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Jores T, Mueth NA, Tonnies J, Char SN, Liu B, Grillo-Alvarado V, Abbitt S, Anand A, Deschamps S, Diehn S, Gordon-Kamm B, Jiao S, Munkvold K, Snowgren H, Sardesai N, Fields S, Yang B, Cuperus JT, Queitsch C. Small DNA elements that act as both insulators and silencers in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612883. [PMID: 39345455 PMCID: PMC11429706 DOI: 10.1101/2024.09.13.612883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Insulators are cis-regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of eight large insulators to identify more than 100 fragments that block enhancer activity. The short fragments can be combined to generate more powerful insulators that abolish the capacity of the strong viral 35S enhancer to activate the 35S minimal promoter. Unexpectedly, when tested upstream of weak enhancers, these fragments act as silencers and repress transcription. Thus, these elements are capable of both insulating or repressing transcription dependent upon regulatory context. We validate our findings in stable transgenic Arabidopsis, maize, and rice plants. The short elements identified here should be useful building blocks for plant biotechnology efforts.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- CEPLAS – Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Nicholas A. Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, USA
| | - Si Nian Char
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Bo Liu
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Valentina Grillo-Alvarado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular & Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Ajith Anand
- Corteva Agriscience, Johnston, IA, USA
- Present address: MyFloraDNA, Sacramento, CA, USA
| | | | | | | | | | - Kathy Munkvold
- Corteva Agriscience, Johnston, IA, USA
- Present address: Foundation for Food & Agriculture Research, Washington, DC, USA
| | | | | | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Bing Yang
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Josh T. Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
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2
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Jiang L, Liu Y, Wen Z, Yang Y, Singer SD, Bennett D, Xu W, Su Z, Yu Z, Cohn J, Luo X, Liu Z, Chae H, Que Q, Liu Z. CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants. Transgenic Res 2022; 31:647-660. [PMID: 36053433 DOI: 10.1007/s11248-022-00326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 08/15/2022] [Indexed: 01/20/2023]
Abstract
Insulators in vertebrates play a role in genome architecture and orchestrate temporo-spatial enhancer-promoter interactions. In plants, insulators and their associated binding factors have not been documented as of yet, largely as a result of a lack of characterized insulators. In this study, we took a comprehensive strategy to identify and validate the enhancer-blocking insulator CW198. We show that a 1.08-kb CW198 fragment from Arabidopsis can, when interposed between an enhancer and a promoter, efficiently abrogate the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and tobacco plants. In plants, both transcriptional crosstalk and spreading of histone modifications were rarely detectable across CW198, which resembles the insulation property observed across the CTCF insulator in the mammalian genome. Taken together, our findings support that CW198 acts as an enhancer-blocking insulator in both Arabidopsis and tobacco. The significance of the present findings and their relevance to the mitigation of mutual interference between enhancers and promoters, as well as multiple promoters in transgenes, is discussed.
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Affiliation(s)
- Li Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhifeng Wen
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.,College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingjun Yang
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.,Forestry College, Henan University of Science and Technology, Luoyang, 471023, China
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Dennis Bennett
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhifang Yu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Josh Cohn
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Hyunsook Chae
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Qiudeng Que
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Zongrang Liu
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.
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Liu H, Jiang L, Wen Z, Yang Y, Singer SD, Bennett D, Xu W, Su Z, Yu Z, Cohn J, Chae H, Que Q, Liu Y, Liu C, Liu Z. Rice RS2-9, which is bound by transcription factor OSH1, blocks enhancer-promoter interactions in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:541-554. [PMID: 34773305 PMCID: PMC9303810 DOI: 10.1111/tpj.15574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/02/2021] [Indexed: 05/13/2023]
Abstract
Insulators characterized in Drosophila and mammals have been shown to play a key role in the restriction of promiscuous enhancer-promoter interactions, as well as reshaping the topological landscape of chromosomes. Yet the role of insulators in plants remains poorly understood, in large part because of a lack of well-characterized insulators and binding factor(s). In this study, we isolated a 1.2-kb RS2-9 insulator from the Oryza sativa (rice) genome that can, when interposed between an enhancer and promoter, efficiently block the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and Nicotiana tabacum (tobacco). In the rice genome, the genes flanking RS2-9 exhibit an absence of mutual transcriptional interactions, as well as a lack of histone modification spread. We further determined that O. sativa Homeobox 1 (OSH1) bound two regions of RS2-9, as well as over 50 000 additional sites in the rice genome, the majority of which resided in intergenic regions. Mutation of one of the two OSH1-binding sites in RS2-9 impaired insulation activity by up to 60%, whereas the mutation of both binding sites virtually abolished insulator function. We also demonstrated that OSH1 binding sites were associated with 72% of the boundaries of topologically associated domains (TADs) identified in the rice genome, which is comparable to the 77% of TAD boundaries bound by the insulator CCCTC-binding factor (CTCF) in mammals. Taken together, our findings indicate that OSH1-RS2-9 acts as a true insulator in plants, and highlight a potential role for OSH1 in gene insulation and topological organization in plant genomes.
