151
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Wen Y, Liao G, Pritchard T, Zhao TT, Connelly JP, Pruett-Miller SM, Blanc V, Davidson NO, Madison BB. A stable but reversible integrated surrogate reporter for assaying CRISPR/Cas9-stimulated homology-directed repair. J Biol Chem 2017; 292:6148-6162. [PMID: 28228480 DOI: 10.1074/jbc.m117.777722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The discovery and application of CRISPR/Cas9 technology for genome editing has greatly accelerated targeted mutagenesis in a variety of organisms. CRISPR/Cas9-mediated site-specific cleavage is typically exploited for the generation of insertions or deletions (indels) after aberrant dsDNA repair via the endogenous non-homology end-joining (NHEJ) pathway or, alternatively, for enhancing homology-directed repair to facilitate the generation of a specific mutation (or "knock-in"). However, there is a need for efficient cellular assays that can measure Cas9/guide RNA activity. Reliable methods for enriching and identifying desired mutants are also lacking. Here we describe a method using the Piggybac transposon for stable genomic integration of an H2B-GFP reporter or a hygromycin resistance gene for assaying Cas9 target cleavage and homology-directed repair. The H2B-GFP fusion protein provides increased stability and an obvious pattern of nuclear localization. This method, called SRIRACCHA (i.e. a stable, but reversible, integrated reporter for assaying CRISPR/Cas-stimulated HDR activity), enables the enrichment of mutants via selection of GFP-positive or hygromycin-resistant mammalian cells (immortalized or non-immortalized) as a surrogate for the modification of the endogenous target site. Currently available hyperactive Piggybac transposase mutants allow both delivery and removal of the surrogate reporters, with minimal risk of generating undesirable mutations. This assay permits rapid screening for efficient guide RNAs and the accelerated identification of mutant clones and is applicable to many cell types. We foresee the utility of this approach in contexts in which the maintenance of genomic integrity is essential, for example, when engineering cells for therapeutic purposes.
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Affiliation(s)
- Yahong Wen
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Grace Liao
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Thomas Pritchard
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Ting-Ting Zhao
- First Hospital of China Medical University, Department of Breast Surgery, Shenyang, China 110001
| | - Jon P Connelly
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University, Saint Louis, Missouri 63110, and
| | - Shondra M Pruett-Miller
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University, Saint Louis, Missouri 63110, and
| | - Valerie Blanc
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Nicholas O Davidson
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Blair B Madison
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110,
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152
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Recent advances in the identification of the host factors involved in dengue virus replication. Virol Sin 2017; 32:23-31. [PMID: 28124222 PMCID: PMC6598876 DOI: 10.1007/s12250-016-3902-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/04/2017] [Indexed: 12/28/2022] Open
Abstract
Dengue virus (DENV) belongs to the genus Flavivirus of the family Flaviviridae and it is primarily transmitted via Aedes aegypti and Aedes albopictus mosquitoes. The life cycle of DENV includes attachment, endocytosis, protein translation, RNA synthesis, assembly, egress, and maturation. Recent researches have indicated that a variety of host factors, including cellular proteins and microRNAs, positively or negatively regulate the DENV replication process. This review summarizes the latest findings (from 2014 to 2016) in the identification of the host factors involved in the DENV life cycle and Dengue infection.
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153
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Chen WH, Lu G, Chen X, Zhao XM, Bork P. OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Res 2017; 45:D940-D944. [PMID: 27799467 PMCID: PMC5210522 DOI: 10.1093/nar/gkw1013] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 01/14/2023] Open
Abstract
OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations. Developments since the last public release include increased numbers of species and gene essentiality data sets, inclusion of non-coding essential sequences and genes with intermediate essentiality statuses. In addition, we included 16 essentiality data sets from cancer cell lines, corresponding to 9 human cancers; with OGEE, users can easily explore the shared and differentially essential genes within and between cancer types. These genes, especially those derived from cell lines that are similar to tumor samples, could reveal the oncogenic drivers, paralogous gene expression pattern and chromosomal structure of the corresponding cancer types, and can be further screened to identify targets for cancer therapy and/or new drug development. OGEE is freely available at http://ogee.medgenius.info.
