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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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2
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Bull T, Khakhar A. Design principles for synthetic control systems to engineer plants. PLANT CELL REPORTS 2023; 42:1875-1889. [PMID: 37789180 DOI: 10.1007/s00299-023-03072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE Synthetic control systems have led to significant advancement in the study and engineering of unicellular organisms, but it has been challenging to apply these tools to multicellular organisms like plants. The ability to predictably engineer plants will enable the development of novel traits capable of alleviating global problems, such as climate change and food insecurity. Engineering predictable multicellular phenotypes will require the development of synthetic control systems that can precisely regulate how the information encoded in genomes is translated into phenotypes. Many efficient control systems have been developed for unicellular organisms. However, it remains challenging to use such tools to study or engineer multicellular organisms. Plants are a good chassis within which to develop strategies to overcome these challenges, thanks to their capacity to withstand large-scale reprogramming without lethality. Additionally, engineered plants have great potential for solving major societal problems. Here we briefly review the progress of control system development in unicellular organisms, and how that information can be leveraged to characterize control systems in plants. Further, we discuss strategies for developing control systems designed to regulate the expression of transgenes or endogenous loci and generate dosage-dependent or discrete traits. Finally, we discuss the utility that mathematical models of biological processes have for control system deployment.
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Affiliation(s)
- Tawni Bull
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
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3
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Teper D, White FF, Wang N. The Dynamic Transcription Activator-Like Effector Family of Xanthomonas. PHYTOPATHOLOGY 2023; 113:651-666. [PMID: 36449529 DOI: 10.1094/phyto-10-22-0365-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins that are injected into the eukaryotic nucleus to act as transcriptional factors and function as key virulence factors of the phytopathogen Xanthomonas. TALEs are translocated into plant host cells via the type III secretion system and induce the expression of host susceptibility (S) genes to facilitate disease. The unique modular DNA binding domains of TALEs comprise an array of nearly identical direct repeats that enable binding to DNA targets based on the recognition of a single nucleotide target per repeat. The very nature of TALE structure and function permits the proliferation of TALE genes and evolutionary adaptations in the host to counter TALE function, making the TALE-host interaction the most dynamic story in effector biology. The TALE genes appear to be a relatively young effector gene family, with a presence in all virulent members of some species and absent in others. Genome sequencing has revealed many TALE genes throughout the xanthomonads, and relatively few have been associated with a cognate S gene. Several species, including Xanthomonas oryzae pv. oryzae and X. citri pv. citri, have near absolute requirement for TALE gene function, while the genes appear to be just now entering the disease interactions with new fitness contributions to the pathogens of tomato and pepper among others. Deciphering the simple and effective DNA binding mechanism also has led to the development of DNA manipulation tools in fields of gene editing and transgenic research. In the three decades since their discovery, TALE research remains at the forefront of the study of bacterial evolution, plant-pathogen interactions, and synthetic biology. We also discuss critical questions that remain to be addressed regarding TALEs.
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Affiliation(s)
- Doron Teper
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Frank F White
- Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, U.S.A
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4
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Leben K, Strmšek Ž, Lebar T, Verbič A, Dragovan M, Omersa N, Anderluh G, Jerala R. Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor. Nucleic Acids Res 2022; 50:6562-6574. [PMID: 35670660 PMCID: PMC9226504 DOI: 10.1093/nar/gkac454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 01/27/2023] Open
Abstract
DNA transcription is regulated by a range of diverse mechanisms and primarily by transcription factors that recruit the RNA polymerase complex to the promoter region on the DNA. Protein binding to DNA at nearby or distant sites can synergistically affect this process in a variety of ways, but mainly through direct interactions between DNA-binding proteins. Here we show that a Transcription Activator-Like Effector (TALE), which lacks an activation domain, can enhance transcription in mammalian cells when it binds in the vicinity of and without direct interaction with several different dimeric or monomeric transcription factors. This effect was observed for several TALEs regardless of the recognition sequences and their DNA-bound orientation. TALEs can exert an effect over the distance of tens of nucleotides and it also potentiated KRAB-mediated repression. The augmentation of transcriptional regulation of another transcription factor is characteristic of TALEs, as it was not observed for dCas9/gRNA, zinc finger, or Gal4 DNA-binding domains. We propose that this mechanism involves an allosteric effect exerted on DNA structure or dynamics. This mechanism could be used to modulate transcription but may also play a role in the natural context of TALEs.
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Affiliation(s)
- Katja Leben
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Matej Dragovan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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5
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Kar S, Bordiya Y, Rodriguez N, Kim J, Gardner EC, Gollihar JD, Sung S, Ellington AD. Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. PLANT METHODS 2022; 18:42. [PMID: 35351174 PMCID: PMC8966344 DOI: 10.1186/s13007-022-00867-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/01/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The construction and application of synthetic genetic circuits is frequently improved if gene expression can be orthogonally controlled, relative to the host. In plants, orthogonality can be achieved via the use of CRISPR-based transcription factors that are programmed to act on natural or synthetic promoters. The construction of complex gene circuits can require multiple, orthogonal regulatory interactions, and this in turn requires that the full programmability of CRISPR elements be adapted to non-natural and non-standard promoters that have few constraints on their design. Therefore, we have developed synthetic promoter elements in which regions upstream of the minimal 35S CaMV promoter are designed from scratch to interact via programmed gRNAs with dCas9 fusions that allow activation of gene expression. RESULTS A panel of three, mutually orthogonal promoters that can be acted on by artificial gRNAs bound by CRISPR regulators were designed. Guide RNA expression targeting these promoters was in turn controlled by either Pol III (U6) or ethylene-inducible Pol II promoters, implementing for the first time a fully artificial Orthogonal Control System (OCS). Following demonstration of the complete orthogonality of the designs, the OCS was tied to cellular metabolism by putting gRNA expression under the control of an endogenous plant signaling molecule, ethylene. The ability to form complex circuitry was demonstrated via the ethylene-driven, ratiometric expression of fluorescent proteins in single plants. CONCLUSIONS The design of synthetic promoters is highly generalizable to large tracts of sequence space, allowing Orthogonal Control Systems of increasing complexity to potentially be generated at will. The ability to tie in several different basal features of plant molecular biology (Pol II and Pol III promoters, ethylene regulation) to the OCS demonstrates multiple opportunities for engineering at the system level. Moreover, given the fungibility of the core 35S CaMV promoter elements, the derived synthetic promoters can potentially be utilized across a variety of plant species.