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Affiliation(s)
- Huawei Liu
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Li Jiang
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Zhifeng Wen
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of HorticultureFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Yingjun Yang
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- Forestry CollegeHenan University of Science and TechnologyLuoyang471023China
| | - Stacy D. Singer
- Agriculture and Agri‐Food CanadaLethbridge Research and Development CentreLethbridgeAlbertaT1J 4B1Canada
| | - Dennis Bennett
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Zhifang Yu
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Jonathan Cohn
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Hyunsook Chae
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Qiudeng Que
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Yue Liu
- College of HorticultureQingdao Agricultural UniversityQingdao266109China
| | - Chang Liu
- Department of EpigeneticsUniversity of HohenheimStuttgart70599Germany
| | - Zongrang Liu
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
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4
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Chien CH, Huang LY, Lo SF, Chen LJ, Liao CC, Chen JJ, Chu YW. Using Machine Learning Approaches to Predict Target Gene Expression in Rice T-DNA Insertional Mutants. Front Genet 2021; 12:798107. [PMID: 34976025 PMCID: PMC8718795 DOI: 10.3389/fgene.2021.798107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
To change the expression of the flanking genes by inserting T-DNA into the genome is commonly used in rice functional gene research. However, whether the expression of a gene of interest is enhanced must be validated experimentally. Consequently, to improve the efficiency of screening activated genes, we established a model to predict gene expression in T-DNA mutants through machine learning methods. We gathered experimental datasets consisting of gene expression data in T-DNA mutants and captured the PROMOTER and MIDDLE sequences for encoding. In first-layer models, support vector machine (SVM) models were constructed with nine features consisting of information about biological function and local and global sequences. Feature encoding based on the PROMOTER sequence was weighted by logistic regression. The second-layer models integrated 16 first-layer models with minimum redundancy maximum relevance (mRMR) feature selection and the LADTree algorithm, which were selected from nine feature selection methods and 65 classified methods, respectively. The accuracy of the final two-layer machine learning model, referred to as TIMgo, was 99.3% based on fivefold cross-validation, and 85.6% based on independent testing. We discovered that the information within the local sequence had a greater contribution than the global sequence with respect to classification. TIMgo had a good predictive ability for target genes within 20 kb from the 35S enhancer. Based on the analysis of significant sequences, the G-box regulatory sequence may also play an important role in the activation mechanism of the 35S enhancer.
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Affiliation(s)
- Ching-Hsuan Chien
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Lan-Ying Huang
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Shuen-Fang Lo
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center National Chung Hsing University, Taichung, Taiwan
| | - Chi-Chou Liao
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Jia-Jyun Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Yen-Wei Chu
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Yen-Wei Chu,
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5
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6
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Liao CC, Chen LJ, Lo SF, Chen CW, Chu YW. EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches. PLoS Comput Biol 2019; 15:e1006942. [PMID: 31067213 PMCID: PMC6505892 DOI: 10.1371/journal.pcbi.1006942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/09/2019] [Indexed: 11/17/2022] Open
Abstract
T-DNA activation-tagging technology is widely used to study rice gene functions. When T-DNA inserts into genome, the flanking gene expression may be altered using CaMV 35S enhancer, but the affected genes still need to be validated by biological experiment. We have developed the EAT-Rice platform to predict the flanking gene expression of T-DNA insertion site in rice mutants. The three kinds of DNA sequences including UPS1K, DISTANCE, and MIDDLE were retrieved to encode and build a forecast model of two-layer machine learning. In the first-layer models, the features nucleotide context (N-gram), cis-regulatory elements (Motif), nucleotide physicochemical properties (NPC), and CG-island (CGI) were used to build SVM models by analysing the concealed information embedded within the three kinds of sequences. Logistic regression was used to estimate the probability of gene activation which as feature-encoding weighting within first-layer model. In the second-layer models, the NaiveBayesUpdateable algorithm was used to integrate these first layer-models, and the system performance was 88.33% on 5-fold cross-validation, and 79.17% on independent-testing finally. In the three kinds of sequences, the model constructed by Middle had the best contribution to the system for identifying the activated genes. The EAT-Rice system provided better performance and gene expression prediction at further distances when compared to the TRIM database. An online server based on EAT-rice is available at http://predictor.nchu.edu.tw/EAT-Rice.
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Affiliation(s)
- Chi-Chou Liao
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center National Chung Hsing University, Taichung, Taiwan
| | - Shuen-Fang Lo
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Wei Chen
- Department of Computer Science and Engineering, National Chung Hsing University, Taichung, Taiwan
| | - Yen-Wei Chu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.,Rong Hsing Research Center For Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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7
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Dolgova AS, Dolgov SV. Matrix attachment regions as a tool to influence plant transgene expression. 3 Biotech 2019; 9:176. [PMID: 30997313 DOI: 10.1007/s13205-019-1709-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/08/2019] [Indexed: 12/29/2022] Open
Abstract
The inclusion of special regulatory sequences known as matrix attachment regions (MARs) in transgene constructs has been suggested as a possible approach to stabilise the expression of foreign heterological genes. The present review provides a brief summary regarding the MARs that have been used in investigations studying their influence on plant transgene expression in different plants with different promoters and reporter genes, and the comparison of these investigations.
