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Yang J, Gao L, Zhang X, Zheng R, Liu X, Cui Y, Wang Z, Wang X. Identification and functional characterization of bidirectional gene pairs and their intergenic regions in cotton. BMC PLANT BIOLOGY 2024; 24:829. [PMID: 39232709 PMCID: PMC11373494 DOI: 10.1186/s12870-024-05548-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND In research to improve the quality of transgenic crops, it is often necessary to introduce multiple functionally related genes into recipient plants simultaneously to improve crop genetic traits effectively. Compared with unidirectional promoters, bidirectional promoters simultaneously regulate the expression of multiple genes and improve the efficiency of biotechnology. Therefore, in this study, bidirectional gene pairs were systematically analyzed in Gossypium hirsutum TM-1, and the structure, function and evolutionary relationships of the bidirectional genes were analyzed. The endogenous bidirectional promoters of cotton were mined, and their specific regulatory elements and biological functions were explored to provide useful promoter resources and a theoretical basis for cultivating new cotton germplasms with excellent fiber quality. RESULTS Using an improved search model, a total of 1,383 bidirectional transcript pairs were identified in the Gossypium hirsutum TM-1 genome, and their gene structure and functional annotations were systematically analyzed. Thirty bidirectional intergenic sequences were randomly screened for promoter activity analysis via a transient expression system, and 25 intergenic sequences were found to have bidirectional promoter activity. Comparative analysis of the bidirectional gene profiles of the four cotton subspecies revealed that these subspecies presented abundant bidirectional gene pairs with high homology and that the bidirectional genes in the cotton subspecies were more similar in terms of their molecular functions, cellular components and biological processes. In addition, parallel analysis of bidirectional genes in dicotyledons and monocotyledons revealed that abundant bidirectional gene pairs exist in different species. Although the total number of orthologous bidirectional genes was similar, there was a significant difference in the number of orthologous bidirectional gene pairs between dicotyledons and monocotyledons. This evolutionary analysis of the function and structure of homologous bidirectional gene pairs in different varieties and different subspecies of the same species revealed potential pathways by which these gene pairs originated, which may be necessary for the evolution of a new species. CONCLUSION In this study, many bidirectional gene pairs in Gossypium hirsutum TM-1 were identified using computer programming, and systematic analysis was conducted to explore their functions and evolutionary relationships. In addition, the promoter activity of the bidirectional intergenic sequences was verified. The combination of computer programming screening, experimental validation and other methods is expected to provide preferred bidirectional promoters for transgenic breeding work via multigene cotransformation methods, and this information is valuable for genetic engineering research and applications.
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Affiliation(s)
- Jiangtao Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Lihua Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Xiaochun Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Ran Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Xuan Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Yuxin Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China.
| | - Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China.
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Yang Y, Liu J, Singer SD, Yan G, Bennet DR, Liu Y, Hily JM, Xu W, Yang Y, Wang X, Zhong GY, Liu Z, An YC, Liu H, Liu Z. Ectopic enhancer-enhancer interactions as causal forces driving RNA-directed DNA methylation in gene regulatory regions. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39021281 DOI: 10.1111/pbi.14435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/21/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024]
Abstract
Cis-regulatory elements (CREs) are integral to the spatiotemporal and quantitative expression dynamics of target genes, thus directly influencing phenotypic variation and evolution. However, many of these CREs become highly susceptible to transcriptional silencing when in a transgenic state, particularly when organised as tandem repeats. We investigated the mechanism of this phenomenon and found that three of the six selected flower-specific CREs were prone to transcriptional silencing when in a transgenic context. We determined that this silencing was caused by the ectopic expression of non-coding RNAs (ncRNAs), which were processed into 24-nt small interfering RNAs (siRNAs) that drove RNA-directed DNA methylation (RdDM). Detailed analyses revealed that aberrant ncRNA transcription within the AGAMOUS enhancer (AGe) in a transgenic context was significantly enhanced by an adjacent CaMV35S enhancer (35Se). This particular enhancer is known to mis-activate the regulatory activities of various CREs, including the AGe. Furthermore, an insertion of 35Se approximately 3.5 kb upstream of the AGe in its genomic locus also resulted in the ectopic induction of ncRNA/siRNA production and de novo methylation specifically in the AGe, but not other regions, as well as the production of mutant flowers. This confirmed that interactions between the 35Se and AGe can induce RdDM activity in both genomic and transgenic states. These findings highlight a novel epigenetic role for CRE-CRE interactions in plants, shedding light on the underlying forces driving hypermethylation in transgenes, duplicate genes/enhancers, and repetitive transposons, in which interactions between CREs are inevitable.