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Affiliation(s)
- Shaunak Kar
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
| | - Yogendra Bordiya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, TX, USA
| | - Nestor Rodriguez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C Gardner
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sibum Sung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
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6
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Li Y, Nowak CM, Pham U, Nguyen K, Bleris L. Cell morphology-based machine learning models for human cell state classification. NPJ Syst Biol Appl 2021; 7:23. [PMID: 34039992 PMCID: PMC8155075 DOI: 10.1038/s41540-021-00180-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Herein, we implement and access machine learning architectures to ascertain models that differentiate healthy from apoptotic cells using exclusively forward (FSC) and side (SSC) scatter flow cytometry information. To generate training data, colorectal cancer HCT116 cells were subjected to miR-34a treatment and then classified using a conventional Annexin V/propidium iodide (PI)-staining assay. The apoptotic cells were defined as Annexin V-positive cells, which include early and late apoptotic cells, necrotic cells, as well as other dying or dead cells. In addition to fluorescent signal, we collected cell size and granularity information from the FSC and SSC parameters. Both parameters are subdivided into area, height, and width, thus providing a total of six numerical features that informed and trained our models. A collection of logistical regression, random forest, k-nearest neighbor, multilayer perceptron, and support vector machine was trained and tested for classification performance in predicting cell states using only the six aforementioned numerical features. Out of 1046 candidate models, a multilayer perceptron was chosen with 0.91 live precision, 0.93 live recall, 0.92 live f value and 0.97 live area under the ROC curve when applied on standardized data. We discuss and highlight differences in classifier performance and compare the results to the standard practice of forward and side scatter gating, typically performed to select cells based on size and/or complexity. We demonstrate that our model, a ready-to-use module for any flow cytometry-based analysis, can provide automated, reliable, and stain-free classification of healthy and apoptotic cells using exclusively size and granularity information.
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Affiliation(s)
- Yi Li
- Bioengineering Department, University of Texas at Dallas, Richardson, TX, USA.,Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
| | - Chance M Nowak
- Bioengineering Department, University of Texas at Dallas, Richardson, TX, USA.,Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA.,Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Uyen Pham
- Bioengineering Department, University of Texas at Dallas, Richardson, TX, USA.,Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
| | - Khai Nguyen
- Bioengineering Department, University of Texas at Dallas, Richardson, TX, USA.,Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, Richardson, TX, USA. .,Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA. .,Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA.
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7
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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8
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Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
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Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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9
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Gutiérrez-González M, Latorre Y, Zúñiga R, Aguillón JC, Molina MC, Altamirano C. Transcription factor engineering in CHO cells for recombinant protein production. Crit Rev Biotechnol 2019; 39:665-679. [PMID: 31030575 DOI: 10.1080/07388551.2019.1605496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The continuous increase of approved biopharmaceutical products drives the development of more efficient recombinant protein expression systems. Chinese hamster ovary (CHO) cells are the mainstay for this purpose but have some drawbacks, such as low levels of expression. Several strategies have been applied to increase the productivity of CHO cells with different outcomes. Transcription factor (TF) engineering has emerged as an interesting and successful approach, as these proteins can act as master regulators; the expression and function of a TF can be controlled by small molecules, and it is possible to design tailored TFs and promoters with desired features. To date, the majority of studies have focused on the use of TFs with growth, metabolic, cell cycle or endoplasmic reticulum functions, although there is a trend to develop new, synthetic TFs. Moreover, new synthetic biological approaches are showing promising advances for the development of specific TFs, even with tailored ligand sensitivity. In this article, we summarize the strategies to increase recombinant protein expression by modulating and designing TFs and with advancements in synthetic biology. We also illustrate how this class of proteins can be used to develop more robust expression systems.
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Affiliation(s)
| | - Yesenia Latorre
- b Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso , Valparaíso , Chile
| | - Roberto Zúñiga
- a Centro de InmunoBiotecnología, Universidad de Chile , Santiago , Chile
| | | | | | - Claudia Altamirano
- b Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso , Valparaíso , Chile
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10
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Schreiber T, Prange A, Hoppe T, Tissier A. Split-TALE: A TALE-Based Two-Component System for Synthetic Biology Applications in Planta. PLANT PHYSIOLOGY 2019; 179:1001-1012. [PMID: 30643014 PMCID: PMC6393785 DOI: 10.1104/pp.18.01218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/02/2019] [Indexed: 05/20/2023]
Abstract
Transcription activator-like effectors (TALEs) are bacterial Type-III effector proteins from phytopathogenic Xanthomonas species that act as transcription factors in plants. The modular DNA-binding domain of TALEs can be reprogrammed to target nearly any DNA sequence. Here, we designed and optimized a two-component AND-gate system for synthetic circuits in plants based on TALEs. In this system, named split-TALE (sTALE), the TALE DNA binding domain and the transcription activation domain are separated and each fused to protein interacting domains. Physical interaction of interacting domains leads to TALE-reconstitution and can be monitored by reporter gene induction. This setup was used for optimization of the sTALE scaffolds, which result in an AND-gate system with an improved signal-to-noise ratio. We also provide a toolkit of ready-to-use vectors and single modules compatible with Golden Gate cloning and MoClo syntax. In addition to its implementation in synthetic regulatory circuits, the sTALE system allows the analysis of protein-protein interactions in planta.
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Affiliation(s)
- Tom Schreiber
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Anja Prange
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Tina Hoppe
- Department of Genetics, Institute for Biology, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
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11
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Geiger-Schuller K, Mitra J, Ha T, Barrick D. Functional instability allows access to DNA in longer transcription Activator-Like effector (TALE) arrays. eLife 2019; 8:38298. [PMID: 30810525 PMCID: PMC6461438 DOI: 10.7554/elife.38298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
Transcription activator-like effectors (TALEs) bind DNA through an array of tandem 34-residue repeats. How TALE repeat domains wrap around DNA, often extending more than 1.5 helical turns, without using external energy is not well understood. Here, we examine the kinetics of DNA binding of TALE arrays with varying numbers of identical repeats. Single molecule fluorescence analysis and deterministic modeling reveal conformational heterogeneity in both the free- and DNA-bound TALE arrays. Our findings, combined with previously identified partly folded states, indicate a TALE instability that is functionally important for DNA binding. For TALEs forming less than one superhelical turn around DNA, partly folded states inhibit DNA binding. In contrast, for TALEs forming more than one turn, partly folded states facilitate DNA binding, demonstrating a mode of ‘functional instability’ that facilitates macromolecular assembly. Increasing repeat number slows down interconversion between the various DNA-free and DNA-bound states. The DNA contains all the information needed to build an organism. It is made up of two strands that wind around each other like a twisted ladder to form the double helix. The strands consist of sugar and phosphate molecules, which attach to one of for bases. Genes are built from DNA, and contain specific sequences of these bases. Being able to modify DNA by deleting, inserting or changing certain sequences allows researchers to engineer tissues or even organisms for therapeutical and practical applications. One of these gene editing tools is the so-called transcription activator-like effector protein (or TALE for short). TALE proteins are derived from bacteria and are built from simple repeating units that can be linked to form a string-like structure. They have been found to be unstable proteins. To bind to DNA, TALES need to follow the shape of the double helix, adopting a spiral structure, but how exactly TALE proteins thread their way around the DNA is not clear. To investigate this, Geiger-Schuller et al. monitored single TALE units using fluorescent microscopy. This way, they could exactly measure the time it takes for single TALE proteins to bind and release DNA. The results showed that some TALE proteins bind DNA quickly, whereas others do this slowly. Using a computer model to analyze the different speeds of binding suggested that the fast binding comes from partly unfolded proteins that quickly associate with DNA, and that the slow binding comes from rigid, folded TALE proteins, which have a harder time wrapping around DNA. This suggest that the unstable nature of TALEs, helps these proteins to bind to DNA and turn on genes. These findings will help to design future TALE-based gene editing tools and also provide more insight into how large molecules can assemble into complex structures. A next step will be to identify TALE repeats with unstable states and to test TALE gene editing tools that have intentionally placed unstable units.
