repeat arrays for imaging genomic loci and irregular repeats to visualize RNA or proteins via signal amplification.
Collapse
Affiliation(s)
- Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Christina Jean Su
- Department of Molecular and Cellular Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Behnam Enghiad
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Meng Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shekhar Mishra
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
77
|
Chaudhary N, Nho SH, Cho H, Gantumur N, Ra JS, Myung K, Kim H. Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore. Genome Res 2020; 30:1306-1316. [PMID: 32887690 PMCID: PMC7545142 DOI: 10.1101/gr.260018.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/23/2020] [Indexed: 12/30/2022]
Abstract
The higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure–function relationship, it is necessary to directly visualize genomic elements in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited applicability due to background signals and nonspecific aggregation of fluorophores within nuclei. To address this issue, we developed a novel visualization scheme combining tripartite fluorescent proteins with the SunTag system and demonstrated that it strongly suppressed background fluorescence and amplified locus-specific signals, allowing long-term tracking of genomic loci. We integrated the multicomponent CRISPR system into stable cell lines to allow quantitative and reliable analysis of dynamic behaviors of genomic loci. Due to the greatly elevated signal-to-background ratio, target loci with only small numbers of sequence repeats could be successfully tracked, even under a conventional fluorescence microscope. This feature enables the application of CRISPR-based imaging to loci throughout the genome and opens up new possibilities for the study of nuclear processes in living cells.
Collapse
Affiliation(s)
- Narendra Chaudhary
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Si-Hyeong Nho
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Narangerel Gantumur
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| |
Collapse
|
78
|
Uno N, Kaku N, Morinaga Y, Hasegawa H, Yanagihara K. Flow cytometry assay for the detection of single-copy DNA in human lymphocytes. Nucleic Acids Res 2020; 48:e86. [PMID: 32544240 PMCID: PMC7470942 DOI: 10.1093/nar/gkaa515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/09/2020] [Accepted: 06/05/2020] [Indexed: 11/23/2022] Open
Abstract
Specific nucleic acid sequences can be detected in individual cells by in situ hybridization. However, when very few copies of a target sequence are present per cell, its signal is undetectable by flow cytometry. Although various approaches have been developed to increase fluorescence signals for in situ hybridization, flow cytometric detection of specific genomic DNA sequences has not been established. Here, we present a flow cytometry assay for detection of single-copy genomic sequences in human lymphocytes using in situ PCR with universal energy transfer-labelled primers.
Collapse
Affiliation(s)
- Naoki Uno
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| |
Collapse
|
79
|
Sun NH, Chen DY, Ye LP, Sheng G, Gong JJ, Chen BH, Lu YM, Han F. CRISPR-Sunspot: Imaging of endogenous low-abundance RNA at the single-molecule level in live cells. Theranostics 2020; 10:10993-11012. [PMID: 33042266 PMCID: PMC7532675 DOI: 10.7150/thno.43094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based mRNA imaging has been developed to labeling of high-abundance mRNAs. A lack of non-genetically encoded mRNA-tagged imaging tools has limited our ability to explore the functional distributions of endogenous low-abundance mRNAs in cells. Here, we developed a CRISPR-Sunspot method based on the SunTag signal amplification system that allows efficient imaging of low-abundance mRNAs with CRISPR/Cas9. Methods: We created a stable TRE3G-dCas9-EGFP cell line and generated an Inducible dCas9-EGFP imaging system for assessment of two factors, sgRNA and dCas9, which influence imaging quality. Based on SunTag system, we established a CRISPR-Sunspot imaging system for amplifying signals from single-molecule mRNA in live cells. CRISPR-Sunspot was used to track co-localization of Camk2a mRNA with regulatory protein Xlr3b in neurons. CRISPR-Sunspot combined with CRISPRa was used to determine elevated mRNA molecules. Results: Our results showed that manipulating the expression of fluorescent proteins and sgRNA increased the efficiency of RNA imaging in cells. CRISPR-Sunspot could target endogenous mRNAs in the cytoplasm and amplified signals from single-molecule mRNA. Furthermore, CRISPR-Sunspot was also applied to visualize mRNA distributions with its regulating proteins in neurons. CRISPR-Sunspot detected the co-localization of Camk2a mRNA with overexpressed Xlr3b proteins in the neuronal dendrites. Moreover, we also manipulated CRISPR-Sunspot to detect transcriptional activation of target gene such as HBG1 in live cells. Conclusion: Our findings suggest that CRISPR-Sunspot is a novel applicable imaging tool for visualizing the distributions of low-abundance mRNAs in cells. This study provides a novel strategy to unravel the molecular mechanisms of diseases caused by aberrant mRNA molecules.