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Affiliation(s)
- Yazhou Yang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jia Liu
- College of Landscape, Architecture and Life science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Guohua Yan
- The Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Dennis R Bennet
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jean-Michel Hily
- Institut Français de la Vigne et du Vin (IFV), Le Grau du Roi, France
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, Ningxia, China
| | - Yingzhen Yang
- USDA-ARS, Grape Genetic Research Unit, Geneva, New York, USA
| | - Xiping Wang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Gan-Yuan Zhong
- USDA-ARS, Grape Genetic Research Unit, Geneva, New York, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Yong-Chiang An
- USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, Missouri, USA
| | - Huawei Liu
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Zongrang Liu
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
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Genetic Transformation of Quercus ilex Somatic Embryos with a Gnk2-like Protein That Reveals a Putative Anti-Oomycete Action. PLANTS 2022; 11:plants11030304. [PMID: 35161285 PMCID: PMC8838351 DOI: 10.3390/plants11030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022]
Abstract
Holm oak is a key tree species in Mediterranean ecosystems, whose populations have been increasingly threatened by oak decline syndrome, a disease caused by the combined action of Phytophthora cinnamomi and abiotic stresses. The aim of the present study was to produce holm oak plants that overexpress the Ginkbilobin-2 homologous domain gene (Cast_Gnk2-like) that it is known to possess antifungal properties. Proembryogenic masses (PEMs) isolated from four embryogenic lines (Q8, E2, Q10-16 and E00) were used as target explants. PEMs were co-cultured for 5 days with Agrobacterium EHA105pGnk2 and then cultured on selective medium containing kanamycin (kan) and carbenicillin. After 14 weeks on selective medium, the transformation events were observed in somatic embryos of lines Q8 and E2 and a total of 4 transgenic lines were achieved. The presence of the Cast_Gnk2-like gene on transgenic embryos was verified by PCR, and the number of transgene copies and gene expression was estimated by qPCR. Transgenic plants were obtained from all transgenic lines after cold storage of the somatic embryos for 2 months and subsequent transfer to germination medium. In an in vitro tolerance assay with the pathogen P. cinnamomi, we observed that transgenic plants were able to survive longer than wild type.
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Li T, Liu JX, Deng YJ, Xu ZS, Xiong AS. Overexpression of a carrot BCH gene, DcBCH1, improves tolerance to drought in Arabidopsis thaliana. BMC PLANT BIOLOGY 2021; 21:475. [PMID: 34663216 PMCID: PMC8522057 DOI: 10.1186/s12870-021-03236-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/28/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Carrot (Daucus carota L.), an important root vegetable, is very popular among consumers as its taproot is rich in various nutrients. Abiotic stresses, such as drought, salt, and low temperature, are the main factors that restrict the growth and development of carrots. Non-heme carotene hydroxylase (BCH) is a key regulatory enzyme in the β-branch of the carotenoid biosynthesis pathway, upstream of the abscisic acid (ABA) synthesis pathway. RESULTS In this study, we characterized a carrot BCH encoding gene, DcBCH1. The expression of DcBCH1 was induced by drought treatment. The overexpression of DcBCH1 in Arabidopsis thaliana resulted in enhanced tolerance to drought, as demonstrated by higher antioxidant capacity and lower malondialdehyde content after drought treatment. Under drought stress, the endogenous ABA level in transgenic A. thaliana was higher than that in wild-type (WT) plants. Additionally, the contents of lutein and β-carotene in transgenic A. thaliana were lower than those in WT, whereas the expression levels of most endogenous carotenogenic genes were significantly increased after drought treatment. CONCLUSIONS DcBCH1 can increase the antioxidant capacity and promote endogenous ABA levels of plants by regulating the synthesis rate of carotenoids, thereby regulating the drought resistance of plants. These results will help to provide potential candidate genes for plant drought tolerance breeding.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Yuan-Jie Deng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
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Yi C, Hong Y. Estimating the Copy Number of Transgenes in Transformed Cotton by Real-Time Quantitative PCR. Methods Mol Biol 2019; 1902:137-157. [PMID: 30543067 DOI: 10.1007/978-1-4939-8952-2_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transgenic cotton has been widely employed both in commercial cultivation and basic research. It is essential to determine which plants contain the transgene and in how many copies after transgenic cotton plants are generated. A TaqMan quantitative real-time polymerase chain reaction (Tq RT-PCR) method is described here to examine transgene copy number in transgenic cotton plants. The estimation of two transgene elements, the target gene of green fluorescence protein (GFP) and the selective gene of neomycin phosphotransferase II (NPTII), is used as an example to detail each step in Tq RT-PCR procedure, including endogenous reference gene selection, reference plasmid construction, primer-probe design, DNA extraction, real-time PCR, and data analysis. Comparing with traditional Southern hybridization analysis, this method can be used efficiently in screening large number of seedlings of T0 transgenic cotton at early stage of transformation process as well as in identifying transgene homozygotes in a segregation population.