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Affiliation(s)
- Kathryn Geiger-Schuller
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, United States
| | - Jaba Mitra
- Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, United States
| | - Taekjip Ha
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, United States.,Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, United States.,Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States.,Howard Hughes Medical Institute, Baltimore, United States
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, United States
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12
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Wheat genome editing expedited by efficient transformation techniques: Progress and perspectives. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2017.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Abstract
The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.
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Affiliation(s)
- Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708; , .,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708; , .,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710
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14
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Techniques and strategies employing engineered transcription factors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Geiger-Schuller K, Barrick D. Broken TALEs: Transcription Activator-like Effectors Populate Partly Folded States. Biophys J 2017; 111:2395-2403. [PMID: 27926841 DOI: 10.1016/j.bpj.2016.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/14/2023] Open
Abstract
Transcription activator-like effector proteins (TALEs) contain large numbers of repeats that bind double-stranded DNA, wrapping around DNA to form a continuous superhelix. Since unbound TALEs retain superhelical structure, it seems likely that DNA binding requires a significant structural distortion or partial unfolding. In this study, we use nearest-neighbor "Ising" analysis of consensus TALE (cTALE) repeat unfolding to quantify intrinsic folding free energies, coupling energies between repeats, and the free energy distribution of partly unfolded states, and to determine how those energies depend on the sequence that determines DNA-specificity (called the "RVD"). We find a moderate level of cooperativity for both the HD and NS RVD sequences (stabilizing interfaces combined with unstable repeats), as has been seen in other linear repeat proteins. Surprisingly, RVD sequence identity influences both the overall stability and the balance of intrinsic repeat stability and interfacial coupling energy. Using parameters from the Ising analysis, we have analyzed the distribution of partly folded states as a function of cTALE length and RVD sequence. We find partly unfolded states where one or more repeats are unfolded to be energetically accessible. Mixing repeats with different RVD sequences increases the population of partially folded states. Local folding free energies plateau for central repeats, suggesting that TALEs access partially folded states where a single internal repeat is unfolded while adjacent repeats remain folded. This breakage should allow TALEs to access superhelically-broken states, and may facilitate DNA binding.
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Affiliation(s)
- Kathryn Geiger-Schuller
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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16
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Abstract
Epigenome editing aims for an introduction or removal of chromatin marks at a defined genomic region using artificial EpiEffectors resulting in a modulation of the activity of the targeted functional DNA elements. Rationally designed EpiEffectors consist of a targeting DNA-binding module (such as a zinc finger protein, TAL effector, or CRISPR/Cas complex) and usually, but not exclusively, a catalytic domain of a chromatin-modifying enzyme. Epigenome editing opens a completely new strategy for basic research of the central nervous system and causal treatment of psychiatric and neurological diseases, because rewriting of epigenetic information can lead to the direct and durable control of the expression of disease-associated genes. Here, we review current advances in the design of locus- and allele-specific DNA-binding modules, approaches for spatial, and temporal control of EpiEffectors and discuss some examples of existing and propose new potential therapeutic strategies based on epigenome editing for treatment of neurodegenerative and psychiatric diseases. These include the targeted silencing of disease-associated genes or activation of neuroprotective genes which may be applied in Alzheimer's and Parkinson's diseases or the control of addiction and depression. Moreover, we discuss allele-specific epigenome editing as novel therapeutic approach for imprinting disorders, Huntington's disease and Rett syndrome.
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17
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Axton RA, Haideri SS, Lopez-Yrigoyen M, Taylor HA, Forrester LM. SplitAx: A novel method to assess the function of engineered nucleases. PLoS One 2017; 12:e0171698. [PMID: 28212417 PMCID: PMC5315338 DOI: 10.1371/journal.pone.0171698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/24/2017] [Indexed: 12/29/2022] Open
Abstract
Engineered nucleases have been used to generate knockout or reporter cell lines and a range of animal models for human disease. These new technologies also hold great promise for therapeutic genome editing. Current methods to evaluate the activity of these nucleases are time consuming, require extensive optimization and are hampered by readouts with low signals and high background. We have developed a simple and easy to perform method (SplitAx) that largely addresses these issues and provides a readout of nuclease activity. The assay involves splitting the N-terminal (amino acid 1-158) coding region of GFP and an out-of-frame of C-terminal region with a nuclease binding site sequence. Following exposure to the test nuclease, cutting and repair by error prone non-homologous end joining (NHEJ) restores the reading frame resulting in the production of a full length fluorescent GFP protein. Fluorescence can also be restored by complementation between the N-terminal and C-terminal coding sequences in trans. We demonstrate successful use of the SplitAx assay to assess the function of zinc finger nucleases, CRISPR hCAS9 and TALENS. We also test the activity of multiple gRNAs in CRISPR/hCas9/D10A systems. The zinc finger nucleases and guide RNAs that showed functional activity in the SplitAx assay were then used successfully to target the endogenous AAVS1, SOX6 and Cfms loci. This simple method can be applied to other unrelated proteins such as ZsGreen1 and provides a test system that does not require complex optimization.