Collapse
Affiliation(s)
- Ning-He Sun
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan-Yang Chen
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lu-Peng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Gang Sheng
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Jun-Jie Gong
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Bao-Hui Chen
- Department of Cell Biology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Feng Han
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Center for Global Health of Nanjing Medical University, Nanjing, 211166, China
| |
Collapse
|
80
|
Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing. Trends Biotechnol 2020; 39:262-273. [PMID: 32828556 DOI: 10.1016/j.tibtech.2020.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
CRISPR technology is a universal tool for genome engineering that has revolutionized biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered Cas proteins, have rapidly expanded the functions and applications of CRISPR/Cas systems. The structures of Cas proteins are complex, containing multiple functional domains. These protein domains are evolutionarily conserved polypeptide units that generally show independent structural or functional properties. In this review, we propose using protein domains as a new way to classify protein engineering strategies for these proteins and discuss common ways to engineer key domains to modify the functions of CRISPR/Cas systems.
Collapse
|
81
|
Sun W, Wang H. Recent advances of genome editing and related technologies in China. Gene Ther 2020; 27:312-320. [DOI: 10.1038/s41434-020-0181-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/24/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022]
|
82
|
Lau CH, Tin C. The Synergy between CRISPR and Chemical Engineering. Curr Gene Ther 2020; 19:147-171. [PMID: 31267870 DOI: 10.2174/1566523219666190701100556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 02/06/2023]
Abstract
Gene therapy and transgenic research have advanced quickly in recent years due to the development of CRISPR technology. The rapid development of CRISPR technology has been largely benefited by chemical engineering. Firstly, chemical or synthetic substance enables spatiotemporal and conditional control of Cas9 or dCas9 activities. It prevents the leaky expression of CRISPR components, as well as minimizes toxicity and off-target effects. Multi-input logic operations and complex genetic circuits can also be implemented via multiplexed and orthogonal regulation of target genes. Secondly, rational chemical modifications to the sgRNA enhance gene editing efficiency and specificity by improving sgRNA stability and binding affinity to on-target genomic loci, and hence reducing off-target mismatches and systemic immunogenicity. Chemically-modified Cas9 mRNA is also more active and less immunogenic than the native mRNA. Thirdly, nonviral vehicles can circumvent the challenges associated with viral packaging and production through the delivery of Cas9-sgRNA ribonucleoprotein complex or large Cas9 expression plasmids. Multi-functional nanovectors enhance genome editing in vivo by overcoming multiple physiological barriers, enabling ligand-targeted cellular uptake, and blood-brain barrier crossing. Chemical engineering can also facilitate viral-based delivery by improving vector internalization, allowing tissue-specific transgene expression, and preventing inactivation of the viral vectors in vivo. This review aims to discuss how chemical engineering has helped improve existing CRISPR applications and enable new technologies for biomedical research. The usefulness, advantages, and molecular action for each chemical engineering approach are also highlighted.