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Affiliation(s)
- Chengxin Yi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- JOil (S) Pte Ltd, Singapore, Singapore
| | - Yan Hong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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6
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Structural and Functional Analysis of a Bidirectional Promoter from Gossypium hirsutum in Arabidopsis. Int J Mol Sci 2018; 19:ijms19113291. [PMID: 30360512 PMCID: PMC6274729 DOI: 10.3390/ijms19113291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Stacked traits have become an important trend in the current development of genomically modified crops. The bidirectional promoter can not only prevent the co-suppression of multigene expression, but also increase the efficiency of the cultivation of transgenic plants with multigenes. In Gossypium hirsutum, Ghrack1 and Ghuhrf1 are head-to-head gene pairs located on chromosome D09. We cloned the 1429-bp intergenic region between the Ghrack1 and Ghuhrf1 genes from Gossypium hirsutum. The cloned DNA fragment GhZU had the characteristics of a bidirectional promoter, with 38.7% G+C content, three CpG islands and no TATA-box. Using gfp and gus as reporter genes, a series of expression vectors were constructed into young leaves of tobacco. The histochemical GUS (Beta-glucuronidase) assay and GFP (green fluorescence protein) detection results indicated that GhZU could drive the expression of the reporter genes gus and gfp simultaneously in both orientations. Furthermore, we transformed the expression vectors into Arabidopsis and found that GUS was concentrated at vigorous growth sites, such as the leaf tip, the base of the leaves and pod, and the stigma. GFP was also mainly expressed in the epidermis of young leaves. In summary, we determined that the intergenic region GhZU was an orientation-dependent bidirectional promoter, and this is the first report on the bidirectional promoter from Gossypium hirsutum. Our findings in this study are likely to enhance understanding on the regulatory mechanisms of plant bidirectional promoters.
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Colicchio JM, Miura F, Kelly JK, Ito T, Hileman LC. DNA methylation and gene expression in Mimulus guttatus. BMC Genomics 2015; 16:507. [PMID: 26148779 PMCID: PMC4492170 DOI: 10.1186/s12864-015-1668-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
Abstract
Background The presence of methyl groups on cytosine nucleotides across an organism’s genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. The capacity for DNA methylation to be altered by environmental conditions, and potentially passed between generations, makes it a prime candidate for transgenerational epigenetic inheritance. Here we conduct the first analysis of the Mimulus guttatus methylome, with a focus on the relationship between DNA methylation and gene expression. Results We present a whole genome methylome for the inbred line Iron Mountain 62 (IM62). DNA methylation varies across chromosomes, genomic regions, and genes. We develop a model that predicts gene expression based on DNA methylation (R2 = 0.2). Post hoc analysis of this model confirms prior relationships, and identifies novel relationships between methylation and gene expression. Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions. Conclusions The establishment here of a reference methylome will be a useful resource for the continued advancement of M. guttatus as a model system. Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression. This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1668-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jack M Colicchio
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
| | - Fumihito Miura
- Department of Medical Biochemistry, Department of Biochemistry, Fukuoka 812-8581, Fukuoka 812-8582, Japan
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Takashi Ito
- Department of Medical Biochemistry, Department of Biochemistry, Fukuoka 812-8581, Fukuoka 812-8582, Japan
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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Nahampun HN, Bosworth B, Cunnick J, Mogler M, Wang K. Expression of H3N2 nucleoprotein in maize seeds and immunogenicity in mice. PLANT CELL REPORTS 2015; 34:969-80. [PMID: 25677970 DOI: 10.1007/s00299-015-1758-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/22/2015] [Accepted: 01/28/2015] [Indexed: 05/27/2023]