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Affiliation(s)
- Richard A. Axton
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Sharmin S. Haideri
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Martha Lopez-Yrigoyen
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Helen A. Taylor
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Lesley M. Forrester
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
- * E-mail:
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18
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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: 148] [Impact Index Per Article: 18.5] [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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19
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Schukur L, Fussenegger M. Engineering of synthetic gene circuits for (re-)balancing physiological processes in chronic diseases. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:402-22. [DOI: 10.1002/wsbm.1345] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/12/2016] [Accepted: 04/26/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Lina Schukur
- Department of Biosystems Science and Engineering; ETH Zurich; Basel Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zurich; Basel Switzerland
- Faculty of Science; University of Basel; Basel Switzerland
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20
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Barbon E, Pignani S, Branchini A, Bernardi F, Pinotti M, Bovolenta M. An engineered tale-transcription factor rescues transcription of factor VII impaired by promoter mutations and enhances its endogenous expression in hepatocytes. Sci Rep 2016; 6:28304. [PMID: 27341548 PMCID: PMC4920032 DOI: 10.1038/srep28304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/02/2016] [Indexed: 01/24/2023] Open
Abstract
Tailored approaches to restore defective transcription responsible for severe diseases have been poorly explored. We tested transcription activator-like effectors fused to an activation domain (TALE-TFs) in a coagulation factor VII (FVII) deficiency model. In this model, the deficiency is caused by the −94C > G or −61T > G mutation, which abrogate the binding of Sp1 or HNF-4 transcription factors. Reporter assays in hepatoma HepG2 cells naturally expressing FVII identified a single TALE-TF (TF4) that, by targeting the region between mutations, specifically trans-activated both the variant (>100-fold) and wild-type (20–40-fold) F7 promoters. Importantly, in the genomic context of transfected HepG2 and transduced primary hepatocytes, TF4 increased F7 mRNA and protein levels (2- to 3-fold) without detectable off-target effects, even for the homologous F10 gene. The ectopic F7 expression in renal HEK293 cells was modestly affected by TF4 or by TALE-TF combinations. These results provide experimental evidence for TALE-TFs as gene-specific tools useful to counteract disease-causing promoter mutations.
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Affiliation(s)
- Elena Barbon
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Silvia Pignani
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy.,LTTA Center, University of Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy.,LTTA Center, University of Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy.,LTTA Center, University of Ferrara, Italy
| | - Matteo Bovolenta
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
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21
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Lee HB, Sundberg BN, Sigafoos AN, Clark KJ. Genome Engineering with TALE and CRISPR Systems in Neuroscience. Front Genet 2016; 7:47. [PMID: 27092173 PMCID: PMC4821859 DOI: 10.3389/fgene.2016.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/16/2016] [Indexed: 12/26/2022] Open
Abstract
Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience.
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Affiliation(s)
- Han B Lee
- Neurobiology of Disease Graduate Program, Mayo Graduate School Rochester, MN, USA
| | - Brynn N Sundberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Ashley N Sigafoos
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Karl J Clark
- Neurobiology of Disease Graduate Program, Mayo Graduate SchoolRochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo ClinicRochester, MN, USA
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22
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Copeland MF, Politz MC, Johnson CB, Markley AL, Pfleger BF. A transcription activator-like effector (TALE) induction system mediated by proteolysis. Nat Chem Biol 2016; 12:254-60. [PMID: 26854666 PMCID: PMC4809019 DOI: 10.1038/nchembio.2021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/31/2015] [Indexed: 12/16/2022]
Abstract
Simple and predictable trans-acting regulatory tools are needed in the fields of synthetic biology and metabolic engineering to build complex genetic circuits and optimize the levels of native and heterologous gene products. Transcription activator-like effectors (TALEs) are bacterial virulence factors that have recently gained traction in biotechnology applications due to their customizable DNA binding specificity. In this work we expand the versatility of these transcription factors to create an inducible TALE system by inserting tobacco-etch virus (TEV) protease recognition sites into the TALE backbone. The resulting engineered TALEs maintain transcriptional repression of their target genes in Escherichia coli, but are degraded following the induction of the TEV protease, thereby promoting expression of the previously repressed target gene of interest. This TALE-TEV technology enables both repression and induction of plasmid or chromosomal target genes in a manner analogous to traditional repressor proteins but with the added flexibility of being operator agnostic.
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Affiliation(s)
- Matthew F Copeland
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Mark C Politz
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Charles B Johnson
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Andrew L Markley
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Brian F Pfleger
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
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23
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Li Y, Mendiratta S, Ehrhardt K, Kashyap N, White MA, Bleris L. Exploiting the CRISPR/Cas9 PAM Constraint for Single-Nucleotide Resolution Interventions. PLoS One 2016; 11:e0144970. [PMID: 26788852 PMCID: PMC4720446 DOI: 10.1371/journal.pone.0144970] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/27/2015] [Indexed: 01/03/2023] Open
Abstract
CRISPR/Cas9 is an enabling RNA-guided technology for genome targeting and engineering. An acute DNA binding constraint of the Cas9 protein is the Protospacer Adjacent Motif (PAM). Here we demonstrate that the PAM requirement can be exploited to specifically target single-nucleotide heterozygous mutations while exerting no aberrant effects on the wild-type alleles. Specifically, we target the heterozygous G13A activating mutation of KRAS in colorectal cancer cells and we show reversal of drug resistance to a MEK small-molecule inhibitor. Our study introduces a new paradigm in genome editing and therapeutic targeting via the use of gRNA to guide Cas9 to a desired protospacer adjacent motif.
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Affiliation(s)
- Yi Li
- Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
- Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
| | - Saurabh Mendiratta
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States of America
| | - Kristina Ehrhardt
- Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
- Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
| | - Neha Kashyap
- Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
- Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
| | - Michael A. White
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States of America
| | - Leonidas Bleris
- Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
- Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
- Electrical Engineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States of America
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24
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Lonzarić J, Lebar T, Majerle A, Manček-Keber M, Jerala R. Locked and proteolysis-based transcription activator-like effector (TALE) regulation. Nucleic Acids Res 2016; 44:1471-81. [PMID: 26748097 PMCID: PMC4756844 DOI: 10.1093/nar/gkv1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/26/2015] [Indexed: 11/13/2022] Open
Abstract
Development of orthogonal, designable and adjustable transcriptional regulators is an important goal of synthetic biology. Their activity has been typically modulated through stimulus-induced oligomerization or interaction between the DNA-binding and activation/repression domain. We exploited a feature of the designable Transcription activator-like effector (TALE) DNA-binding domain that it winds around the DNA which allows to topologically prevent it from binding by intramolecular cyclization. This new approach was investigated through noncovalent ligand-induced cyclization or through a covalent split intein cyclization strategy, where the topological inhibition of DNA binding by cyclization and its restoration by a proteolytic release of the topologic constraint was expected. We show that locked TALEs indeed have diminished DNA binding and regain full transcriptional activity by stimulation with the rapamycin ligand or site-specific proteolysis of the peptide linker, with much higher level of activation than rapamycin-induced heterodimerization. Additionally, we demonstrated reversibility, activation of genomic targets and implemented logic gates based on combinations of protein cyclization, proteolytic cleavage and ligand-induced dimerization, where the strongest fold induction was achieved by the proteolytic cleavage of a repression domain from a linear TALE.
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Affiliation(s)
- Jan Lonzarić
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Tina Lebar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Andreja Majerle
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Mateja Manček-Keber
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
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25
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Thakore PI, Gersbach CA. Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors. Methods Mol Biol 2016; 1338:71-88. [PMID: 26443215 DOI: 10.1007/978-1-4939-2932-0_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versatile method to activate or repress gene expression. Described here are methods to design, assemble, and test TALE transcription factors (TALE-TFs) for control of endogenous gene expression. In this protocol, TALE arrays are constructed by Golden Gate cloning and tested for activity by transfection and quantitative RT-PCR. These methods for engineering TALE-TFs are useful for studies in reverse genetics and genomics, synthetic biology, and gene therapy.