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Affiliation(s)
- Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Guanting Lu
- Department of Blood Transfusion, Tangdu Hospital, the Fourth Military Medical University, No 1, Xinsi Road, Chanba District, 710000 Xi'an, China
| | - Xiao Chen
- Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Xing-Ming Zhao
- Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Peer Bork
- European molecular biology laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
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154
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Validation of Synthetic CRISPR Reagents as a Tool for Arrayed Functional Genomic Screening. PLoS One 2016; 11:e0168968. [PMID: 28030641 PMCID: PMC5193459 DOI: 10.1371/journal.pone.0168968] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/10/2016] [Indexed: 12/03/2022] Open
Abstract
To date, lentiviral-based CRISPR-Cas9 screens have largely been conducted in pooled format. However, numerous assays are not amenable to pooled approaches, and lentiviral screening in arrayed format presents many challenges. We sought to examine synthetic CRISPR reagents in the context of arrayed screening. Experiments were performed using aberrant DNA replication as an assay. Using synthetic CRISPR RNAs targeting the known control gene GMNN in HCT-116 cells stably expressing Cas9, we observed statistically significant phenotype among the majority of transfected cells within 72 hours. Additional studies revealed near complete loss of GMNN protein and editing of GMNN DNA. We next conducted a screen of synthetic CRISPR RNAs directed against 640 ubiquitin-related genes. Screening identified known and novel DNA replication regulators that were also supported by siRNA gene knockdown. Notably, CRISPR screening identified more statistically significant hits than corresponding siRNA screens run in parallel. These results highlight the possibility of using synthetic CRISPR reagents as an arrayed screening tool.
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155
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Bagchi P, Inoue T, Tsai B. EMC1-dependent stabilization drives membrane penetration of a partially destabilized non-enveloped virus. eLife 2016; 5. [PMID: 28012275 PMCID: PMC5224922 DOI: 10.7554/elife.21470] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/23/2016] [Indexed: 11/13/2022] Open
Abstract
Destabilization of a non-enveloped virus generates a membrane transport-competent viral particle. Here we probe polyomavirus SV40 endoplasmic reticulum (ER)-to-cytosol membrane transport, a decisive infection step where destabilization initiates this non-enveloped virus for membrane penetration. We find that a member of the ER membrane protein complex (EMC) called EMC1 promotes SV40 ER membrane transport and infection. Surprisingly, EMC1 does so by using its predicted transmembrane residue D961 to bind to and stabilize the membrane-embedded partially destabilized SV40, thereby preventing premature viral disassembly. EMC1-dependent stabilization enables SV40 to engage a cytosolic extraction complex that ejects the virus into the cytosol. Thus EMC1 acts as a molecular chaperone, bracing the destabilized SV40 in a transport-competent state. Our findings reveal the novel principle that coordinated destabilization-stabilization drives membrane transport of a non-enveloped virus. DOI:http://dx.doi.org/10.7554/eLife.21470.001
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Affiliation(s)
- Parikshit Bagchi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Takamasa Inoue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
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156
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Doerflinger M, Forsyth W, Ebert G, Pellegrini M, Herold MJ. CRISPR/Cas9-The ultimate weapon to battle infectious diseases? Cell Microbiol 2016; 19. [PMID: 27860197 DOI: 10.1111/cmi.12693] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/30/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022]
Abstract
Infectious diseases are a leading cause of death worldwide. Novel therapeutics are urgently required to treat multidrug-resistant organisms such as Mycobacterium tuberculosis and to mitigate morbidity and mortality caused by acute infections such as malaria and dengue fever virus as well as chronic infections such as human immunodeficiency virus-1 and hepatitis B virus. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, which has revolutionized biomedical research, holds great promise for the identification and validation of novel drug targets. Since its discovery as an adaptive immune system in prokaryotes, the CRISPR/Cas9 system has been developed into a multi-faceted genetic modification tool, which can now be used to induce gene deletions or specific gene insertions, such as conditional alleles or endogenous reporters in virtually any organism. The generation of CRISPR/Cas9 libraries that can be used to perform phenotypic whole genome screens provides an important new tool that will aid in the identification of critical host factors involved in the pathogenesis of infectious diseases. In this review, we will discuss the development and recent applications of the CRISPR/Cas9 system used to identify novel regulators, which might become important in the fight against infectious diseases.