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Affiliation(s)
- Anna Sergeevna Dolgova
- 1Central Research Institute of Epidemiology, Moscow, Russia
- 2Saint-Petersburg Pasteur Institute, St. Petersburg, Russia
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8
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Wang D, Ma J, Sun D, Li H, Jiang C, Li X. Expression of bioactive anti-CD20 antibody fragments and induction of ER stress response in Arabidopsis seeds. Appl Microbiol Biotechnol 2015; 99:6753-64. [PMID: 25957150 DOI: 10.1007/s00253-015-6601-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/01/2015] [Accepted: 04/05/2015] [Indexed: 11/25/2022]
Abstract
Seed-based expression system is an attractive platform for the production of recombinant proteins in molecular farming. Despite the many advantages of molecular farming, little is known about the effect of the different subcellular accumulation of recombinant proteins on the endoplasmic reticulum (ER) quality control system in host plants. In this study, we analyzed the expression of anti-CD20 antibody fragments in seeds of Arabidopsis thaliana (ecotype Columbia) and corresponding glycosylation mutants, and evaluated the influence of three different signal sequences on the expression levels of scFv-Fc of C2B8. The highest protein accumulation level, with a maximum of 6.12 % total soluble proteins, was observed upon fusing proteins to the signal peptide of Arabidopsis seed storage albumin 2. The ER stress responses in developing seeds at 13 days post-anthesis were also compared across different transgenic lines under normal and heat shock conditions. Based on the gene expression profiles of ER stress transducers, our results suggest that accumulation of antibody fragments in the ER exerts more stress on ER homeostasis. In addition, quantitative PCR results also implicate enhanced activation of ER-associated degradation in transgenic lines. Last but not the least, we also demonstrate the anti-tumor potency of plant-derived proteins by showing the anti-tumor activity of purified scFv-Fc proteins against Daudi cells. Together, our data implies that better understanding of the interaction between exogenous protein production and the cellular quality control system of the host plant is necessary for the development of an optimal expression strategy that will be especially beneficial to commercial protein manufacturing.
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Affiliation(s)
- Dezhong Wang
- College of Life Sciences, Jilin University, Changchun, 130021, China
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9
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Chen MX, Zheng SX, Yang YN, Xu C, Liu JS, Yang WD, Chye ML, Li HY. Strong seed-specific protein expression from the Vigna radiata storage protein 8SGα promoter in transgenic Arabidopsis seeds. J Biotechnol 2014; 174:49-56. [PMID: 24503210 DOI: 10.1016/j.jbiotec.2014.01.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/23/2014] [Accepted: 01/27/2014] [Indexed: 11/16/2022]
Abstract
Vigna radiata (mung bean) is an important crop plant and is a major protein source in developing countries. Mung bean 8S globulins constitute nearly 90% of total seed storage protein and consist of three subunits designated as 8SGα, 8SGα' and 8SGβ. The 5'-flanking sequences of 8SGα' has been reported to confer high expression in transgenic Arabidopsis seeds. In this study, a 472-bp 5'-flanking sequence of 8SGα was identified by genome walking. Computational analysis subsequently revealed the presence of numerous putative seed-specific cis-elements within. The 8SGα promoter was then fused to the gene encoding β-glucuronidase (GUS) to create a reporter construct for Arabidopsis thaliana transformation. The spatial and temporal expression of 8SGα∷GUS, as investigated using GUS histochemical assays, showed GUS expression exclusively in transgenic Arabidopsis seeds. Quantitative GUS assays revealed that the 8SGα promoter showed 2- to 4-fold higher activity than the Cauliflower Mosaic Virus (CaMV) 35S promoter. This study has identified a seed-specific promoter of high promoter strength, which is potentially useful for directing foreign protein expression in seed bioreactors.
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Affiliation(s)
- Mo-Xian Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shu-Xiao Zheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yue-Ning Yang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Chao Xu
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jie-Sheng Liu
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wei-Dong Yang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Hong-Ye Li
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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10
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Singer SD, Liu Z, Cox KD. Minimizing the unpredictability of transgene expression in plants: the role of genetic insulators. PLANT CELL REPORTS 2012; 31:13-25. [PMID: 21987122 DOI: 10.1007/s00299-011-1167-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 09/27/2011] [Indexed: 05/20/2023]
Abstract
The genetic transformation of plants has become a necessary tool for fundamental plant biology research, as well as the generation of engineered plants exhibiting improved agronomic and industrial traits. However, this technology is significantly hindered by the fact that transgene expression is often highly variable amongst independent transgenic lines. Two of the major contributing factors to this type of inconsistency are inappropriate enhancer-promoter interactions and chromosomal position effects, which frequently result in mis-expression or silencing of the transgene, respectively. Since the precise, often tissue-specific, expression of the transgene(s) of interest is often a necessity for the successful generation of transgenic plants, these undesirable side effects have the potential to pose a major challenge for the genetic engineering of these organisms. In this review, we discuss strategies for improving foreign gene expression in plants via the inclusion of enhancer-blocking insulators, which function to impede enhancer-promoter communication, and barrier insulators, which block the spread of heterochromatin, in transgenic constructs. While a complete understanding of these elements remains elusive, recent studies regarding their use in genetically engineered plants indicate that they hold great promise for the improvement of transgene expression, and thus the future of plant biotechnology.