Abstract
Oral administration of maize-expressed H3N2 nucleoprotein induced antibody responses in mice showing the immunogenicity of plant-derived antigen and its potential to be utilized as a universal flu vaccine. Influenza A viruses cause influenza epidemics that are devastating to humans and livestock. The vaccine for influenza needs to be reformulated every year to match the circulating strains due to virus mutation. Influenza virus nucleoprotein (NP) is a multifunctional RNA-binding protein that is highly conserved among strains, making it a potential candidate for a universal vaccine. In this study, the NP gene of H3N2 swine origin influenza virus was expressed in maize endosperm. Twelve transgenic maize lines were generated and analyzed for recombinant NP (rNP) expression. Transcript analysis showed the main accumulation of rNP in seed. Protein level of rNP in T1 transgenic maize seeds ranged from 8.0 to 35 µg of NP/g of corn seed. The level increased up to 70 µg of NP/g in T3 seeds. A mouse study was performed to test the immunogenicity of one line of maize-derived rNP (MNP). Mice were immunized with MNP in a prime-boost design. Oral gavage administration showed that a humoral immune response was elicited in the mice treated with MNP indicating the immunogenicity of MNP. NP-specific antibody responses in the MNP group showed comparable antibody titer with the groups receiving positive controls such as Vero cell-derived NP (VNP) or alphavirus replicon particle-derived NP (ANP). Cytokine analysis showed antigen-specific stimulation of IL-4 cytokine elicited in splenocytes from mice treated with MNP further confirming a TH2 humoral immune response induced by MNP administration.
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Affiliation(s)
- Hartinio N Nahampun
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, 50011-1010, USA
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Pinheiro TT, Figueira A, Latado RR. Early-flowering sweet orange mutant 'x11' as a model for functional genomic studies of Citrus. BMC Res Notes 2014; 7:511. [PMID: 25108567 PMCID: PMC4267115 DOI: 10.1186/1756-0500-7-511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There had been many reports on genetic transformation of Citrus for functional genomic studies but few included genes associated with flower or fruit traits. A major reason for this might derive from the extensive juvenile stage of Citrus plants when regenerated from juvenile explants (epicotyls, cotyledon or calli), which delays the observation of the resulting phenotype. Alternatives include the use of explants from adult tissues, which sometimes may be recalcitrant to regeneration or transformation, or of early-flowering genotypes. However, there is no report about the use of early-flowering sweet orange mutants for functional genomic studies. RESULTS Here, we propose a sweet orange spontaneous early-flowering mutant, named 'x11', as a platform for Citrus functional genomic studies, particularly for genes associated with flower or fruit traits. We report a procedure for efficient regeneration and transformation using epicotyl segment explants of 'x11' and Agrobacterium tumefaciens as a proof-of-concept. The average transformation efficiency was 18.6%, but reached 29.6% in the best protocol tested. Among 270 positive shoots, five were in vitro micrografted and acclimatized, followed by evaluation of transgene expression by quantitative amplification of reversed transcripts (RT-qPCR) and determination of the number of copies inserted. Four of these plants, containing from one to four copies of the transgene, exhibited the first flowers within three months after ex vitro establishment, and the other, two months later, regardless of the period of the year. Flowers of transgenic plants displayed fertile pollen and gynoecium, with self-pollination inducing fruit development with seeds. Histochemical staining for β-glucuronidase activity using stem segments, flowers and fruits from 5 to 7 month-old acclimatized transgenic plants confirmed the constitutive transgene expression in these organs. CONCLUSION The 'x11' sweet orange is suitable for functional genomics studies with a satisfactory transformation rate, and it can be considered a good model for functional genomic studies in commercial sweet oranges, for traits related to flower and fruit.