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Affiliation(s)
- M Doerflinger
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - W Forsyth
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - G Ebert
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - M Pellegrini
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - M J Herold
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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157
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Liu J, Shui SL. Delivery methods for site-specific nucleases: Achieving the full potential of therapeutic gene editing. J Control Release 2016; 244:83-97. [PMID: 27865852 DOI: 10.1016/j.jconrel.2016.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/30/2016] [Accepted: 11/07/2016] [Indexed: 12/20/2022]
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158
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Gaj T, Sirk SJ, Shui SL, Liu J. Genome-Editing Technologies: Principles and Applications. Cold Spring Harb Perspect Biol 2016; 8:a023754. [PMID: 27908936 PMCID: PMC5131771 DOI: 10.1101/cshperspect.a023754] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Targeted nucleases have provided researchers with the ability to manipulate virtually any genomic sequence, enabling the facile creation of isogenic cell lines and animal models for the study of human disease, and promoting exciting new possibilities for human gene therapy. Here we review three foundational technologies-clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs). We discuss the engineering advances that facilitated their development and highlight several achievements in genome engineering that were made possible by these tools. We also consider artificial transcription factors, illustrating how this technology can complement targeted nucleases for synthetic biology and gene therapy.
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Affiliation(s)
- Thomas Gaj
- Department of Bioengineering, University of California, Berkeley, California 94720
| | - Shannon J Sirk
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Sai-Lan Shui
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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159
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Phongphaew W, Kobayashi S, Sasaki M, Carr M, Hall WW, Orba Y, Sawa H. Valosin-containing protein (VCP/p97) plays a role in the replication of West Nile virus. Virus Res 2016; 228:114-123. [PMID: 27914931 PMCID: PMC7114552 DOI: 10.1016/j.virusres.2016.11.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/25/2016] [Accepted: 11/25/2016] [Indexed: 12/16/2022]
Abstract
Inhibition of VCP by chemical inhibitors decreased WNV infection in a dose-dependent manner. Knockdown of endogenous VCP level using siRNA suppressed WNV infection. Depletion of VCP levels suppressed WNV infection at the early stages of WNV replication cycle. Depletion of VCP levels lowered nascent WNV genomic RNA. VCP participates in early stages and viral genomic RNA replication.
Valosin-containing protein (VCP) is classified as a member of the type II AAA+ ATPase protein family. VCP functions in several cellular processes, including protein degradation, membrane fusion, vesicular trafficking and disassembly of stress granules. Moreover, VCP is considered to play a role in the replication of several viruses, albeit through different mechanisms. In the present study, we have investigated the role of VCP in West Nile virus (WNV) infection. Endogenous VCP expression was inhibited using either VCP inhibitors or by siRNA knockdown. It could be shown that the inhibition of endogenous VCP expression significantly inhibited WNV infection. The entry assay revealed that silencing of endogenous VCP caused a significant reduction in the expression levels of WNV-RNA compared to control siRNA-treated cells. This indicates that VCP may play a role in early steps either the binding or entry steps of the WNV life cycle. Using WNV virus like particles and WNV-DNA-based replicon, it could be demonstrated that perturbation of VCP expression decreased levels of newly synthesized WNV genomic RNA. These findings suggest that VCP is involved in early steps and during genome replication of the WNV life cycle.