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Affiliation(s)
- Stacy D Singer
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
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11
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Singer SD, Hily JM, Cox KD. Analysis of the enhancer-blocking function of the TBS element from Petunia hybrida in transgenic Arabidopsis thaliana and Nicotiana tabacum. PLANT CELL REPORTS 2011; 30:2013-25. [PMID: 21706298 DOI: 10.1007/s00299-011-1109-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/01/2011] [Accepted: 06/13/2011] [Indexed: 05/31/2023]
Abstract
Transcriptional enhancers possess the ability to override the tissue-specificity and efficiency of nearby promoters, which is of concern when generating transgenic constructs bearing multiple cassettes. One means of preventing these inappropriate interactions is through the use of enhancer-blocking insulators. The 2-kb transformation booster sequence (TBS) from Petunia hybrida has been shown previously to exhibit this function when inserted between an enhancer and promoter in transgenic Arabidopsis thaliana. In this study, we attempted to further characterize the ability of this fragment to impede enhancer-promoter interference through an analysis of transgenic Arabidopsis and Nicotiana tabacum lines bearing various permutations of the TBS element between the cauliflower mosaic virus (CaMV) 35S enhancer and an assortment of tissue-specific promoters fused to the β-glucuronidase (GUS) reporter gene. The full-length TBS fragment was found to function in both orientations, although to a significantly lesser degree in the reverse orientation, and was operational in both plant species tested. While multiple deletion fragments were found to exhibit activity, it appeared that several regions of the TBS were required for maximal enhancer-blocking function. Furthermore, we found that this element exhibited promoter-like activity, which has implications in terms of possible mechanisms behind its ability to impede enhancer-promoter communication in plants.
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Affiliation(s)
- Stacy D Singer
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
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12
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Singer SD, Cox KD, Liu Z. Enhancer-promoter interference and its prevention in transgenic plants. PLANT CELL REPORTS 2011; 30:723-31. [PMID: 21170713 DOI: 10.1007/s00299-010-0977-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 12/07/2010] [Accepted: 12/07/2010] [Indexed: 05/22/2023]
Abstract
Biotechnology has several advantages over conventional breeding for the precise engineering of gene function and provides a powerful tool for the genetic improvement of agronomically important traits in crops. In particular, it has been exploited for the improvement of multiple traits through the simultaneous introduction or stacking of several genes driven by distinct tissue-specific promoters. Since transcriptional enhancer elements have been shown to override the specificity of nearby promoters in a position- and orientation-independent manner, the co-existence of multiple enhancers/promoters within a single transgenic construct could be problematic as it has the potential to cause the mis-expression of transgene product(s). In order to develop strategies with, which to prevent such interference, a clear understanding of the mechanisms underlying enhancer-mediated activation of target promoters, as well as the identification of DNA sequences that function to block these interactions in plants, will be necessary. To date, little is known concerning enhancer function in plants and only a very limited number of enhancer-blocking insulators that operate in plant species have been identified. In this review, we discuss the current knowledge surrounding enhancer-promoter interactions, as well as possible means of minimizing such interference during plant transformation experiments.
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Affiliation(s)
- Stacy D Singer
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
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13
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Nguyen HT, Mishra G, Whittle E, Pidkowich MS, Bevan SA, Merlo AO, Walsh TA, Shanklin J. Metabolic engineering of seeds can achieve levels of omega-7 fatty acids comparable with the highest levels found in natural plant sources. PLANT PHYSIOLOGY 2010; 154:1897-904. [PMID: 20943853 PMCID: PMC2996033 DOI: 10.1104/pp.110.165340] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 10/08/2010] [Indexed: 05/20/2023]
Abstract
Plant oils containing ω-7 fatty acids (FAs; palmitoleic 16:1Δ(9) and cis-vaccenic 18:1Δ(11)) have potential as sustainable feedstocks for producing industrially important octene via metathesis chemistry. Engineering plants to produce seeds that accumulate high levels of any unusual FA has been an elusive goal. We achieved high levels of ω-7 FA accumulation by systematic metabolic engineering of Arabidopsis (Arabidopsis thaliana). A plastidial 16:0-ACP desaturase has been engineered to convert 16:0 to 16:1Δ(9) with specificity >100-fold than that of naturally occurring paralogs, such as that from cat's claw vine (Doxantha unguis-cati). Expressing this engineered enzyme (Com25) in seeds increased ω-7 FA accumulation from <2% to 14%. Reducing competition for 16:0-ACP by down-regulating the β-ketoacyl-ACP synthase II 16:0 elongase further increased accumulation of ω-7 FA to 56%. The level of 16:0 exiting the plastid without desaturation also increased to 21%. Coexpression of a pair of fungal 16:0 desaturases in the cytosol reduced the 16:0 level to 11% and increased ω-7 FA to as much as 71%, equivalent to levels found in Doxantha seeds.
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Affiliation(s)
| | | | | | | | | | | | | | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Upton, New York 11973 (H.T.N., G.M., E.W., M.S.P., J.S.); Discovery Research, Dow AgroSciences, Indianapolis, Indiana 46268 (S.A.B., A.O.M., T.A.W.)