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Affiliation(s)
- Thaísa Tessutti Pinheiro
- />Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP 13400-970 Brazil
- />Centro de Citricultura “Sylvio Moreira”, Instituto Agronômico, CP 04, Cordeirópolis, SP 13490-970 Brazil
| | - Antonio Figueira
- />Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP 13400-970 Brazil
| | - Rodrigo Rocha Latado
- />Centro de Citricultura “Sylvio Moreira”, Instituto Agronômico, CP 04, Cordeirópolis, SP 13490-970 Brazil
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Abstract
The evolutionary mechanisms underlying duplicate gene maintenance and divergence remain highly debated. Epigenetic modifications, such as DNA methylation, may contribute to duplicate gene evolution by facilitating tissue-specific regulation. However, the role of epigenetic divergence on duplicate gene evolution remains little understood. Here we show, using comprehensive data across 10 diverse human tissues, that DNA methylation plays critical roles in several aspects of duplicate gene evolution. We first demonstrate that duplicate genes are initially heavily methylated, before gradually losing DNA methylation as they age. Within each pair, DNA methylation divergence between duplicate partners increases with evolutionary age. Importantly, tissue-specific DNA methylation of duplicates correlates with tissue-specific expression, implicating DNA methylation as a causative factor for functional divergence of duplicate genes. These patterns are apparent in promoters but not in gene bodies, in accord with the complex relationship between gene-body DNA methylation and transcription. Remarkably, many duplicate gene pairs exhibit consistent division of DNA methylation across multiple, divergent tissues: For the majority (73%) of duplicate gene pairs, one partner is always hypermethylated compared with the other. This is indicative of a common underlying determinant of DNA methylation. The division of DNA methylation is also consistent with their chromatin accessibility profiles. Moreover, at least two sequence motifs known to interact with the Sp1 transcription factor mark promoters of more hypomethylated duplicate partners. These results demonstrate critical roles of DNA methylation, as well as complex interaction between genome and epigenome, on duplicate gene evolution.
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11
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Maessen G. Genomic stability and stability of expression in genetically modified plants. ACTA ACUST UNITED AC 2013. [DOI: 10.1111/plb.1997.46.1.3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nahampun HN, Lee CJ, Jane JL, Wang K. Ectopic expression of bacterial amylopullulanase enhances bioethanol production from maize grain. PLANT CELL REPORTS 2013; 32:1393-1405. [PMID: 23652819 DOI: 10.1007/s00299-013-1453-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/18/2013] [Accepted: 04/25/2013] [Indexed: 06/02/2023]
Abstract
Heterologous expression of amylopullulanase in maize seeds leads to partial starch degradation into fermentable sugars, which enhances direct bioethanol production from maize grain. Utilization of maize in bioethanol industry in the United States reached ±13.3 billion gallons in 2012, most of which was derived from maize grain. Starch hydrolysis for bioethanol industry requires the addition of thermostable alpha amylase and amyloglucosidase (AMG) enzymes to break down the α-1,4 and α-1,6 glucosidic bonds of starch that limits the cost effectiveness of the process on an industrial scale due to its high cost. Transgenic plants expressing a thermostable starch-degrading enzyme can overcome this problem by omitting the addition of exogenous enzymes during the starch hydrolysis process. In this study, we generated transgenic maize plants expressing an amylopullulanase (APU) enzyme from the bacterium Thermoanaerobacter thermohydrosulfuricus. A truncated version of the dual functional APU (TrAPU) that possesses both alpha amylase and pullulanase activities was produced in maize endosperm tissue using a seed-specific promoter of 27-kD gamma zein. A number of analyses were performed at 85 °C, a temperature typically used for starch processing. Firstly, enzymatic assay and thin layer chromatography analysis showed direct starch hydrolysis into glucose. In addition, scanning electron microscopy illustrated porous and broken granules, suggesting starch autohydrolysis. Finally, bioethanol assay demonstrated that a 40.2 ± 2.63 % (14.7 ± 0.90 g ethanol per 100 g seed) maize starch to ethanol conversion was achieved from the TrAPU seeds. Conversion efficiency was improved to reach 90.5 % (33.1 ± 0.66 g ethanol per 100 g seed) when commercial amyloglucosidase was added after direct hydrolysis of TrAPU maize seeds. Our results provide evidence that enzymes for starch hydrolysis can be produced in maize seeds to enhance bioethanol production.
