1
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Jakobsen ST, Jensen RAM, Madsen MS, Ravnsborg T, Vaagenso CS, Siersbæk MS, Einarsson H, Andersson R, Jensen ON, Siersbæk R. MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch. Nat Genet 2024; 56:663-674. [PMID: 38454021 DOI: 10.1038/s41588-024-01676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.
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Affiliation(s)
- Simon T Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rikke A M Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria S Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hjorleifur Einarsson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robin Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rasmus Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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2
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Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Rep 2022; 41:111630. [PMID: 36351387 PMCID: PMC9687083 DOI: 10.1016/j.celrep.2022.111630] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
A scarcity of functionally validated enhancers in the human genome presents a significant hurdle to understanding how these cis-regulatory elements contribute to human diseases. We carry out highly multiplexed CRISPR-based perturbation and sequencing to identify enhancers required for cell proliferation and fitness in 10 human cancer cell lines. Our results suggest that the cell fitness enhancers, unlike their target genes, display high cell-type specificity of chromatin features. They typically adopt a modular structure, comprised of activating elements enriched for motifs of oncogenic transcription factors, surrounded by repressive elements enriched for motifs recognized by transcription factors with tumor suppressor functions. We further identify cell fitness enhancers that are selectively accessible in clinical tumor samples, and the levels of chromatin accessibility are associated with patient survival. These results reveal functional enhancers across multiple cancer cell lines, characterize their context-dependent chromatin organization, and yield insights into altered transcription programs in cancer cells.
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Affiliation(s)
- Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Singapore
| | - Patrick C Fiaux
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Kai Zhang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shan Jiang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Emma Rooholfada
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Mengchi Wang
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Paul S Mischel
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA; Institute of Genome Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, San Diego, La Jolla, CA 92093, USA.
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3
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Tokumoto S, Miyata Y, Deviatiiarov R, Yamada TG, Hiki Y, Kozlova O, Yoshida Y, Cornette R, Funahashi A, Shagimardanova E, Gusev O, Kikawada T. Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11. Int J Mol Sci 2021; 22:5798. [PMID: 34071490 PMCID: PMC8197945 DOI: 10.3390/ijms22115798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 01/10/2023] Open
Abstract
The Pv11, an insect cell line established from the midge Polypedilum vanderplanki, is capable of extreme hypometabolic desiccation tolerance, so-called anhydrobiosis. We previously discovered that heat shock factor 1 (HSF1) contributes to the acquisition of desiccation tolerance by Pv11 cells, but the mechanistic details have yet to be elucidated. Here, by analyzing the gene expression profiles of newly established HSF1-knockout and -rescue cell lines, we show that HSF1 has a genome-wide effect on gene regulation in Pv11. The HSF1-knockout cells exhibit a reduced desiccation survival rate, but this is completely restored in HSF1-rescue cells. By comparing mRNA profiles of the two cell lines, we reveal that HSF1 induces anhydrobiosis-related genes, especially genes encoding late embryogenesis abundant proteins and thioredoxins, but represses a group of genes involved in basal cellular processes, thus promoting an extreme hypometabolism state in the cell. In addition, HSF1 binding motifs are enriched in the promoters of anhydrobiosis-related genes and we demonstrate binding of HSF1 to these promoters by ChIP-qPCR. Thus, HSF1 directly regulates the transcription of anhydrobiosis-related genes and consequently plays a pivotal role in the induction of anhydrobiotic ability in Pv11 cells.
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Affiliation(s)
- Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan;
| | - Yugo Miyata
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan; (Y.M.); (R.C.)
| | - Ruslan Deviatiiarov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (R.D.); (O.K.); (E.S.); (O.G.)
| | - Takahiro G. Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan; (T.G.Y.); (Y.H.); (A.F.)
| | - Yusuke Hiki
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan; (T.G.Y.); (Y.H.); (A.F.)
| | - Olga Kozlova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (R.D.); (O.K.); (E.S.); (O.G.)
| | - Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan;
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-8520, Japan
| | - Richard Cornette
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan; (Y.M.); (R.C.)
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan; (T.G.Y.); (Y.H.); (A.F.)
| | - Elena Shagimardanova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (R.D.); (O.K.); (E.S.); (O.G.)
| | - Oleg Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (R.D.); (O.K.); (E.S.); (O.G.)
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama 230-0045, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan;
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan; (Y.M.); (R.C.)