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14
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Hily JM, Singer SD, Yang Y, Liu Z. A transformation booster sequence (TBS) from Petunia hybrida functions as an enhancer-blocking insulator in Arabidopsis thaliana. PLANT CELL REPORTS 2009; 28:1095-104. [PMID: 19373469 DOI: 10.1007/s00299-009-0700-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/20/2009] [Accepted: 03/29/2009] [Indexed: 05/18/2023]
Abstract
Several matrix-attachment regions (MARs) from animals have been shown to block interactions between an enhancer and promoter when situated between the two. Since a similar function for plant MARs has not been discerned, we tested the Zea mays ADH1 5' MAR, Nicotiana tabacum Rb7 3' MAR and a transformation booster sequence (TBS) MAR from Petunia hybrida for their ability to impede enhancer-promoter interactions in Arabidopsis thaliana. Stable transgenic lines containing vectors in which one of the three MAR elements or a 4 kb control sequence were interposed between the cauliflower mosaic virus 35S enhancer and a flower-specific AGAMOUS second intron-derived promoter (AGIP)::beta-glucuronidase (GUS) fusion were assayed for GUS expression in vegetative tissues. We demonstrate that the TBS MAR element, but not the ADH1 or Rb7 MARs, is able to block interactions between the 35S enhancer and AGIP without compromising the function of either with elements from which they are not insulated.
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Affiliation(s)
- Jean-Michel Hily
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA
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15
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Zhang J, Lu L, Ji L, Yang G, Zheng C. Functional characterization of a tobacco matrix attachment region-mediated enhancement of transgene expression. Transgenic Res 2009; 18:377-85. [PMID: 19043795 DOI: 10.1007/s11248-008-9230-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
TM2, a new matrix attachment region (MAR) isolated from tobacco, increases transgene expression in plants. We have carried out a more detailed analysis of the DNA elements in TM2 with the aim of improving its effect on transcription activation. Our study of the location effect of individual MARs on the expression of the adjacent 35S:gusA cassette indicated that the TM2 functions in a bidirectional manner, with the 5'-MAR being more efficient in enhancing beta-glucuronidase expression than the 3'-MAR. The influence of 5'-MAR on different linked mini-promoters in transgenic tobacco cells suggested that the role of TM2 depends on the basic expression of the transgenes. Deletion analysis of one topo II site and two unwinding sites together with one T-box revealed that all these sites contribute most (93.3%) of the transcription activation mediated from the TM2 sequence. Additionally, micrococcal nuclease accessibility of the 35S promoter region can be strengthened by linked TM2, suggesting that the TM2 mediates the spreading of nucleosome opening. Taken together, our results reveal that the TM2 mediates a more open and accessible chromatin DNA structure for promoter-dependent active transcription, which in turn enhances transgene expression.
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Affiliation(s)
- Jiedao Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong, People's Republic of China
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16
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Nguyen T, Shanklin J. Altering Arabidopsis Oilseed Composition by a Combined Antisense-Hairpin RNAi Gene Suppression Approach. J AM OIL CHEM SOC 2008. [DOI: 10.1007/s11746-008-1322-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Kim MS, Lim HS, Ahn SJ, Jeong YK, Kim CG, Lee HH. Enhanced expression of EGFP gene in CHSE-214 cells by an ARS element from mud loach (Misgurnus mizolepis). Plasmid 2007; 58:228-39. [PMID: 17586046 DOI: 10.1016/j.plasmid.2007.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 04/16/2007] [Accepted: 05/01/2007] [Indexed: 10/23/2022]
Abstract
The origins of replication are associated with nuclear matrices or are found in close proximity to matrix attachment regions (MARs). In this report, fish MARs were cloned into an autonomously replicating sequence (ARS) cloning vector and were screened for ARS elements in Saccharomyces cerevisiae. Sixteen clones were isolated that were able to grow on the selective plates. In particular, an ARS905 that shows high efficiency among them was selected for this study. Southern hybridization indicated the autonomous replication of the transformation vector containing the ARS905 element. DNA sequences analysis showed that the ARS905 contained two ARS consensus sequences as well as MAR motifs, such as AT tracts, ORI patterns, and ATC tracts. In vitro matrix binding analysis, major matrix binding activity and ARS function coincided in a subfragment of the ARS905. To analyze the effects of ARS905 on expression of a reporter gene, an ARS905(E1158) with ARS activity was inserted into pBaEGFP(+) containing mud loach beta-actin promoter, EGFP as a reporter gene, and SV40 poly(A) signal. The pBaEGFP(+)-ARS905(E1158) was transfected into a fish cell line, CHSE-214. The intensity of EGFP transfected cells was a 7-fold of the control at 11days post-transfection. These results indicate that ARS905 enhances the expression of the EGFP gene and that it should be as a component of expression vectors in further fish biotechnological studies.
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Affiliation(s)
- Moo-Sang Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan 608-737, Republic of Korea
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18
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Tao Y, Shang-long Z, Jing-mei L, De-ming C. Approaches to improve heterogeneous gene expression in transgenic plants. ACTA ACUST UNITED AC 2007. [DOI: 10.1079/cjb200697] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
AbstractWith the development of plant genetic engineering, many transformation methods can be used to transfer heterogeneous genes into plants to develop genetic crops. However, a lot of research results have shown that transgene expression remains largely unpredictable and there is great variation of expression level in different transgenic plant lines. Plant genetic engineering research is reviewed in the present paper. We analysed the reasons why low efficiency of heterogeneous gene expression has happened in transgenic plants in terms of DNA modification, localization of proteins and methods of transformation used. Some strategies for improving heterogeneous gene expression in transgenic plants are also discussed.