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Affiliation(s)
- Hartinio N Nahampun
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA 50011-1010, USA
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Wang JY, Lai LD, Tong SM, Li QL. Constitutive and salt-inducible expression of SlBADH gene in transgenic tomato (Solanum lycopersicum L. cv. Micro-Tom) enhances salt tolerance. Biochem Biophys Res Commun 2013; 432:262-7. [PMID: 23402752 DOI: 10.1016/j.bbrc.2013.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/03/2013] [Indexed: 11/18/2022]
Abstract
To improve the stress tolerance of crops, many genes, including transcription factors, have been expressed in transgenic plants using either constitutive or stress-inducible promoters. However, transgenic plants that show strong constitutive expression of transcription factors often suffer from many undesirable phenotypes, such as stunted growth and reduced yield. In the present study, the betaine aldehyde dehydrogenase (BADH) gene, cloned from Suaeda liaotungensis and, controlled by the Cauliflower mosaic virus (CaMV) 35S promoter or stress-inducible promoter of BADH (P5: -300 to +62 bp), was transformed into tomato (Solanum lycopersicum). The transformants with single copy of SlBADH were determined by real time PCR. Expression of SlBADH in the P5:BADH transgenic plants exhibited salt induced and was higher than that in CaMV35S:BADH under salt stress. The SlBADH enhanced salt tolerance of P5:BADH and CaMV35S:BADH transformants. And SlBADH in P5:BADH plants did not affect the growth of transformants. Consequently, we conclude that the P5 promoter can drive increased expression of SlBADH in transgenic tomato under salt stress and increase salt tolerance without affecting plant growth.
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Affiliation(s)
- Jing-yu Wang
- College of Life Sciences, Liaoning Normal University, 1 South Liushu Street, Ganjingzi District, Dalian, Liaoning 116081, China
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Patro S, Maiti IB, Dey N. Development of an efficient bi-directional promoter with tripartite enhancer employing three viral promoters. J Biotechnol 2013; 163:311-7. [PMID: 23183382 DOI: 10.1016/j.jbiotec.2012.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/15/2012] [Accepted: 11/16/2012] [Indexed: 10/27/2022]
Abstract
We have developed a novel bi-directional promoter (FsFfCBD) by placing two heterogeneous core-promoters from the Figwort mosaic virus sub-genomic transcript promoter (FsCP, -69 to +31) and Cauliflower mosaic virus 35S promoter (CCP, -89 to +1) respectively on upstream (5') and downstream (3') ends of a tri-hybrid enhancer (FsEFfECE), in reverse orientation. The FsEFfECE domain encompasses three heterologous enhancer fragments from Figwort mosaic virus sub-genomic transcript promoter (FsE, 101 bp, -70 to -170), Figwort mosaic virus full-length transcript promoter (FfE, 196 bp, -249 to -54) and Cauliflower mosaic virus 35S promoter (CE, 254 bp, -343 to -90). The bi-directional nature of the FsFfCBD promoter (coupled to GFP and GUS) was established both in transient systems (onion epidermal cells and tobacco protoplasts) and transgenic plant (Nicotiana tabacum samsun NN) by monitoring the simultaneous expression of GFP and GUS employing fluorescence (for GFP) and biochemical (for GUS) based assays. In transgenic plants, the FsFfCBD promoter was found to be 6.8 and 2.5 times stronger than two parent promoters; Fs and FfC respectively. The bi-directional compound promoter FsFfCBD, composed of three heterologous enhancers with enhanced activity could become a valuable additional tool for efficient plant metabolic engineering and molecular pharming.
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Affiliation(s)
- Sunita Patro
- Division of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Govt. of India, Nalco Square, Chandrasekherpur, Bhubaneswar 751 023, Odisha, India
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Yi C, Hong Y. Estimating the copy number of transgenes in transformed cotton by real-time quantitative PCR. Methods Mol Biol 2013; 958:109-30. [PMID: 23143487 DOI: 10.1007/978-1-62703-212-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transgenic cotton has widely been employed both in commercial cultivation and basic research. It is essential to determine which plants contain the transgene and in how many copies after transgenic cotton plants are generated. A TaqMan quantitative real-time polymerase chain reaction (Tq RT-PCR) method is described here to examine transgene copy number in transgenic cotton plants. The estimation of two transgene elements, the target gene of green fluorescence protein (GFP) and the selective gene of neomycin phosphotransferase II (NPTII), is used as an example to detail each step in Tq RT-PCR procedure, including endogenous reference gene selection, reference plasmid construction, primer-probe design, DNA extraction, real-time PCR, and data analysis. Comparing with traditional approach-Southern hybridization -analysis, this method can be used efficiently in screening large number of T0 transgenic cotton plants at early stage of transformation process as well as identifying transgene homozygotes in a segregation population.
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Affiliation(s)
- Chengxin Yi
- JOil (S) Pte Ltd, 1 Research Link, National University of Singapore, Singapore, Singapore
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Abstract
Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.