Collapse
Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong
| |
Collapse
|
83
|
Kunii A, Yamamoto T, Sakuma T. Various strategies of effector accumulation to improve the efficiency of genome editing and derivative methodologies. In Vitro Cell Dev Biol Anim 2020; 56:359-366. [PMID: 32514717 DOI: 10.1007/s11626-020-00469-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022]
Abstract
CRISPR-Cas9 is a sophisticated tool in which Cas9/sgRNA complexes bind to the programmed target sequences and induce DNA double-strand breaks (DSBs) enabling highly efficient genome editing. Moreover, when nuclease-inactive Cas9 (dCas9) is employed, its specific DNA-binding activity provides a variety of derivative technologies such as transcriptional activation/repression, epigenome editing, and chromosome visualization. In these derivative technologies, particular effector molecules are fused with dCas9 or recruited to the target site. However, there had been room for improvement, because both genome editing and derivative technologies require not only the DNA-binding tools but also the additional components for their efficient and flexible outcomes. For genome editing, DSB repair molecules and knock-in donor templates need to act at the DSB sites. Derivative technologies also require their various effector domains to be gathered onto the target sites. Recently, many groups have developed and utilized inventive platforms to accumulate these additional components to the target sequence by modifying Cas9 protein and/or sgRNA. Here, we summarize the strategies of CRISPR-based effector accumulation and the improved methodologies using these creative platforms.
Collapse
Affiliation(s)
- Atsushi Kunii
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| |
Collapse
|
84
|
Li G. The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome. SCIENCE CHINA-LIFE SCIENCES 2020; 63:791-794. [PMID: 32394246 DOI: 10.1007/s11427-020-1723-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Guohong Li
- National laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.
| |
Collapse
|
85
|
Abstract
Until recently, our understanding of chromosome organization in higher eukaryotic cells has been based on analyses of large-scale, low-resolution changes in chromosomes structure. More recently, CRISPR-Cas9 technologies have allowed us to "zoom in" and visualize specific chromosome regions in live cells so that we can begin to examine in detail the dynamics of chromosome organization in individual cells. In this review, we discuss traditional methods of chromosome locus visualization and look at how CRISPR-Cas9 gene-targeting methodologies have helped improve their application. We also describe recent developments of the CRISPR-Cas9 technology that enable visualization of specific chromosome regions without the requirement for complex genetic manipulation.
Collapse
Affiliation(s)
- John K Eykelenboom
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
| |
Collapse
|
86
|
Advances in technologies for 3D genomics research. SCIENCE CHINA-LIFE SCIENCES 2020; 63:811-824. [PMID: 32394244 DOI: 10.1007/s11427-019-1704-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023]
Abstract
The spatial structure of the orderly organized chromatin in the nucleus has important roles in maintaining normal cell function and in regulation of gene expression, and the high-throughput Hi-C and ChIA-PET methods have been widely used in various biological studies for determining potential spatial genome structures and their functions. However, there are still great difficulties and challenges in three-dimensional (3D) genomics research. More efficient, economical, and unbiased approaches to studying 3D genomics need to be developed for more widespread and easier applications. Here, we review the most recent studies on new 3D genomics research technologies, such as improvements of the traditional Hi-C and ChIA-PET methods, new approaches based on non-proximal-ligation strategies, and imaging-based methods improved in recent years. Especially, we review the CRISPR-based methods for functional validations in 3D genomics, which could be the forthcoming directions. We hope this review can show some insights into the potential improvements for future 3D genomics.
Collapse
|
87
|
Shaban HA, Seeber A. Monitoring the spatio-temporal organization and dynamics of the genome. Nucleic Acids Res 2020; 48:3423-3434. [PMID: 32123910 PMCID: PMC7144944 DOI: 10.1093/nar/gkaa135] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/17/2020] [Accepted: 02/23/2020] [Indexed: 12/22/2022] Open
Abstract
The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixed snapshots as a result of techniques like FISH and Hi-C, little is known about chromatin dynamics in living cells. The rapid development of flexible genomic loci imaging approaches can address fundamental questions on chromatin dynamics in a range of model organisms. Moreover, it is now possible to visualize not only single genomic loci but the whole genome simultaneously. These advances have opened many doors leading to insight into several nuclear processes including transcription and DNA repair. In this review, we discuss new chromatin imaging methods and how they have been applied to study transcription.
Collapse
Affiliation(s)
- Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
88
|
Sato H, Das S, Singer RH, Vera M. Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Annu Rev Biochem 2020; 89:159-187. [PMID: 32176523 DOI: 10.1146/annurev-biochem-011520-104955] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.