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19
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Razin SV, Iarovaia OV. Spatial Organization of DNA in the Nucleus May Determine Positions of Recombination Hot Spots. Mol Biol 2005. [DOI: 10.1007/s11008-005-0070-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Jost W, Link S, Horstmann V, Decker EL, Reski R, Gorr G. Isolation and characterisation of three moss-derived beta-tubulin promoters suitable for recombinant expression. Curr Genet 2004; 47:111-20. [PMID: 15605251 DOI: 10.1007/s00294-004-0555-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Revised: 11/12/2004] [Accepted: 11/16/2004] [Indexed: 10/26/2022]
Abstract
The moss Physcomitrella patens is an excellent tool to study plant gene-function relationships due to its high rate of homologous recombination (HR). It has also been shown to be very useful in the production of recombinant proteins which are secreted into a simple medium. Thus, there is a need for suitable promoters functional in this well established model organism. We isolated genomic flanking regions of the beta-tubulin gene family from Physcomitrella, concentrating on those family members showing high transcript abundance integrated over gametophytic tissues. Using a novel, fast and reliable quantification assay based on the transient expression and secretion of a recombinant human protein, three genomic upstream regions were characterised in serial deletion constructs. Expression rates were up to three times higher than those obtained with the 35S cauliflower mosaic virus (35S) promoter, which served as a reference.
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Affiliation(s)
- Wolfgang Jost
- Greenovation Biotech GmbH, Bötzinger Strasse 29b, 79111 Freiburg, Germany
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21
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Namciu SJ, Fournier REK. Human matrix attachment regions are necessary for the establishment but not the maintenance of transgene insulation in Drosophila melanogaster. Mol Cell Biol 2004; 24:10236-45. [PMID: 15542833 PMCID: PMC529032 DOI: 10.1128/mcb.24.23.10236-10245.2004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Revised: 07/06/2004] [Accepted: 09/01/2004] [Indexed: 11/20/2022] Open
Abstract
Human matrix attachment regions (MARs) can insulate transgene expression from chromosomal position effects in Drosophila melanogaster. To gain insight into the mechanism(s) by which chromosomal insulation occurs, we studied the expression phenotypes of Drosophila transformants expressing mini-white transgenes in which MAR sequences from the human apoB gene were arranged in a variety of ways. In agreement with previous reports, we found that a single copy of the insulating element was not sufficient for position-independent transgene expression; rather, two copies were required. However, the arrangement of the two elements within the transgene was unimportant, since chromosomal insulation was equally apparent when both copies of the insulator were upstream of the mini-white reporter as when the transcription unit was flanked by insulator elements. Moreover, experiments in which apoB 3' MAR sequences were removed from integrated transgenes in vivo by site-specific recombination demonstrated that MAR sequences were required for the establishment but not for the maintenance of chromosomal insulation. These observations are not compatible with the chromosomal loop model in its simplest form. Alternate mechanisms for MAR function in this system are proposed.
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Affiliation(s)
- Stephanie J Namciu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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22
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Carranco R, Chandrasekharan MB, Townsend JC, Hall TC. Interaction of PvALF and VP1 B3 domains with the beta -phaseolin promoter. PLANT MOLECULAR BIOLOGY 2004; 55:221-37. [PMID: 15604677 DOI: 10.1007/s11103-004-0512-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The phas promoter is potently transcribed during embryogenesis but in vegetative tissues it is completely silenced by a rotationally positioned nucleosome. Ectopic expression in leaves of PvALF, a seed-specific transcription factor belonging to the plant-exclusive B3 domain-containing VP1/ABI3 family, leads to chromatin remodeling of the phas promoter, permitting transcriptional activation by the growth regulator abscisic acid (ABA). Specific interaction with RY elements present in 40-42 bp oligonucleotide probes has been shown in vitro for Arabidopsis ABI3 and the isolated B3 domain of maize VP1. Here, both in vivo and in vitro approaches were used to show physical interaction of the B3 domain of VP1 or PvALF to RY elements in the native phas promoter. In electrophoretic mobility shift assays, small changes in B3 domain concentration differentiated between RY element-specific and sequence non-specific DNA binding. Increased affinity of the PvALF B3 domain to RY elements was observed in the presence of histones and other basic proteins, possibly reflecting the ability of this B3 factor to interact with the phas promoter in its nucleosomal configuration.
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Affiliation(s)
- Raúl Carranco
- Institute of Developmental and Molecular Biology and Department of Biology, Texas A & M University, College Station, TX 77843-3155, USA
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23
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Lincker F, Philipps G, Chabouté ME. UV-C response of the ribonucleotide reductase large subunit involves both E2F-mediated gene transcriptional regulation and protein subcellular relocalization in tobacco cells. Nucleic Acids Res 2004; 32:1430-8. [PMID: 14990748 PMCID: PMC390297 DOI: 10.1093/nar/gkh310] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2004] [Revised: 02/05/2004] [Accepted: 02/05/2004] [Indexed: 12/22/2022] Open
Abstract
E2F factors are implicated in various cellular processes including specific gene induction at the G1/S transition of the cell cycle. We present in this study a novel regulatory aspect for the tobacco large subunit of ribonucleotide reductase (R1a) and its encoding gene (RNR1a) in the UV-C response. By structural analyses, two E2F sites were identified on the promoter of this gene. Functional analysis showed that, in addition to their role in the specific G1/S induction of the RNR1a gene, both E2F sites were important for regulating specific RNR1a gene expression in response to UV-C irradiation in non-synchronized and synchronized cells. Concomitantly, western blot and cellular analyses showed an increase of a 60 kDa E2F factor and a transient translocation of a GFP-R1a protein fusion from cytoplasm to nucleus in response to UV irradiation.