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Affiliation(s)
- Pratiksha I Thakore
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708-0281, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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26
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Brown AJ, James DC. Precision control of recombinant gene transcription for CHO cell synthetic biology. Biotechnol Adv 2015; 34:492-503. [PMID: 26721629 DOI: 10.1016/j.biotechadv.2015.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/11/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology.
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Affiliation(s)
- Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, England, United Kingdom
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, England, United Kingdom.
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27
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Discriminating direct and indirect connectivities in biological networks. Proc Natl Acad Sci U S A 2015; 112:12893-8. [PMID: 26420864 DOI: 10.1073/pnas.1507168112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Reverse engineering of biological pathways involves an iterative process between experiments, data processing, and theoretical analysis. Despite concurrent advances in quality and quantity of data as well as computing resources and algorithms, difficulties in deciphering direct and indirect network connections are prevalent. Here, we adopt the notions of abstraction, emulation, benchmarking, and validation in the context of discovering features specific to this family of connectivities. After subjecting benchmark synthetic circuits to perturbations, we inferred the network connections using a combination of nonparametric single-cell data resampling and modular response analysis. Intriguingly, we discovered that recovered weights of specific network edges undergo divergent shifts under differential perturbations, and that the particular behavior is markedly different between topologies. Our results point to a conceptual advance for reverse engineering beyond weight inference. Investigating topological changes under differential perturbations may address the longstanding problem of discriminating direct and indirect connectivities in biological networks.
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28
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Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, Reddy TE, Gersbach CA. Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. ACS Synth Biol 2015; 4:689-99. [PMID: 25494287 PMCID: PMC4475448 DOI: 10.1021/sb500322u] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genetic reprogramming holds great potential for disease modeling, drug screening, and regenerative medicine. Genetic reprogramming of mammalian cells is typically achieved by forced expression of natural transcription factors that control master gene networks and cell lineage specification. However, in many instances, the natural transcription factors do not induce a sufficiently robust response to completely reprogram cell phenotype. In this study, we demonstrate that protein engineering of the master transcription factor MyoD can enhance the conversion of human dermal fibroblasts and adult stem cells to a skeletal myocyte phenotype. Fusion of potent transcriptional activation domains to MyoD led to increased myogenic gene expression, myofiber formation, cell fusion, and global reprogramming of the myogenic gene network. This work supports a general strategy for synthetically enhancing the direct conversion between cell types that can be applied in both synthetic biology and regenerative medicine.
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Affiliation(s)
| | | | | | | | | | - Farshid Guilak
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | | | - Charles A. Gersbach
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
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29
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Cuculis L, Abil Z, Zhao H, Schroeder CM. Direct observation of TALE protein dynamics reveals a two-state search mechanism. Nat Commun 2015; 6:7277. [PMID: 26027871 PMCID: PMC4458887 DOI: 10.1038/ncomms8277] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/24/2015] [Indexed: 11/29/2022] Open
Abstract
Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process—a search state and a recognition state—facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state. TALEs are programmable DNA-binding proteins with practical use in genome engineering and synthetic biology. Here the authors use single-molecule fluorescence microscopy to establish that TALE proteins function using two distinct DNA-interaction modes during sequence-specific target search.
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Affiliation(s)
- Luke Cuculis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Zhanar Abil
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Huimin Zhao
- 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [3] Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [4] Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801 USA [5] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Charles M Schroeder
- 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [3] Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801 USA [4] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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30
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Falahi F, Sgro A, Blancafort P. Epigenome engineering in cancer: fairytale or a realistic path to the clinic? Front Oncol 2015; 5:22. [PMID: 25705610 PMCID: PMC4319383 DOI: 10.3389/fonc.2015.00022] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/19/2015] [Indexed: 01/15/2023] Open
Abstract
Epigenetic modifications such as histone post-transcriptional modifications, DNA methylation, and non-protein-coding RNAs organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations) are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs) have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide “off-target” effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA-binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering). Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.
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Affiliation(s)
- Fahimeh Falahi
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Agustin Sgro
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
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31
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Li Y, Jiang Y, Chen H, Liao W, Li Z, Weiss R, Xie Z. Modular construction of mammalian gene circuits using TALE transcriptional repressors. Nat Chem Biol 2015; 11:207-213. [PMID: 25643171 PMCID: PMC4333066 DOI: 10.1038/nchembio.1736] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 11/25/2014] [Indexed: 01/14/2023]
Abstract
An important goal of synthetic biology is the rational design and predictable implementation of synthetic gene circuits using standardized and interchangeable parts. However, engineering of complex circuits in mammalian cells is currently limited by the availability of well-characterized and orthogonal transcriptional repressors. Here, we introduce a library of 26 reversible transcription activator-like effector repressors (TALERs) that bind newly designed hybrid promoters and exert transcriptional repression through steric hindrance of key transcriptional initiation elements. We demonstrate that using the input-output transfer curves of our TALERs enables accurate prediction of the behavior of modularly assembled TALER cascade and switch circuits. We also show that TALER switches employing feedback regulation exhibit improved accuracy for microRNA-based HeLa cancer cell classification versus HEK293 cells. Our TALER library is a valuable toolkit for modular engineering of synthetic circuits, enabling programmable manipulation of mammalian cells and helping elucidate design principles of coupled transcriptional and microRNA-mediated post-transcriptional regulation.