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4
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Zhang M, Yang C, Tasan I, Zhao H. Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. ACS Synth Biol 2021; 10:429-446. [PMID: 33596056 DOI: 10.1021/acssynbio.0c00576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inserting custom designed DNA sequences into the mammalian genome plays an essential role in synthetic biology. In particular, the ability to introduce foreign DNA in a site-specific manner offers numerous advantages over random DNA integration. In this review, we focus on two mechanistically distinct systems that have been widely adopted for targeted DNA insertion in mammalian cells, the CRISPR/Cas9 system and site-specific recombinases. The CRISPR/Cas9 system has revolutionized the genome engineering field thanks to its high programmability and ease of use. However, due to its dependence on linearized DNA donor and endogenous cellular pathways to repair the induced double-strand break, CRISPR/Cas9-mediated DNA insertion still faces limitations such as small insert size, and undesired editing outcomes via error-prone repair pathways. In contrast, site-specific recombinases, in particular the Serine integrases, demonstrate large-cargo capability and no dependence on cellular repair pathways for DNA integration. Here we first describe recent advances in improving the overall efficacy of CRISPR/Cas9-based methods for DNA insertion. Moreover, we highlight the advantages of site-specific recombinases over CRISPR/Cas9 in the context of targeted DNA integration, with a special focus on the recent development of programmable recombinases. We conclude by discussing the importance of protein engineering to further expand the current toolkit for targeted DNA insertion in mammalian cells.
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Affiliation(s)
- Meng Zhang
- Department of Chemical and Biomolecular Engineering, 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
| | - Che Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ipek Tasan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, 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 Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham PE, Chen JG, Weston DJ, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee JH, Cottingham RW, Martin S, Lu M, Tschaplinski TJ, Yuan G, Lu H, Ranjan P, Mitchell JC, Wullschleger SD, Tuskan GA. Plant Biosystems Design Research Roadmap 1.0. BIODESIGN RESEARCH 2020; 2020:8051764. [PMID: 37849899 PMCID: PMC10521729 DOI: 10.34133/2020/8051764] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 10/19/2023] Open
Abstract
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Henrique C. De Paoli
- Department of Biodesign, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cong T. Trinh
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1858, Frederiksberg, Copenhagen, Denmark
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jessy Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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6
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Ying Y, Wang Y, Huang X, Sun Y, Zhang J, Li M, Zeng J, Wang M, Xiao W, Zhong L, Xu B, Li L, Tao Q, Wang X, Shu XS. Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1. Oncogene 2019; 39:1004-1017. [DOI: 10.1038/s41388-019-1013-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022]
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7
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Niu W, Parent JM. Modeling genetic epilepsies in a dish. Dev Dyn 2019; 249:56-75. [DOI: 10.1002/dvdy.79] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wei Niu
- Department of Neurology and Neuroscience Graduate ProgramUniversity of Michigan Medical Center and VA Ann Arbor Healthcare System Ann Arbor Michigan
| | - Jack M. Parent
- Department of Neurology and Neuroscience Graduate ProgramUniversity of Michigan Medical Center and VA Ann Arbor Healthcare System Ann Arbor Michigan
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8
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Ahmadzadeh V, Farajnia S, Baghban R, Rahbarnia L, Zarredar H. CRISPR-Cas system: Toward a more efficient technology for genome editing and beyond. J Cell Biochem 2019; 120:16379-16392. [PMID: 31219653 DOI: 10.1002/jcb.29140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022]
Abstract
Genome engineering technology is of great interest for biomedical research that enables scientists to make specific manipulation in the DNA sequence. Early methods for introducing double-stranded DNA breaks relies on protein-based systems. These platforms have enabled fascinating advances, but all are costly and time-consuming to engineer, preventing these from gaining high-throughput applications. The CRISPR-Cas9 system, co-opted from bacteria, has generated considerable excitement in gene targeting. In this review, we describe gene targeting techniques with an emphasis on recent strategies to improve the specificities of CRISPR-Cas systems for nuclease and non-nuclease applications.
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Affiliation(s)
- Vahideh Ahmadzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roghayyeh Baghban
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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9
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Nakade S, Mochida K, Kunii A, Nakamae K, Aida T, Tanaka K, Sakamoto N, Sakuma T, Yamamoto T. Biased genome editing using the local accumulation of DSB repair molecules system. Nat Commun 2018; 9:3270. [PMID: 30115916 PMCID: PMC6095859 DOI: 10.1038/s41467-018-05773-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/24/2018] [Indexed: 01/31/2023] Open
Abstract
Selective genome editing such as gene knock-in has recently been achieved by administration of chemical enhancer or inhibitor of particular DNA double-strand break (DSB) repair pathways, as well as overexpression of pathway-specific genes. In this study, we attempt to enhance the efficiency further to secure robust gene knock-ins, by using the local accumulation of DSB repair molecules (LoAD) system. We identify CtIP as a strong enhancer of microhomology-mediated end-joining (MMEJ) repair by genetic screening, and show the knock-in-enhancing effect of CtIP LoADing. Next-generation sequencing reveals that CtIP LoADing highly increases the frequency of MMEJ-mediated integration. Selection-free, simultaneous triple gene knock-ins are also achieved with the CtIP-LoADing strategy. Moreover, by replacing the LoADing molecules and targeting strategies, this system can be applied for other specific genome engineering purposes, such as introducing longer deletions for gene disruption, independently introducing multiple mutations without chromosomal deletion, and efficiently incorporating a single-stranded oligodeoxynucleotide donor.