Collapse
Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada;
| |
Collapse
|
89
|
Li Y, Tao T, Du L, Zhu X. Three-dimensional genome: developmental technologies and applications in precision medicine. J Hum Genet 2020; 65:497-511. [PMID: 32152365 DOI: 10.1038/s10038-020-0737-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 12/17/2022]
Abstract
In the 20th century, our familiar structure of DNA was the double helix. Due to technical limitations, we do not have a good way to understand the finer structure of the genome, let alone its transcriptional regulation. Until the advent of 3C technologies, we were no longer blind to this one. Three-dimensional (3D) genomics is a new subject, which mainly studies the 3D structure and transcriptional regulation of eukaryotic genomes. Now, this field mainly has Hi-C series and CHIA-PET series technologies. Through 3D genomics, we can understand the basic structure of DNA, understand the growth and development of organisms and the occurrence of diseases, so as to promote human medical and health undertakings. The review introduces the main research techniques of 3D genomics and their characteristics, the latest development of 3D genome structure, the relationship between diseases and 3D genome structure, the applications of 3D genome in precision medicine, and the development of the 4D nucleome project.
Collapse
Affiliation(s)
- Yingqi Li
- Marine Medical Research Institute of Guangdong Zhanjiang (GDZJMMRI), Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, 255000, China
| | - Likun Du
- First Affiliated Hospital, Heilongjiang University of Traditional Chinese Medicine, Harbin, 150040, China.
| | - Xiao Zhu
- Marine Medical Research Institute of Guangdong Zhanjiang (GDZJMMRI), Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.
| |
Collapse
|
90
|
Rubio K, Castillo-Negrete R, Barreto G. Non-coding RNAs and nuclear architecture during epithelial-mesenchymal transition in lung cancer and idiopathic pulmonary fibrosis. Cell Signal 2020; 70:109593. [PMID: 32135188 DOI: 10.1016/j.cellsig.2020.109593] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/13/2022]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. On the other hand, idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease showing a prevalence of 20 new cases per 100,000 persons per year. Despite differences in cellular origin and pathological phenotypes, LC and IPF are lung diseases that share common features, including hyperproliferation of specific cell types in the lung, involvement of epithelial-mesenchymal transition (EMT) and enhanced activity of signaling pathways, such as tissue growth factor (TGFB), epidermal growth factor (EGF), fibroblast growth factor (FGF), wingless secreted glycoprotein (WNT) signaling, among others. EMT is a process during which epithelial cells lose their cell polarity and cell-cell adhesion, and acquire migratory and invasive properties to become mesenchymal cells. EMT involves numerous morphological hallmarks of hyperproliferative diseases, like cell plasticity, resistance to apoptosis, dedifferentiation and proliferation, thereby playing a central role during organ fibrosis and cancer progression. EMT was considered as an "all-or-none" process. In contrast to these outdated dichotomist interpretations, recent reports suggest that EMT occurs gradually involving different epithelial cell intermediate states with mesenchyme-like characteristics. These cell intermediate states of EMT differ from each other in their cell plasticity, invasiveness and metastatic potential, which in turn are induced by signals from their microenvironment. EMT is regulated by several transcription factors (TFs), which are members of prominent families of master regulators of transcription. In addition, there is increasing evidence for the important contribution of noncoding RNAs (ncRNAs) to EMT. In our review we highlight articles dissecting the function of different ncRNAs subtypes and nuclear architecture in cell intermediate states of EMT, as well as their involvement in LC and IPF.