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Affiliation(s)
- Frédéric Lincker
- Institut de Biologie Moléculaire des Plantes du CNRS, Université Louis Pasteur, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
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24
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Abstract
Insulators might regulate gene expression by establishing and maintaining the organization of the chromatin fiber within the nucleus. Biochemical fractionation and in situ high salt extraction of lysed cells show that two known protein components of the gypsy insulator are present in the nuclear matrix. Using FISH with DNA probes located between two endogenous Su(Hw) binding sites, we show that the intervening DNA is arranged in a loop, with the two insulators located at the base. Mutations in insulator proteins, subjecting the cells to a brief heat shock, or destruction of the nuclear matrix lead to disruption of the loop. Insertion of an additional gypsy insulator in the center of the loop results in the formation of paired loops through the attachment of the inserted sequences to the nuclear matrix. These results suggest that the gypsy insulator might establish higher-order domains of chromatin structure and regulate nuclear organization by tethering the DNA to the nuclear matrix and creating chromatin loops.
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Affiliation(s)
- Keith Byrd
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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25
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Sidorenko L, Bruce W, Maddock S, Tagliani L, Li X, Daniels M, Peterson T. Functional analysis of two matrix attachment region (MAR) elements in transgenic maize plants. Transgenic Res 2003; 12:137-54. [PMID: 12739882 DOI: 10.1023/a:1022908614356] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Matrix attachment regions (MARs) are binding sites for nuclear scaffold proteins in vitro, and are proposed to mediate the attachment of chromatin to the nuclear scaffold in vivo. Previous reports suggest that MAR elements may stabilize transgene expression. Here, we tested the effects of two maize MAR elements (P-MAR from the P1-rr gene, and Adh1-MAR from the adh1 gene) on the expression of a gusA reporter gene driven by three different promoters: the maize p1 gene promoter, a wheat peroxidase (WP) gene promoter, or a synthetic promoter (Rsyn7). The inclusion of P-MAR or Adh1-MAR on P::GUS transgene constructs did not reduce variation in the levels of GUS activity among independent transformation events, nor among the progeny derived from each event. The Adh1-MAR element did not affect GUS expression driven by the WP promoter, but did modify the spatial pattern of expression of the Rsyn7::GUS transgene. These results indicate that, in transgenic maize plants, the effects of MAR elements can vary significantly depending upon the promoter used to drive the transgene.
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Affiliation(s)
- Lyudmila Sidorenko
- Department of Zoology and Genetics, Iowa State University, IA 50011, Ames, USA
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26
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Chandrasekharan MB, Bishop KJ, Hall TC. Module-specific regulation of the beta-phaseolin promoter during embryogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 33:853-66. [PMID: 12609027 DOI: 10.1046/j.1365-313x.2003.01678.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phas promoter displays stringent spatial regulation, being very highly expressed during embryogenesis and completely silent during all phases of vegetative development in bean, Phaseolus vulgaris. This pattern is maintained in transgenic tobacco and, as shown here, Arabidopsis. Dimethyl sulphate in vivo footprinting analyses revealed that over 20 cis-elements within the proximal 295 bp of the phas promoter are protected by factor binding in seed tissues whereas none are bound in leaves. The hypothesis that this complex profile represents a summation of several module (cotyledon, hypocotyl, and radicle)-specific factor-DNA interactions has been explored by the incorporation of site-directed substitution mutations into 10 locations within the -295phas promoter. Only 2.6% of -295phas promoter activity remained after mutation of the G-box; the CCAAAT box, the E-box and the RY elements were also found to mediate high levels of expression in embryos. Whereas the CACA element has dual positive and negative regulatory roles, the vicilin box was identified as a strong negative regulatory element. The proximal (-70 to -64) RY motif was found to bestow expression in the hypocotyl while all the RY elements contribute to expression in cotyledons but not to vascular tissue expression during embryogenesis. RY elements at positions -277 to -271, -260 to -254, and -237 to -231 were found to orchestrate radicle-specific repression. The G-box appears to be the functional abscisic acid responsive element and the E-site may be a coupling element. The results substantiate the concept that autarkical cis-element functions generate modular patterning during embryogenesis. They also reflect the existence of both redundancy and hierarchy in cis-element interactions. Importantly, the virtually identical expression patterns observed for the two distantly related plants studied argue strongly for the generality of function for the observed factor-element interactions.