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Affiliation(s)
- Yinqing Li
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames St, Cambridge MA 02142, USA
| | - Yun Jiang
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - He Chen
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Weixi Liao
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zhihua Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118
| | - Ron Weiss
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames St, Cambridge MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames St, Cambridge MA 02142, USA
| | - Zhen Xie
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics; Department of Automation, Tsinghua University, Beijing 100084, China
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32
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Abdallah NA, Prakash CS, McHughen AG. Genome editing for crop improvement: Challenges and opportunities. GM CROPS & FOOD 2015; 6:183-205. [PMID: 26930114 PMCID: PMC5033222 DOI: 10.1080/21645698.2015.1129937] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Genome or gene editing includes several new techniques to help scientists precisely modify genome sequences. The techniques also enables us to alter the regulation of gene expression patterns in a pre-determined region and facilitates novel insights into the functional genomics of an organism. Emergence of genome editing has brought considerable excitement especially among agricultural scientists because of its simplicity, precision and power as it offers new opportunities to develop improved crop varieties with clear-cut addition of valuable traits or removal of undesirable traits. Research is underway to improve crop varieties with higher yields, strengthen stress tolerance, disease and pest resistance, decrease input costs, and increase nutritional value. Genome editing encompasses a wide variety of tools using either a site-specific recombinase (SSR) or a site-specific nuclease (SSN) system. Both systems require recognition of a known sequence. The SSN system generates single or double strand DNA breaks and activates endogenous DNA repair pathways. SSR technology, such as Cre/loxP and Flp/FRT mediated systems, are able to knockdown or knock-in genes in the genome of eukaryotes, depending on the orientation of the specific sites (loxP, FLP, etc.) flanking the target site. There are 4 main classes of SSN developed to cleave genomic sequences, mega-nucleases (homing endonuclease), zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and the CRISPR/Cas nuclease system (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein). The recombinase mediated genome engineering depends on recombinase (sub-) family and target-site and induces high frequencies of homologous recombination. Improving crops with gene editing provides a range of options: by altering only a few nucleotides from billions found in the genomes of living cells, altering the full allele or by inserting a new gene in a targeted region of the genome. Due to its precision, gene editing is more precise than either conventional crop breeding methods or standard genetic engineering methods. Thus this technology is a very powerful tool that can be used toward securing the world's food supply. In addition to improving the nutritional value of crops, it is the most effective way to produce crops that can resist pests and thrive in tough climates. There are 3 types of modifications produced by genome editing; Type I includes altering a few nucleotides, Type II involves replacing an allele with a pre-existing one and Type III allows for the insertion of new gene(s) in predetermined regions in the genome. Because most genome-editing techniques can leave behind traces of DNA alterations evident in a small number of nucleotides, crops created through gene editing could avoid the stringent regulation procedures commonly associated with GM crop development. For this reason many scientists believe plants improved with the more precise gene editing techniques will be more acceptable to the public than transgenic plants. With genome editing comes the promise of new crops being developed more rapidly with a very low risk of off-target effects. It can be performed in any laboratory with any crop, even those that have complex genomes and are not easily bred using conventional methods.
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Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol 2014; 3:880-91. [PMID: 25360681 PMCID: PMC4277766 DOI: 10.1021/sb5002856] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotic regulatory proteins respond to diverse signals and represent a rich resource for building synthetic sensors and circuits. The TetR family contains >10(5) members that use a simple mechanism to respond to stimuli and bind distinct DNA operators. We present a platform that enables the transfer of these regulators to mammalian cells, which is demonstrated using human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells. The repressors are modified to include nuclear localization signals (NLS) and responsive promoters are built by incorporating multiple operators. Activators are also constructed by modifying the protein to include a VP16 domain. Together, this approach yields 15 new regulators that demonstrate 19- to 551-fold induction and retain both the low levels of crosstalk in DNA binding specificity observed between the parent regulators in Escherichia coli, as well as their dynamic range of activity. By taking advantage of the DAPG small molecule sensing mediated by the PhlF repressor, we introduce a new inducible system with 50-fold induction and a threshold of 0.9 μM DAPG, which is comparable to the classic Dox-induced TetR system. A set of NOT gates is constructed from the new repressors and their response function quantified. Finally, the Dox- and DAPG- inducible systems and two new activators are used to build a synthetic enhancer (fuzzy AND gate), requiring the coordination of 5 transcription factors organized into two layers. This work introduces a generic approach for the development of mammalian genetic sensors and circuits to populate a toolbox that can be applied to diverse applications from biomanufacturing to living therapeutics.
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Affiliation(s)
- Brynne C. Stanton
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Velia Siciliano
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amar Ghodasara
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liliana Wroblewska
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin Clancy
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Axel C. Trefzer
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Jonathan D. Chesnut
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Ron Weiss
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Abstract
Engineered transcription activator-like effectors, or TALEs, have emerged as a new class of designer DNA-binding proteins. Their DNA recognition sites can be specified with great flexibility. When fused to appropriate transcriptional regulatory domains, they can serve as designer transcription factors, modulating the activity of targeted promoters. We created tet operator (tetO)-specific TALEs (tetTALEs), with an identical DNA-binding site as the Tet repressor (TetR) and the TetR-based transcription factors that are extensively used in eukaryotic transcriptional control systems. Different constellations of tetTALEs and tetO modified chromosomal transcription units were analyzed for their efficacy in mammalian cells. We find that tetTALE-silencers can entirely abrogate expression from the strong human EF1α promoter when binding upstream of the transcriptional control sequence. Remarkably, the DNA-binding domain of tetTALE alone can effectively counteract trans-activation mediated by the potent tettrans-activator and also directly interfere with RNA polymerase II transcription initiation from the strong CMV promoter. Our results demonstrate that TALEs can act as highly versatile tools in genetic engineering, serving as trans-activators, trans-silencers and also competitive repressors.
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Affiliation(s)
- Jeannette Werner
- Helmholtz-Zentrum Geesthacht (HZG), Institute of Biomaterial Science, Teltow 14513, Germany Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Föhrer Strasse 15, 13353 Berlin, Germany
| | - Manfred Gossen
- Helmholtz-Zentrum Geesthacht (HZG), Institute of Biomaterial Science, Teltow 14513, Germany Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Föhrer Strasse 15, 13353 Berlin, Germany
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35
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Mercer AC, Gaj T, Sirk SJ, Lamb BM, Barbas CF. Regulation of endogenous human gene expression by ligand-inducible TALE transcription factors. ACS Synth Biol 2014; 3:723-30. [PMID: 24251925 PMCID: PMC4097969 DOI: 10.1021/sb400114p] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The construction of increasingly sophisticated synthetic biological circuits is dependent on the development of extensible tools capable of providing specific control of gene expression in eukaryotic cells. Here, we describe a new class of synthetic transcription factors that activate gene expression in response to extracellular chemical stimuli. These inducible activators consist of customizable transcription activator-like effector (TALE) proteins combined with steroid hormone receptor ligand-binding domains. We demonstrate that these ligand-responsive TALE transcription factors allow for tunable and conditional control of gene activation and can be used to regulate the expression of endogenous genes in human cells. Since TALEs can be designed to recognize any contiguous DNA sequence, the conditional gene regulatory system described herein will enable the design of advanced synthetic gene networks.
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Affiliation(s)
- Andrew C. Mercer
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Thomas Gaj
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shannon J. Sirk
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brian M. Lamb
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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36
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Moore R, Chandrahas A, Bleris L. Transcription activator-like effectors: a toolkit for synthetic biology. ACS Synth Biol 2014; 3:708-16. [PMID: 24933470 PMCID: PMC4210167 DOI: 10.1021/sb400137b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Transcription
activator-like effectors (TALEs) are proteins secreted
by Xanthomonas bacteria to aid the infection of plant
species. TALEs assist infections by binding to specific DNA sequences
and activating the expression of host genes. Recent results show that
TALE proteins consist of a central repeat domain, which determines
the DNA targeting specificity and can be rapidly synthesized de novo. Considering the highly modular nature of TALEs,
their versatility, and the ease of constructing these proteins, this
technology can have important implications for synthetic biology applications.