Collapse
Affiliation(s)
- Karla Rubio
- Brain and Lung Epigenetics (BLUE), Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris-Est Créteil (UPEC), 94010 Créteil, France; Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstraße 1, 61231 Bad Nauheim, Germany
| | - Rafael Castillo-Negrete
- Brain and Lung Epigenetics (BLUE), Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris-Est Créteil (UPEC), 94010 Créteil, France; Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstraße 1, 61231 Bad Nauheim, Germany
| | - Guillermo Barreto
- Brain and Lung Epigenetics (BLUE), Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris-Est Créteil (UPEC), 94010 Créteil, France; Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstraße 1, 61231 Bad Nauheim, Germany; Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russian Federation; Universities of Giessen and Marburg Lung Center (UGMLC), The German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Germany.
| |
Collapse
|
91
|
McCord RP, Kaplan N, Giorgetti L. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function. Mol Cell 2020; 77:688-708. [PMID: 32001106 PMCID: PMC7134573 DOI: 10.1016/j.molcel.2019.12.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapidly developing technologies have recently fueled an exciting era of discovery in the field of chromosome structure and nuclear organization. In addition to chromosome conformation capture (3C) methods, new alternative techniques have emerged to study genome architecture and biological processes in the nucleus, often in single or living cells. This sets an unprecedented stage for exploring the mechanisms that link chromosome structure and biological function. Here we review popular as well as emerging approaches to study chromosome organization, focusing on the contribution of complementary methodologies to our understanding of structures revealed by 3C methods and their biological implications, and discuss the next technical and conceptual frontiers.
Collapse
Affiliation(s)
- Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Noam Kaplan
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
92
|
Wu X, Ying Y, Mao S, Krueger CJ, Chen AK. Live-Cell Imaging of Genomic Loci Using CRISPR/Molecular Beacon Hybrid Systems. Methods Mol Biol 2020; 2166:357-372. [PMID: 32710420 DOI: 10.1007/978-1-0716-0712-1_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The ability to monitor the behavior of specific genomic loci in living cells can offer tremendous opportunities for deciphering the molecular basis driving cellular physiology and disease evolution. Toward this goal, clustered regularly interspersed short palindromic repeat (CRISPR)-based imaging systems have been developed, with tagging of either the nuclease-deactivated mutant of the CRISPR-associated protein 9 (dCas9) or the CRISPR single-guide RNA (sgRNA) with fluorescent protein (FP) molecules currently the major strategies for labeling. Recently, we have demonstrated the feasibility of tagging the sgRNA with molecular beacons, a class of small molecule dye-based, fluorogenic oligonucleotide probes, and demonstrated that the resulting system, termed CRISPR/MB, could be more sensitive and quantitative than conventional approaches employing FP reporters in detecting single telomere loci. In this chapter, we describe detailed protocols for the synthesis of CRISPR/MB, as well as its applications for imaging single telomere and centromere loci in live mammalian cells.
Collapse
Affiliation(s)
- Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.
| |
Collapse
|
93
|
Higashikuni Y, Lu TK. Advancing CRISPR-Based Programmable Platforms beyond Genome Editing in Mammalian Cells. ACS Synth Biol 2019; 8:2607-2619. [PMID: 31751114 DOI: 10.1021/acssynbio.9b00297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human diseases are caused by dysregulation of cellular biological programs that are encoded in DNA. Unveiling the endogenous programs and encoding new programs into the genome are key to creating novel diagnostic and therapeutic strategies. CRISPR/Cas9, originally identified in bacteria, has revolutionized genome editing in mammalian cells. Recent advances in CRISPR technologies have provided new programmable platforms for modifying cell function and behavior. CRISPR-based transcriptional regulators and modified gRNAs have enabled multiplexed regulation and visualization of genome dynamics with spatiotemporal precision. Using these toolkits, genome-scale screening platforms can identify key genetic elements or combinations thereof that modulate phenotypes in mammalian cells. In addition, imaging platforms for multiplexed genomic labeling have been created to study the conformation and dynamics of chromatin in living cells, which are essential for genome function. Furthermore, CRISPR-based computation and memory platforms have been built in living mammalian cells by using DNA as a data processing and storage medium to regulate and monitor cellular behaviors. The conditional regulation of CRISPR-based parts has enabled the design of complex multilayered biological programs. CRISPR-based memory platforms can continuously record biological events as mutations in defined DNA loci. By making use of base editors, CRISPR-based computation and memory platforms have been interconnected to perform logic operations based on past events. These technologies open up new avenues for understanding biological phenomena and designing mammalian cells as living machines for biomedical applications.