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Affiliation(s)
- Mahesh B Chandrasekharan
- Department of Biology, Institute of Developmental and Molecular Biology, Texas A&M University, College Station, TX 77843-3155, USA
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27
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Mankin SL, Allen GC, Phelan T, Spiker S, Thompson WF. Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3' MAR. Transgenic Res 2003; 12:3-12. [PMID: 12650520 DOI: 10.1023/a:1022194120518] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have analyzed effects of a matrix attachment region (MAR) from the tobacco RB7 gene on transgene expression from six different promoters in stably transformed tobacco cell cultures. The presence of MARs flanking the transgene increased expression of constructs based on the constitutive CaMV 35S, NOS, and OCS promoters. Expression from an induced heat shock promoter was also increased and MARs did not cause expression in the absence of heat shock. There was also no effect of MARs on the pea ferredoxin promoter, which is not normally expressed in this cell line. Importantly, most transgenes flanked by RB7 MAR elements showed a large reduction in the number of low expressing GUS transformants relative to control constructs without MARs.
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Affiliation(s)
- S Luke Mankin
- Department of Botany, NC State University, Raleigh, NC 27695-7612, USA.
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28
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Dietz-Pfeilstetter A, Arndt N, Kay V, Bode J. Molecular structure and regulatory potential of a T-DNA integration site in petunia. Transgenic Res 2003; 12:83-99. [PMID: 12650527 DOI: 10.1023/a:1022113020049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The genomic structure surrounding a T-DNA integration site in a transgenic petunia plant, which shows deregulation of a root-specific promoter, was investigated. We have already demonstrated that T-DNA integration in this transformant (P13) had occurred close to a scaffold/matrix attachment region (S/MAR). A major question regarding the observed promoter leakiness was whether the T-DNA had integrated into the centre or at the border of the Petun-SAR and whether other regulatory elements are located within this genomic region. While small rearrangements were shown to occur during T-DNA integration in agreement with other reports, we find indications of the presence of a SINE retroposon--an apparent landmark for recombinogenic targets--at the integration site. Binding assays to both plant and animal nuclear scaffolds, supported by biomathematical analyses, reveal that the T-DNA is definitely located at the border of a strong S/MAR, which is in agreement with current models on the structure of integration sites. These results, together with a developmentally regulated leaf-specific enhancer effect of the Petun-SAR on gene expression in transgenic tobacco plants, indicate that the Petun-SAR demarcates the right border of a chromatin domain with genes predominantly active in leaves.
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Affiliation(s)
- Antje Dietz-Pfeilstetter
- Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Messeweg 11/12, D-38104 Braunschweig, Germany.
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29
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Rampitsch C, Jordan MC, Cloutier S. A matrix attachment region is located upstream from the high-molecular-weight glutenin gene Bx7 in wheat (Triticum aestivum L.). Genome 2000; 43:483-6. [PMID: 10902712 DOI: 10.1139/g00-011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 2.2-kb nucleotide sequence rich in AT, located upstream from the Bx7 allele of the high-molecular-weight glutenin Glu-B1 locus in wheat (Triticum aestivum cv. Glenlea) was cloned following amplification by PCR. The 5' region of this sequence contains motifs typically found in matrix attachment regions (MARs) in other plants. We have shown that part of the 2.2-kb DNA binds to wheat nuclear matrix (NM) in vitro, at least as strongly as a known MAR (Adh1) from maize suggesting that there is a MAR upstream of Bx7. This MAR is approximately 800 bases in length running from -750 to -1560 bases, relative to the start codon. Although the MAR is associated with a tissue-specific gene and is beside a strong tissue-specific promoter, the MAR sequence did not lead to tissue-specific expression of the beta-glucuronidase marker gene under the control of the rice actin promoter in various tissues. Presence of the MAR was only slightly beneficial with respect to expression levels, which were not greatly altered in transient expression assays in various wheat tissues although a slight increase in the number of foci was observed in leaves, which have low transformation efficiencies.
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Affiliation(s)
- C Rampitsch
- Agriculture and Agri-Food Canada, Cereal Research Centre, Winnipeg, MB
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30
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Namciu SJ, Blochlinger KB, Fournier RE. Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol 1998; 18:2382-91. [PMID: 9528807 PMCID: PMC121496 DOI: 10.1128/mcb.18.4.2382] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/1997] [Accepted: 01/02/1998] [Indexed: 02/07/2023] Open
Abstract
Germ line transformation of white- Drosophila embryos with P-element vectors containing white expression cassettes results in flies with different eye color phenotypes due to position effects at the sites of transgene insertion. These position effects can be cured by specific DNA elements, such as the Drosophila scs and scs' elements, that have insulator activity in vivo. We have used this system to determine whether human matrix attachment regions (MARs) can function as insulator elements in vivo. Two different human MARs, from the apolipoprotein B and alpha1-antitrypsin loci, insulated white transgene expression from position effects in Drosophila melanogaster. Both elements reduced variability in transgene expression without enhancing levels of white gene expression. In contrast, expression of white transgenes containing human DNA segments without matrix-binding activity was highly variable in Drosophila transformants. These data indicate that human MARs can function as insulator elements in vivo.
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Affiliation(s)
- S J Namciu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
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31
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Abstract
The repertoire of cis-regulatory elements has increased to a level of sophistication that offers considerable spatial and temporal control over transgene expression. Recent advances made with transgenes have revealed that the control of their expression is also influenced by factors that range from transgene copy number and arrangement to nuclear architecture and chromosomal location. These factors must now be included with the standard considerations of transcriptional and translational enhancers of gene expression during transgene design.
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Affiliation(s)
- D R Gallie
- Department of Biochemistry, University of California, Riverside, CA 92521-0129, USA.
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