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Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
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Cao Y, Wu G, Wu Y, Nie S, Zhang L, Lu C. Characterization of the transgenic rice event TT51-1 and construction of a reference plasmid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:8550-8559. [PMID: 21749035 DOI: 10.1021/jf201699s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transgenic rice TT51-1 (BT63) is an insect resistant strain that was granted for safety certificate in China in 2009. This study characterizes the transgenic event TT51-1 using a GenomeWalker strategy. The organization of the transgenes indicated that the transgenes on two plasmids, pFHBT1 and pGL2RC7, had been integrated at the same locus. The sequence of the event TT51-1 spanned 8725 bp, including a truncated Cry1Ab/Ac cassette, an intact Cry1Ab/Ac cassette, two Amp gene segments, and an Hph gene segment. The 5' and 3' plant flanking sequences were isolated and used to locate the transgenes to chromosome 10 in TT51-1. The isolated TT51-1 fragment and a fragment of the rice PLD gene were integrated into a plasmid vector, to create plasmid pK-TT51 as a calibrator for detecting rice containing TT51-1. Analysis of unknown samples indicated that the reference plasmid was a reliable alternative to TT51-1 genomic DNA.
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Affiliation(s)
- Yinglong Cao
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Ribas AF, Dechamp E, Champion A, Bertrand B, Combes MC, Verdeil JL, Lapeyre F, Lashermes P, Etienne H. Agrobacterium-mediated genetic transformation of Coffea arabica (L.) is greatly enhanced by using established embryogenic callus cultures. BMC PLANT BIOLOGY 2011; 11:92. [PMID: 21595964 PMCID: PMC3111370 DOI: 10.1186/1471-2229-11-92] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 05/19/2011] [Indexed: 05/06/2023]
Abstract
BACKGROUND Following genome sequencing of crop plants, one of the main challenges today is determining the function of all the predicted genes. When gene validation approaches are used for woody species, the main obstacle is the low recovery rate of transgenic plants from elite or commercial cultivars. Embryogenic calli have frequently been the target tissue for transformation, but the difficulty in producing or maintaining embryogenic tissues is one of the main problems encountered in genetic transformation of many woody plants, including Coffea arabica. RESULTS We identified the conditions required for successful long-term proliferation of embryogenic cultures in C. arabica and designed a highly efficient and reliable Agrobacterium tumefaciens-mediated transformation method based on these conditions. The transformation protocol with LBA1119 harboring pBin 35S GFP was established by evaluating the effect of different parameters on transformation efficiency by GFP detection. Using embryogenic callus cultures, co-cultivation with LBA1119 OD600 = 0.6 for five days at 20 °C enabled reproducible transformation. The maintenance conditions for the embryogenic callus cultures, particularly a high auxin to cytokinin ratio, the age of the culture (optimum for 7-10 months of proliferation) and the use of a yellow callus phenotype, were the most important factors for achieving highly efficient transformation (> 90%). At the histological level, successful transformation was related to the number of proembryogenic masses present. All the selected plants were proved to be transformed by PCR and Southern blot hybridization. CONCLUSION Most progress in increasing transformation efficiency in coffee has been achieved by optimizing the production conditions of embryogenic cultures used as target tissues for transformation. This is the first time that a strong positive effect of the age of the culture on transformation efficiency was demonstrated. Our results make Agrobacterium-mediated transformation of embryogenic cultures a viable and useful tool both for coffee breeding and for the functional analysis of agronomically important genes.