Here, we review developments in the area with a particular focus on
modifications for custom and controllable gene regulation.
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Affiliation(s)
- Richard Moore
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080 United States
- Center
for Systems Biology, The University of Texas at Dallas, 800 West Campbell
Road, Richardson, Texas 75080 United States
| | - Anita Chandrahas
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080 United States
- Center
for Systems Biology, The University of Texas at Dallas, 800 West Campbell
Road, Richardson, Texas 75080 United States
| | - Leonidas Bleris
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080 United States
- Electrical
Engineering Department, The University of Texas at Dallas, 800
West Campbell Road, Richardson, Texas 75080 United States
- Center
for Systems Biology, The University of Texas at Dallas, 800 West Campbell
Road, Richardson, Texas 75080 United States
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37
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Role of epigenetics in expression of recombinant proteins from mammalian cells. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.47] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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38
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Copeland MF, Politz MC, Pfleger BF. Application of TALEs, CRISPR/Cas and sRNAs as trans-acting regulators in prokaryotes. Curr Opin Biotechnol 2014; 29:46-54. [PMID: 24632195 PMCID: PMC4162867 DOI: 10.1016/j.copbio.2014.02.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/28/2014] [Accepted: 02/13/2014] [Indexed: 01/09/2023]
Abstract
The last several years have witnessed an explosion in the understanding and use of novel, versatile trans-acting elements. TALEs, CRISPR/Cas, and sRNAs can be easily fashioned to bind any specific sequence of DNA (TALEs, CRISPR/Cas) or RNA (sRNAs) because of the simple rules governing their interactions with nucleic acids. This unique property enables these tools to repress the expression of genes at the transcriptional or post-transcriptional levels, respectively, without prior manipulation of cis-acting and/or chromosomal target DNA sequences. These tools are now being harnessed by synthetic biologists, particularly those in the eukaryotic community, for genome-wide regulation, editing, or epigenetic studies. Here we discuss the exciting opportunities for using TALEs, CRISPR/Cas, and sRNAs as synthetic trans-acting regulators in prokaryotes.
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Affiliation(s)
- Matthew F Copeland
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, USA
| | - Mark C Politz
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, USA
| | - Brian F Pfleger
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, USA.
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39
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Oishi K, Klavins E. Framework for engineering finite state machines in gene regulatory networks. ACS Synth Biol 2014; 3:652-65. [PMID: 24932713 DOI: 10.1021/sb4001799] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Finite state machines are fundamental computing devices at the core of many models of computation. In biology, finite state machines are commonly used as models of development in multicellular organisms. However, it remains unclear to what extent cells can remember state, how they can transition from one state to another reliably, and whether the existing parts available to the synthetic biologist are sufficient to implement specified finite state machines in living cells. Furthermore, how complex multicellular behaviors can be realized by multiple cells coordinating their states with signaling, growth, and division is not well understood. Here, we describe a method by which any finite state machine can be built using nothing more than a suitably engineered network of readily available repressing transcription factors. In particular, we show the mathematical equivalence of finite state machines with a Boolean model of gene regulatory networks. We describe how such networks can be realized with a small class of promoters and transcription factors. To demonstrate the effectiveness of our approach, we show that the behavior of the coarse grained ideal Boolean network model approximates a fine grained delay differential equation model of gene expression. Finally, we explore a framework for the design of more complex systems via an example, synthetic bacterial microcolony edge detection, that illustrates how finite state machines could be used together with cell signaling to construct novel multicellular behaviors.
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Affiliation(s)
- Kevin Oishi
- Department of Electrical
Engineering, University of Washington, Seattle 98195, United States
| | - Eric Klavins
- Department of Electrical
Engineering, University of Washington, Seattle 98195, United States
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40
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Scott JNF, Kupinski AP, Boyes J. Targeted genome regulation and modification using transcription activator-like effectors. FEBS J 2014; 281:4583-97. [DOI: 10.1111/febs.12973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/07/2014] [Accepted: 08/13/2014] [Indexed: 11/30/2022]
Affiliation(s)
- James N. F. Scott
- School of Molecular and Cellular Biology; Faculty of Biological Sciences; University of Leeds; UK
| | - Adam P. Kupinski
- School of Molecular and Cellular Biology; Faculty of Biological Sciences; University of Leeds; UK
| | - Joan Boyes
- School of Molecular and Cellular Biology; Faculty of Biological Sciences; University of Leeds; UK
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41
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Abstract
![]()
Decoders
are combinational circuits that convert information from n inputs to a maximum of 2n outputs.
This operation is of major importance in computing systems yet it
is vastly underexplored in synthetic biology. Here, we present a synthetic
gene network architecture that operates as a biological decoder in
human cells, converting 2 inputs to 4 outputs. As a proof-of-principle,
we use small molecules to emulate the two inputs and fluorescent reporters
as the corresponding four outputs. The experiments are performed using
transient transfections in human kidney embryonic cells and the characterization
by fluorescence microscopy and flow cytometry. We show a clear separation
between the ON and OFF mean fluorescent intensity states. Additionally,
we adopt the integrated mean fluorescence intensity for the characterization
of the circuit and show that this metric is more robust to transfection
conditions when compared to the mean fluorescent intensity. To conclude,
we present the first implementation of a genetic decoder. This combinational
system can be valuable toward engineering higher-order circuits as
well as accommodate a multiplexed interface with endogenous cellular
functions.
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Affiliation(s)
- Michael Guinn
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
- Center
for Systems Biology, The University of Texas at Dallas, NSERL 4.708,
800 West Campbell Road, Richardson, Texas 75080, United States
| | - Leonidas Bleris
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
- Electrical
Engineering Department, The University of Texas at Dallas, 800
West Campbell Road, Richardson, Texas 75080, United States
- Center
for Systems Biology, The University of Texas at Dallas, NSERL 4.708,
800 West Campbell Road, Richardson, Texas 75080, United States
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42
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Kabadi AM, Gersbach CA. Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. Methods 2014; 69:188-97. [PMID: 25010559 DOI: 10.1016/j.ymeth.2014.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/22/2022] Open
Abstract
Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications.
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Affiliation(s)
- Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, United States; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, United States.