Collapse
|
94
|
Yang G, Huang X. Methods and applications of CRISPR/Cas system for genome editing in stem cells. CELL REGENERATION (LONDON, ENGLAND) 2019; 8:33-41. [PMID: 31666940 PMCID: PMC6806369 DOI: 10.1016/j.cr.2019.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 12/26/2022]
Abstract
Genome editing technology holds great promise for genome manipulation and gene therapy. While widespread utilization, genome editing has been used to unravel the roles of specific genes in differentiation and pluripotency of stem cells, and reinforce the stem cell-based applications. In this review, we summarize the advances of genome editing technology, as well as the derivative technologies from CRISPR/Cas system, which show tremendous potential in various fields. We also highlight the key findings in the studies of stem cells and regeneration by genome editing technology.
Collapse
Affiliation(s)
- Guang Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
95
|
Zhang S, Feng S, Jiang W, Huang X, Chen J. Construction and optimization of a base editor based on the MS2 system. Animal Model Exp Med 2019; 2:185-190. [PMID: 31773094 PMCID: PMC6762045 DOI: 10.1002/ame2.12080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 07/31/2019] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Catalytic defect Cas9-cytosine deaminase fusion is widely used in base editing. The Multiple copy numbers of the MS2 binding site (MBS) can recruit multiple MS2 coat proteins (MCPs), which are usually applied to amplify signals. Our study aimed to apply the MS2 signal amplification system to the base editing system in order to achieve simultaneous mutations of multiple bases at the target genome site. METHODS Multiple copy numbers of the MS2 were ligated to the 3'-end of sgRNA, and MCP was fused to the 5'-end of cytosine deaminases. The MS2 was recognized by MCP to recruit cytosine deaminase for base substitutions (C-T) at the target site. Different Cas9 variants, different cytosine deaminases and different copy numbers of MS2 were tested in this system, and the different versions of base editors were compared by editing efficiency and window. RESULTS In this study, dCas9, nCas9 (D10A) and nCas9 (H840A) were used. Among these 3 Cas9 variants, dCas9 exhibited higher base mutation efficiency. Two cytosine deaminases were then applied and the efficiency of rAPOBEC1 deaminase was found to be higher than AID. We also increased the copy numbers of MS2 linked to sgRNA from 2 to 12. Disappointingly, the sgRNA-12x MS2 did not improve the editing efficiency or increase the editing window. CONCLUSION An optimal version of base editor based on the MS2 system, MS2-BE-rAPOBEC1 (sgRNA-2x MS2, MCP-rAPOBEC1 and dCas9), was obtained. This tool can simultaneously mutate multiple bases at the target site, providing a new approach for the study of genome functions.
Collapse
Affiliation(s)
- Shuzhen Zhang
- Department of Hematology, Southwest HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Songjie Feng
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wen Jiang
- Department of Hematology, Southwest HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Xingxu Huang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Jieping Chen
- Department of Hematology, Southwest HospitalThird Military Medical University (Army Medical University)ChongqingChina
| |
Collapse
|
96
|
Guo DG, Wang DB, Liu C, Lu S, Hou Y, Zhang XE. CRISPR-based genomic loci labeling revealed ordered spatial organization of chromatin in living diploid human cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118518. [PMID: 31376419 DOI: 10.1016/j.bbamcr.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/05/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
The eukaryotic genome is compacted in the form of chromatin within the nucleus. Whether the spatial distribution of the genome is ordered or not has been a longstanding question. Answering this question would enable us to understand nuclear organization and cellular processes more deeply. Here, we applied a modified CRISPR/dCas9 system to label the randomly selected genomic loci in diploid living cells, which were visualized by high-resolution wide-field imaging. To analyze the spatial positions of three pairs of genomic loci, three sets of parameters were progressively measured: i) the linear distance between alleles; ii) the radial distribution of the genomic loci; and iii) the linear distances between three pairs of genomic loci on nonhomologous chromosomes. By accurate labeling, geometric measuring and statistical analysis, we demonstrated that the distribution of these genomic loci in the 3D space of the nucleus is relatively stable in both late G1 and early S phases. Collectively, our data provided visual evidence in live cells, which implies the orderly spatial organization of chromatin in the nucleus. The combination of orderliness and flexibility ensures the methodical and efficient operation of complex life systems. How the nucleus adopts this ordered 3D structure in living cells is thought-provoking.