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Affiliation(s)
- Wallaya Phongphaew
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Shintaro Kobayashi
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan; Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, N18, W9, Kita-ku, Sapporo 001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Michael Carr
- Global Institution for Collaborative Researches and Education (GI-CoRE), Global Station for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan; National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Global Institution for Collaborative Researches and Education (GI-CoRE), Global Station for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan; Center for Research in Infectious Diseases, University College of Dublin, Belfield, Dublin 4, Dublin, Ireland; Global Virus Network (GVN), The Institute of Human Virology, University of Maryland, 22S. Greene Street, Baltimore, MD 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan; Global Institution for Collaborative Researches and Education (GI-CoRE), Global Station for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan; Global Virus Network (GVN), The Institute of Human Virology, University of Maryland, 22S. Greene Street, Baltimore, MD 21201, USA.
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160
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Abstract
The development of the CRISPR-Cas platform for genome editing has greatly simplified the process of making targeted genetic modifications. Applications of genome editing are expected to have a substantial impact on human therapies through the development of better animal models, new target discovery, and direct therapeutic intervention.
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161
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Chen S, Sun H, Miao K, Deng CX. CRISPR-Cas9: from Genome Editing to Cancer Research. Int J Biol Sci 2016; 12:1427-1436. [PMID: 27994508 PMCID: PMC5166485 DOI: 10.7150/ijbs.17421] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer development is a multistep process triggered by innate and acquired mutations, which cause the functional abnormality and determine the initiation and progression of tumorigenesis. Gene editing is a widely used engineering tool for generating mutations that enhance tumorigenesis. The recent developed clustered regularly interspaced short palindromic repeats-CRISPR-associated 9 (CRISPR-Cas9) system renews the genome editing approach into a more convenient and efficient way. By rapidly introducing genetic modifications in cell lines, organs and animals, CRISPR-Cas9 system extends the gene editing into whole genome screening, both in loss-of-function and gain-of-function manners. Meanwhile, the system accelerates the establishment of animal cancer models, promoting in vivo studies for cancer research. Furthermore, CRISPR-Cas9 system is modified into diverse innovative tools for observing the dynamic bioprocesses in cancer studies, such as image tracing for targeted DNA, regulation of transcription activation or repression. Here, we view recent technical advances in the application of CRISPR-Cas9 system in cancer genetics, large-scale cancer driver gene hunting, animal cancer modeling and functional studies.
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Affiliation(s)
- Si Chen
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Heng Sun
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Kai Miao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
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162
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, a versatile RNA-guided DNA targeting platform, has been revolutionizing our ability to modify, manipulate, and visualize the human genome, which greatly advances both biological research and therapeutics development. Here, we review the current development of CRISPR/Cas9 technologies for gene editing, transcription regulation, genome imaging, and epigenetic modification. We discuss the broad application of this system to the study of functional genomics, especially genome-wide genetic screening, and to therapeutics development, including establishing disease models, correcting defective genetic mutations, and treating diseases.
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Affiliation(s)
- Xin Xiong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158; ,
| | - Meng Chen
- Department of Bioengineering, Stanford University, Stanford, California 94305; ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- ChEM-H, Stanford University, Stanford, California 94305
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158;
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158; ,
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, California 94305; ,
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305; ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- ChEM-H, Stanford University, Stanford, California 94305
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163
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How Polyomaviruses Exploit the ERAD Machinery to Cause Infection. Viruses 2016; 8:v8090242. [PMID: 27589785 PMCID: PMC5035956 DOI: 10.3390/v8090242] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
To infect cells, polyomavirus (PyV) traffics from the cell surface to the endoplasmic reticulum (ER) where it hijacks elements of the ER-associated degradation (ERAD) machinery to penetrate the ER membrane and reach the cytosol. From the cytosol, the virus transports to the nucleus, enabling transcription and replication of the viral genome that leads to lytic infection or cellular transformation. How PyV exploits the ERAD machinery to cross the ER membrane and access the cytosol, a decisive infection step, remains enigmatic. However, recent studies have slowly unraveled many aspects of this process. These emerging insights should advance our efforts to develop more effective therapies against PyV-induced human diseases.