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43
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 6:19-40. [PMID: 25349712 PMCID: PMC4207558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A. A. Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K. R. Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 85:209-18. [PMID: 25349712 DOI: 10.1007/s11103-014-0188-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 05/07/2023] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A A Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K R Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S P Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S M Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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Lange O, Binder A, Lahaye T. From dead leaf, to new life:
TAL
effectors as tools for synthetic biology. THE PLANT JOURNAL 2014; 78:753-771. [PMID: 24602153 DOI: 10.1111/tpj.12431] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Orlando Lange
- Department of General Genetics Centre for Plant Molecular Biology Eberhard‐Karls‐University Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany
| | - Andreas Binder
- Genetics Faculty of Biology I University of Munich Großhaderner Straße 2‐4 82152 Martinsried Germany
| | - Thomas Lahaye
- Department of General Genetics Centre for Plant Molecular Biology Eberhard‐Karls‐University Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany
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Bogdanove AJ. Principles and applications of TAL effectors for plant physiology and metabolism. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:99-104. [PMID: 24907530 PMCID: PMC4086460 DOI: 10.1016/j.pbi.2014.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 05/08/2014] [Accepted: 05/08/2014] [Indexed: 05/27/2023]
Abstract
Recent advances in DNA targeting allow unprecedented control over gene function and expression. Targeting based on TAL effectors is arguably the most promising for systems biology and metabolic engineering. Multiple, orthogonal TAL-effector reagents of different types can be used in the same cell. Furthermore, variation in base preferences of the individual structural repeats that make up the TAL effector DNA recognition domain makes targeting stringency tunable. Realized applications range from genome editing to epigenome modification to targeted gene regulation to chromatin labeling and capture. The principles that govern TAL effector DNA recognition make TAL effectors well suited for applications relevant to plant physiology and metabolism. TAL effector targeting has merits that are distinct from those of the RNA-based DNA targeting CRISPR/Cas9 system.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853, USA.
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47
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Li Y, Ehrhardt K, Zhang MQ, Bleris L. Assembly and validation of versatile transcription activator-like effector libraries. Sci Rep 2014; 4:4857. [PMID: 24798576 PMCID: PMC4010924 DOI: 10.1038/srep04857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/08/2014] [Indexed: 12/11/2022] Open
Abstract
The ability to perturb individual genes in genome-wide experiments has been instrumental in unraveling cellular and disease properties. Here we introduce, describe the assembly, and demonstrate the use of comprehensive and versatile transcription activator-like effector (TALE) libraries. As a proof of principle, we built an 11-mer library that covers all possible combinations of the nucleotides that determine the TALE-DNA binding specificity. We demonstrate the versatility of the methodology by constructing a constraint library, customized to bind to a known p53 motif. To verify the functionality in assays, we applied the 11-mer library in yeast-one-hybrid screens to discover TALEs that activate human SCN9A and miR-34b respectively. Additionally, we performed a genome-wide screen using the complete 11-mer library to confirm known genes that confer cycloheximide resistance in yeast. Considering the highly modular nature of TALEs and the versatility and ease of constructing these libraries we envision broad implications for high-throughput genomic assays.
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Affiliation(s)
- Yi Li
- 1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
| | - Kristina Ehrhardt
- 1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
| | - Michael Q Zhang
- 1] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Molecular and Cell Biology Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
| | - Leonidas Bleris
- 1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [3] Electrical Engineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
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48
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Hu J, Lei Y, Wong WK, Liu S, Lee KC, He X, You W, Zhou R, Guo JT, Chen X, Peng X, Sun H, Huang H, Zhao H, Feng B. Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors. Nucleic Acids Res 2014; 42:4375-90. [PMID: 24500196 PMCID: PMC3985678 DOI: 10.1093/nar/gku109] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/11/2014] [Accepted: 01/13/2014] [Indexed: 12/21/2022] Open
Abstract
The newly developed transcription activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression. In this article, we systematically investigated the potential of these new tools in activating the stringently silenced pluripotency gene Oct4 (Pou5f1) in mouse and human somatic cells. First, with a number of TALEs and sgRNAs targeting various regions in the mouse and human Oct4 promoters, we found that the most efficient TALE-VP64s bound around -120 to -80 bp, while highly effective sgRNAs targeted from -147 to -89-bp upstream of the transcription start sites to induce high activity of luciferase reporters. In addition, we observed significant transcriptional synergy when multiple TFs were applied simultaneously. Although individual TFs exhibited marginal activity to up-regulate endogenous gene expression, optimized combinations of TALE-VP64s could enhance endogenous Oct4 transcription up to 30-fold in mouse NIH3T3 cells and 20-fold in human HEK293T cells. More importantly, the enhancement of OCT4 transcription ultimately generated OCT4 proteins. Furthermore, examination of different epigenetic modifiers showed that histone acetyltransferase p300 could enhance both TALE-VP64 and sgRNA/dCas9-VP64 induced transcription of endogenous OCT4. Taken together, our study suggested that engineered TALE-TF and dCas9-TF are useful tools for modulating gene expression in mammalian cells.
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Affiliation(s)
- Jiabiao Hu
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Yong Lei
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Wing-Ki Wong
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Senquan Liu
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Kai-Chuen Lee
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Xiangjun He
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Wenxing You
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Rui Zhou
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Jun-Tao Guo
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Xiongfong Chen
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Xianlu Peng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Hao Sun
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - He Huang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Hui Zhao
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China, SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China, Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
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49
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A TAL effector repeat architecture for frameshift binding. Nat Commun 2014; 5:3447. [PMID: 24614980 DOI: 10.1038/ncomms4447] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/13/2014] [Indexed: 11/08/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are important Xanthomonas virulence factors that bind DNA via a unique tandem 34-amino-acid repeat domain to induce expression of plant genes. So far, TALE repeats are described to bind as a consecutive array to a consecutive DNA sequence, in which each repeat independently recognizes a single DNA base. This modular protein architecture enables the design of any desired DNA-binding specificity for biotechnology applications. Here we report that natural TALE repeats of unusual amino-acid sequence length break the strict one repeat-to-one base pair binding mode and introduce a local flexibility to TALE-DNA binding. This flexibility allows TALEs and TALE nucleases to recognize target sequence variants with single nucleotide deletions. The flexibility also allows TALEs to activate transcription at allelic promoters that otherwise confer resistance to the host plant.
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50
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Distinct DNA-based epigenetic switches trigger transcriptional activation of silent genes in human dermal fibroblasts. Sci Rep 2014; 4:3843. [PMID: 24457603 PMCID: PMC3900999 DOI: 10.1038/srep03843] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/18/2013] [Indexed: 12/22/2022] Open
Abstract
The influential role of the epigenome in orchestrating genome-wide transcriptional activation instigates the demand for the artificial genetic switches with distinct DNA sequence recognition. Recently, we developed a novel class of epigenetically active small molecules called SAHA-PIPs by conjugating selective DNA binding pyrrole-imidazole polyamides (PIPs) with the histone deacetylase inhibitor SAHA. Screening studies revealed that certain SAHA-PIPs trigger targeted transcriptional activation of pluripotency and germ cell genes in mouse and human fibroblasts, respectively. Through microarray studies and functional analysis, here we demonstrate for the first time the remarkable ability of thirty-two different SAHA-PIPs to trigger the transcriptional activation of exclusive clusters of genes and noncoding RNAs. QRT-PCR validated the microarray data, and some SAHA-PIPs activated therapeutically significant genes like KSR2. Based on the aforementioned results, we propose the potential use of SAHA-PIPs as reagents capable of targeted transcriptional activation.
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