Collapse
Affiliation(s)
- Dong-Ge Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 4300071, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dian-Bing Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chong Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Lu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 4300071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
97
|
Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
Collapse
Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| |
Collapse
|
98
|
Single-cell approaches to understand genome organisation throughout the cell cycle. Essays Biochem 2019; 63:209-216. [PMID: 31092688 DOI: 10.1042/ebc20180043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 01/05/2023]
Abstract
Mammalian genomes are ordered at several scales, ranging from nucleosomes (beads on a string), to topologically associated domains (TADs), laminar associated domains (LADs), and chromosome territories. These are described briefly below and we refer the reader to some recent comprehensive reviews on genome architecture summarising the current state of knowledge of the organisational principles of the nucleus [1,2]. Biological observations from populations of millions of individual cells can reveal consensus behaviour. New methods to study and interpret biological data at the single-cell level have recently been instrumental in revealing new understanding of cell-to-cell variation and novel biology. Here we will summarise the recent advances in single-cell technology that have provided insights into the behaviour of the mammalian genome during a cell cycle. We will focus on the interphase domain structure of chromosomes, including TADs and LADs, and how chromosome architecture changes during the cell cycle. The role of genome architecture relating to gene expression has been reviewed elsewhere [3].
Collapse
|
99
|
Kim T, Lu TK. CRISPR/Cas-based devices for mammalian synthetic biology. Curr Opin Chem Biol 2019; 52:23-30. [PMID: 31136835 DOI: 10.1016/j.cbpa.2019.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 12/26/2022]
Abstract
Since its first demonstration for mammalian gene editing, CRISPR/Cas technology has been widely adopted in research, industry, and medicine. Beyond indel mutations induced by Cas9 activity, recent advances in CRISPR/Cas have enabled DNA or RNA base editing. In addition, multiple orthogonal methods for the spatiotemporal regulation of CRISPR/Cas activity and repurposed Cas proteins for the visualization and relocation of specific genomic loci in living cells have been described. By harnessing the versatility of CRISPR/Cas-based devices and gene circuits, synthetic biologists are developing memory devices for lineage tracing and technologies for unbiased, high-throughput interrogation of combinatorial gene perturbations. We envision that such approaches will enable researchers to gain deeper insights into the translation of genotypes to phenotypes in healthy and diseased states.
Collapse
Affiliation(s)
- Tackhoon Kim
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| |
Collapse
|
100
|
Ma H, Tu LC, Chung YC, Naseri A, Grunwald D, Zhang S, Pederson T. Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. J Cell Biol 2019; 218:1467-1477. [PMID: 30846483 PMCID: PMC6504907 DOI: 10.1083/jcb.201807162] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 02/08/2023] Open
Abstract
In contrast to the well-studied condensation and folding of chromosomes during mitosis, their dynamics during interphase are less understood. We deployed a CRISPR-based DNA imaging system to track the dynamics of genomic loci situated kilobases to megabases apart on a single chromosome. Two distinct modes of dynamics were resolved: local movements as well as ones that might reflect translational movements of the entire domain within the nucleoplasmic space. The magnitude of both of these modes of movements increased from early to late G1, whereas the translational movements were reduced in early S phase. The local fluctuations decreased slightly in early S and more markedly in mid-late S. These newly observed movements and their cell cycle dependence suggest the existence of a hitherto unrecognized compaction-relaxation dynamic of the interphase chromosome fiber, operating concurrently with changes in the extent of overall movements of loci in the 4D genome.
Collapse
Affiliation(s)
- Hanhui Ma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Li-Chun Tu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA
| | - Yu-Chieh Chung
- Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Japan
| | - Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| |
Collapse
|