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164
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Mutlu N, Kumar A. Mapping paths: new approaches to dissect eukaryotic signaling circuitry. F1000Res 2016; 5. [PMID: 27540473 PMCID: PMC4965690 DOI: 10.12688/f1000research.8818.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic cells are precisely “wired” to coordinate changes in external and intracellular signals with corresponding adjustments in the output of complex and often interconnected signaling pathways. These pathways are critical in understanding cellular growth and function, and several experimental trends are emerging with applicability toward more fully describing the composition and topology of eukaryotic signaling networks. In particular, recent studies have implemented CRISPR/Cas-based screens in mouse and human cell lines for genes involved in various cell growth and disease phenotypes. Proteomic methods using mass spectrometry have enabled quantitative and dynamic profiling of protein interactions, revealing previously undiscovered complexes and allele-specific protein interactions. Methods for the single-cell study of protein localization and gene expression have been integrated with computational analyses to provide insight into cell signaling in yeast and metazoans. In this review, we present an overview of exemplary studies using the above approaches, relevant for the analysis of cell signaling and indeed, more broadly, for many modern biological applications.
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Affiliation(s)
- Nebibe Mutlu
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anuj Kumar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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165
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McDade JR, Waxmonsky NC, Swanson LE, Fan M. Practical Considerations for Using Pooled Lentiviral CRISPR Libraries. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2016; 115:31.5.1-31.5.13. [PMID: 27366891 DOI: 10.1002/cpmb.8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CRISPR/Cas9 technology is ideally suited for genome-wide screening applications due to the ease of generating guide RNAs (gRNAs) and the versatility of Cas9 or Cas9 derivatives to knockout, repress, or activate expression of target genes. Several pooled lentiviral CRISPR libraries have been developed and are now publicly available, but while using CRISPR/Cas9 for genetic experiments has become widely adopted, genome-wide screening experiments remain technically challenging. This review covers the basics of CRISPR/Cas9, describes several publicly available CRISPR libraries, and provides a general protocol for conducting genome-wide screening experiments using CRISPR/Cas9. © 2016 by John Wiley & Sons, Inc.
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166
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Savidis G, McDougall WM, Meraner P, Perreira JM, Portmann JM, Trincucci G, John SP, Aker AM, Renzette N, Robbins DR, Guo Z, Green S, Kowalik TF, Brass AL. Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics. Cell Rep 2016; 16:232-246. [PMID: 27342126 DOI: 10.1016/j.celrep.2016.06.028] [Citation(s) in RCA: 286] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/02/2016] [Accepted: 06/10/2016] [Indexed: 01/10/2023] Open
Abstract
The flaviviruses dengue virus (DENV) and Zika virus (ZIKV) are severe health threats with rapidly expanding ranges. To identify the host cell dependencies of DENV and ZIKV, we completed orthologous functional genomic screens using RNAi and CRISPR/Cas9 approaches. The screens recovered the ZIKV entry factor AXL as well as multiple host factors involved in endocytosis (RAB5C and RABGEF), heparin sulfation (NDST1 and EXT1), and transmembrane protein processing and maturation, including the endoplasmic reticulum membrane complex (EMC). We find that both flaviviruses require the EMC for their early stages of infection. Together, these studies generate a high-confidence, systems-wide view of human-flavivirus interactions and provide insights into the role of the EMC in flavivirus replication.