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Affiliation(s)
- Shota Nakade
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Keiji Mochida
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Atsushi Kunii
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Kazuki Nakamae
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tomomi Aida
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, 46-3143A, 43 Vassar Street, Cambridge, MA, 02139, USA
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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Roy B, Zhao J, Yang C, Luo W, Xiong T, Li Y, Fang X, Gao G, Singh CO, Madsen L, Zhou Y, Kristiansen K. CRISPR/Cascade 9-Mediated Genome Editing-Challenges and Opportunities. Front Genet 2018; 9:240. [PMID: 30026755 PMCID: PMC6042012 DOI: 10.3389/fgene.2018.00240] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and Cascade 9 (also known as Cas9, CRISPR associated protein 9) confer protection against invading viruses or plasmids. The CRISPR/Cascade 9 system constitutes one of the most powerful genome technologies available to researchers today. So far, this technology has enabled efficient genome editing and modification in several model organisms and has successfully been used in biomedicine and biomedical engineering. However, challenges for efficient and safe genetic manipulation in several organisms persist. Here, we review functional approaches and future challenges associated with the use of the CRISPR/Cascade 9 genome editing system and discuss opportunities, ethical issues and future directions within this field.
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Affiliation(s)
| | - Jing Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Chao Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wen Luo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Teng Xiong
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Guanjun Gao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chabungbam O Singh
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lise Madsen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Marine Research, Bergen, Norway
| | - Yong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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11
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Dewari PS, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner MC, Plumb C, Kalantzaki M, Blin C, Finch R, Bressan RB, Morrison G, Jacobi AM, Behlke MA, von Kriegsheim A, Tomlinson S, Krijgsveld J, Pollard SM. An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein. eLife 2018; 7:e35069. [PMID: 29638216 PMCID: PMC5947990 DOI: 10.7554/elife.35069] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here, we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5-30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain-tumor-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of 60 different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells.
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Affiliation(s)
- Pooran Singh Dewari
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Benjamin Southgate
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Katrina Mccarten
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - German Monogarov
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Eoghan O'Duibhir
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Niall Quinn
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Ashley Tyrer
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Marie-Christin Leitner
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Colin Plumb
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Maria Kalantzaki
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Carla Blin
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Rebecca Finch
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Raul Bardini Bressan
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Gillian Morrison
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc.CoralvilleUnited States
| | - Alex von Kriegsheim
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Simon Tomlinson
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jeroen Krijgsveld
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Steven M Pollard
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
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12
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Korona D, Koestler SA, Russell S. Engineering the Drosophila Genome for Developmental Biology. J Dev Biol 2017; 5:jdb5040016. [PMID: 29615571 PMCID: PMC5831791 DOI: 10.3390/jdb5040016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
The recent development of transposon and CRISPR-Cas9-based tools for manipulating the fly genome in vivo promises tremendous progress in our ability to study developmental processes. Tools for introducing tags into genes at their endogenous genomic loci facilitate imaging or biochemistry approaches at the cellular or subcellular levels. Similarly, the ability to make specific alterations to the genome sequence allows much more precise genetic control to address questions of gene function.
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Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Stefan A Koestler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
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13
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Sakuma T, Yamamoto T. Magic wands of CRISPR—lots of choices for gene knock-in. Cell Biol Toxicol 2017; 33:501-505. [DOI: 10.1007/s10565-017-9409-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 12/18/2022]
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14
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Lin J, Zhou Y, Liu J, Chen J, Chen W, Zhao S, Wu Z, Wu N. Progress and Application of CRISPR/Cas Technology in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:3061-3071. [DOI: 10.1002/jcb.26198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Internal Medicine, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Department of Breast Surgical Oncology, National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Central Laboratory, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
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15
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Guichard SM. CRISPR–Cas9 for Drug Discovery in Oncology. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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