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Affiliation(s)
- George Savidis
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - William M McDougall
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Paul Meraner
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Jill M Perreira
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Jocelyn M Portmann
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Gaia Trincucci
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Sinu P John
- Signaling Systems Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron M Aker
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Nicholas Renzette
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Douglas R Robbins
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Zhiru Guo
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sharone Green
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Abraham L Brass
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA; Division of Gastroenterology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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167
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Qi X, Zhang J, Zhao Y, Chen T, Xiang Y, Hui J, Cai D, Liu Y, Xia L, Yu T, Li G. The applications of CRISPR screen in functional genomics. Brief Funct Genomics 2016; 16:34-37. [DOI: 10.1093/bfgp/elw020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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168
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Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature 2016; 535:159-63. [PMID: 27383987 PMCID: PMC4964798 DOI: 10.1038/nature18631] [Citation(s) in RCA: 332] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/10/2016] [Indexed: 12/15/2022]
Abstract
The Flaviviridae are a family of viruses that cause severe human diseases. For example, dengue virus (DENV) is a rapidly emerging pathogen causing an estimated 100 million symptomatic infections annually worldwide. No approved antivirals are available to date and clinical trials with a tetravalent dengue vaccine showed disappointingly low protection rates. Hepatitis C virus (HCV) also remains a major medical problem, with 160 million chronically infected patients worldwide and only expensive treatments available. Despite distinct differences in their pathogenesis and modes of transmission, the two viruses share common replication strategies. A detailed understanding of the host functions that determine viral infection is lacking. Here we use a pooled CRISPR genetic screening strategy to comprehensively dissect host factors required for these two highly important Flaviviridae members. For DENV, we identified endoplasmic-reticulum (ER)-associated multi-protein complexes involved in signal sequence recognition, N-linked glycosylation and ER-associated degradation. DENV replication was nearly completely abrogated in cells deficient in the oligosaccharyltransferase (OST) complex. Mechanistic studies pinpointed viral RNA replication and not entry or translation as the crucial step requiring the OST complex. Moreover, we show that viral non-structural proteins bind to the OST complex. The identified ER-associated protein complexes were also important for infection by other mosquito-borne flaviviruses including Zika virus, an emerging pathogen causing severe birth defects. By contrast, the most significant genes identified in the HCV screen were distinct and included viral receptors, RNA-binding proteins and enzymes involved in metabolism. We found an unexpected link between intracellular flavin adenine dinucleotide (FAD) levels and HCV replication. This study shows notable divergence in host-depenency factors between DENV and HCV, and illuminates new host targets for antiviral therapy.
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169
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A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature 2016; 535:164-8. [PMID: 27383988 PMCID: PMC4945490 DOI: 10.1038/nature18625] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/06/2016] [Indexed: 12/17/2022]
Abstract
Flaviviruses infect hundreds of millions of people annually, and no antiviral therapy is available. We performed a genome-wide CRISPR/Cas9-based screen to identify host genes that, when edited, resulted in reduced flavivirus infection. Here, we validated nine human genes required for flavivirus infectivity, and these were associated with endoplasmic reticulum functions including translocation, protein degradation, and N-linked glycosylation. In particular, a subset of endoplasmic reticulum-associated signal peptidase complex (SPCS) proteins was necessary for proper cleavage of the flavivirus structural proteins (prM and E) and secretion of viral particles. Loss of SPCS1 expression resulted in markedly reduced yield of all Flaviviridae family members tested (West Nile, Dengue, Zika, yellow fever, Japanese encephalitis, and hepatitis C viruses), but had little impact on alphavirus, bunyavirus, or rhabdovirus infection or the surface expression or secretion of diverse host proteins. We found that SPCS1 dependence could be bypassed by replacing the native prM protein leader sequences with a class I major histocompatibility complex (MHC) antigen leader sequence. Thus, SPCS1, either directly or indirectly via its interactions with unknown host proteins, preferentially promotes the processing of specific protein cargo, and Flaviviridae have a unique dependence on this signal peptide processing pathway. SPCS1 and other signal processing pathway members could represent pharmacological targets for inhibiting infection by the expanding number of flaviviruses of medical concern.
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170
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Weaver SC, Costa F, Garcia-Blanco MA, Ko AI, Ribeiro GS, Saade G, Shi PY, Vasilakis N. Zika virus: History, emergence, biology, and prospects for control. Antiviral Res 2016; 130:69-80. [PMID: 26996139 PMCID: PMC4851879 DOI: 10.1016/j.antiviral.2016.03.010] [Citation(s) in RCA: 516] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 12/18/2022]
Abstract
Zika virus (ZIKV), a previously obscure flavivirus closely related to dengue, West Nile, Japanese encephalitis and yellow fever viruses, has emerged explosively since 2007 to cause a series of epidemics in Micronesia, the South Pacific, and most recently the Americas. After its putative evolution in sub-Saharan Africa, ZIKV spread in the distant past to Asia and has probably emerged on multiple occasions into urban transmission cycles involving Aedes (Stegomyia) spp. mosquitoes and human amplification hosts, accompanied by a relatively mild dengue-like illness. The unprecedented numbers of people infected during recent outbreaks in the South Pacific and the Americas may have resulted in enough ZIKV infections to notice relatively rare congenital microcephaly and Guillain-Barré syndromes. Another hypothesis is that phenotypic changes in Asian lineage ZIKV strains led to these disease outcomes. Here, we review potential strategies to control the ongoing outbreak through vector-centric approaches as well as the prospects for the development of vaccines and therapeutics.
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Affiliation(s)
- Scott C Weaver
- Institute for Human Infections and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston TX, USA; Institute for Human Infections and Immunity, Department of Pathology, University of Texas Medical Branch, Galveston TX, USA.
| | - Federico Costa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil; Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Mariano A Garcia-Blanco
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Albert I Ko
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Guilherme S Ribeiro
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil; Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - George Saade
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA; Department of Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston TX, USA; Institute for Human Infections and Immunity, Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
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171
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Making Bunyaviruses Talk: Interrogation Tactics to Identify Host Factors Required for Infection. Viruses 2016; 8:v8050130. [PMID: 27187446 PMCID: PMC4885085 DOI: 10.3390/v8050130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/03/2016] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
The identification of host cellular genes that act as either proviral or antiviral factors has been aided by the development of an increasingly large number of high-throughput screening approaches. Here, we review recent advances in which these new technologies have been used to interrogate host genes for the ability to impact bunyavirus infection, both in terms of technical advances as well as a summary of biological insights gained from these studies.
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172
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Heigwer F, Zhan T, Breinig M, Winter J, Brügemann D, Leible S, Boutros M. CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biol 2016; 17:55. [PMID: 27013184 PMCID: PMC4807595 DOI: 10.1186/s13059-016-0915-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. RESULTS Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CONCLUSION CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.
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Affiliation(s)
- Florian Heigwer
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Tianzuo Zhan
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
- />Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Marco Breinig
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Jan Winter
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Dirk Brügemann
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Svenja Leible
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Michael Boutros
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
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173
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Zhang H, Zhang X, Fan C, Xie Q, Xu C, Zhao Q, Liu Y, Wu X, Zhang H. A novel sgRNA selection system for CRISPR-Cas9 in mammalian cells. Biochem Biophys Res Commun 2016; 471:528-32. [PMID: 26879140 DOI: 10.1016/j.bbrc.2016.02.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/11/2016] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas9 mediated genome editing system has been developed as a powerful tool for elucidating the function of genes through genetic engineering in multiple cells and organisms. This system takes advantage of a single guide RNA (sgRNA) to direct the Cas9 endonuclease to a specific DNA site to generate mutant alleles. Since the targeting efficiency of sgRNAs to distinct DNA loci can vary widely, there remains a need for a rapid, simple and efficient sgRNA selection method to overcome this limitation of the CRISPR-Cas9 system. Here we report a novel system to select sgRNA with high efficacy for DNA sequence modification by a luciferase assay. Using this sgRNAs selection system, we further demonstrated successful examples of one sgRNA for generating one gene knockout cell lines where the targeted genes are shown to be functionally defective. This system provides a potential application to optimize the sgRNAs in different species and to generate a powerful CRISPR-Cas9 genome-wide screening system with minimum amounts of sgRNAs.
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Affiliation(s)
- Haiwei Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xixi Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cunxian Fan
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qun Xie
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Department of Anesthesiology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Chengxian Xu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qun Zhao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yongbo Liu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoxia Wu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haibing Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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174
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Functional Genomic Strategies for Elucidating Human-Virus Interactions: Will CRISPR Knockout RNAi and Haploid Cells? Adv Virus Res 2016; 94:1-51. [PMID: 26997589 PMCID: PMC7112329 DOI: 10.1016/bs.aivir.2015.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Over the last several years a wealth of transformative human–virus interaction discoveries have been produced using loss-of-function functional genomics. These insights have greatly expanded our understanding of how human pathogenic viruses exploit our cells to replicate. Two technologies have been at the forefront of this genetic revolution, RNA interference (RNAi) and random retroviral insertional mutagenesis using haploid cell lines (haploid cell screening), with the former technology largely predominating. Now the cutting edge gene editing of the CRISPR/Cas9 system has also been harnessed for large-scale functional genomics and is poised to possibly displace these earlier methods. Here we compare and contrast these three screening approaches for elucidating host–virus interactions, outline their key strengths and weaknesses including a comparison of an arrayed multiple orthologous RNAi reagent screen to a pooled CRISPR/Cas9 human rhinovirus 14–human cell interaction screen, and recount some notable insights made possible by each. We conclude with a brief perspective on what might lie ahead for the fast evolving field of human–virus functional genomics.
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175
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Xue HY, Ji LJ, Gao AM, Liu P, He JD, Lu XJ. CRISPR-Cas9 for medical genetic screens: applications and future perspectives. J Med Genet 2015; 53:91-7. [DOI: 10.1136/jmedgenet-2015-103409] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/13/2015] [Indexed: 12/26/2022]
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176
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Dang Y, Jia G, Choi J, Ma H, Anaya E, Ye C, Shankar P, Wu H. Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency. Genome Biol 2015; 16:280. [PMID: 26671237 PMCID: PMC4699467 DOI: 10.1186/s13059-015-0846-3] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Single-guide RNA (sgRNA) is one of the two key components of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome-editing system. The current commonly used sgRNA structure has a shortened duplex compared with the native bacterial CRISPR RNA (crRNA)–transactivating crRNA (tracrRNA) duplex and contains a continuous sequence of thymines, which is the pause signal for RNA polymerase III and thus could potentially reduce transcription efficiency. Results Here, we systematically investigate the effect of these two elements on knockout efficiency and showed that modifying the sgRNA structure by extending the duplex length and mutating the fourth thymine of the continuous sequence of thymines to cytosine or guanine significantly, and sometimes dramatically, improves knockout efficiency in cells. In addition, the optimized sgRNA structure also significantly increases the efficiency of more challenging genome-editing procedures, such as gene deletion, which is important for inducing a loss of function in non-coding genes. Conclusions By a systematic investigation of sgRNA structure we find that extending the duplex by approximately 5 bp combined with mutating the continuous sequence of thymines at position 4 to cytosine or guanine significantly increases gene knockout efficiency in CRISPR-Cas9-based genome editing experiments. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0846-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ying Dang
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Gengxiang Jia
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Jennie Choi
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Hongming Ma
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Edgar Anaya
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Chunting Ye
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Premlata Shankar
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
| | - Haoquan Wu
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA.
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177
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Abstract
CRISPR-based approaches have quickly become a favored method to perturb genes to uncover their functions. Here, we review the key considerations in the design of genome editing experiments, and survey the tools and resources currently available to assist users of this technology.
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Affiliation(s)
- Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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