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Affiliation(s)
- Alessandra F Ribas
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Département des Systèmes Biologiques (CIRAD-BIOS). UMR-RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Eveline Dechamp
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Département des Systèmes Biologiques (CIRAD-BIOS). UMR-RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Anthony Champion
- IRD - Institut de Recherche pour le Développement, UMR RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Benoît Bertrand
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Département des Systèmes Biologiques (CIRAD-BIOS). UMR-RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Marie-Christine Combes
- IRD - Institut de Recherche pour le Développement, UMR RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Jean-Luc Verdeil
- CIRAD-BIOS, MRI, UMR-DAP, Plant cell imaging platform (www.PHIV.cirad.fr), Avenue Agropolis, 34398 Montpellier, Cedex 5, France
| | - Fabienne Lapeyre
- CIRAD-BIOS, MRI, UMR-DAP, Plant cell imaging platform (www.PHIV.cirad.fr), Avenue Agropolis, 34398 Montpellier, Cedex 5, France
| | - Philippe Lashermes
- IRD - Institut de Recherche pour le Développement, UMR RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Hervé Etienne
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Département des Systèmes Biologiques (CIRAD-BIOS). UMR-RPB (CIRAD, IRD, Université Montpellier II), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
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Nathwani AC, Rosales C, McIntosh J, Rastegarlari G, Nathwani D, Raj D, Nawathe S, Waddington SN, Bronson R, Jackson S, Donahue RE, High KA, Mingozzi F, Ng CYC, Zhou J, Spence Y, McCarville MB, Valentine M, Allay J, Coleman J, Sleep S, Gray JT, Nienhuis AW, Davidoff AM. Long-term safety and efficacy following systemic administration of a self-complementary AAV vector encoding human FIX pseudotyped with serotype 5 and 8 capsid proteins. Mol Ther 2011; 19:876-85. [PMID: 21245849 DOI: 10.1038/mt.2010.274] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Adeno-associated virus vectors (AAV) show promise for liver-targeted gene therapy. In this study, we examined the long-term consequences of a single intravenous administration of a self-complementary AAV vector (scAAV2/ 8-LP1-hFIXco) encoding a codon optimized human factor IX (hFIX) gene in 24 nonhuman primates (NHPs). A dose-response relationship between vector titer and transgene expression was observed. Peak hFIX expression following the highest dose of vector (2 × 10(12) pcr-vector genomes (vg)/kg) was 21 ± 3 µg/ml (~420% of normal). Fluorescent in-situ hybridization demonstrated scAAV provirus in almost 100% of hepatocytes at that dose. No perturbations of clinical or laboratory parameters were noted and vector genomes were cleared from bodily fluids by 10 days. Macaques transduced with 2 × 10(11) pcr-vg/kg were followed for the longest period (~5 years), during which time expression of hFIX remained >10% of normal level, despite a gradual decline in transgene copy number and the proportion of transduced hepatocytes. All macaques developed serotype-specific antibodies but no capsid-specific cytotoxic T lymphocytes were detected. The liver was preferentially transduced with 300-fold more proviral copies than extrahepatic tissues. Long-term biochemical, ultrasound imaging, and histologic follow-up of this large cohort of NHP revealed no toxicity. These data support further evaluation of this vector in hemophilia B patients.
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Affiliation(s)
- Amit C Nathwani
- Department of Hematology, University College London Cancer Institute, London, UK.
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Abstract
Electrical and chemical synapses provide two distinct modes of direct communication between neurons, and the embryonic development of the two is typically not simultaneous. Instead, in both vertebrates and invertebrates, gap junction-based electrical synapses arise before chemical synaptogenesis, and the early circuits composed of gap junction-based electrical synapses resemble those produced later by chemical synapses. This developmental sequence from electrical to chemical synapses has led to the hypothesis that, in developing neuronal circuits, electrical junctions are necessary forerunners of chemical synapses. Up to now, it has been difficult to test this hypothesis directly, but we can identify individual neurons in the leech nervous system from before the time when synapses are first forming, so we could test the hypothesis. Using RNA interference, we transiently reduced gap junction expression in individual identified neurons during the 2-4 d when chemical synapses normally form. We found that the expected chemical synapses failed to form on schedule, and they were still missing months later when the nervous system was fully mature. We conclude that the formation of gap junctions between leech neurons is a necessary step in the formation of chemical synaptic junctions, confirming the predicted relation between electrical synapses and chemical synaptogenesis.
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Esmaeili F, Bamdad T, Ghasemi S. Stable suppression of gene expression by short interfering RNAs targeted to promoter in a mouse embryonal carcinoma stem cell line. In Vitro Cell Dev Biol Anim 2010; 46:834-40. [PMID: 20872183 DOI: 10.1007/s11626-010-9347-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 08/19/2010] [Indexed: 11/26/2022]
Abstract
RNA interference (RNAi) can induce gene silencing via two pathways: post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). The mediators of gene inactivation in both pathways are 21-bp small interfering RNAs (siRNAs) generated from longer double-stranded RNA (dsRNA). PTGS involves siRNA-mediated targeting and degradation of mRNA. However, siRNAs induce TGS via DNA methylation at the targeted promoter. Synthetic siRNAs can induce loss of gene activity comparable to long dsRNA. The limitation of this method is that the transfected synthetic siRNA works for only a few days. In this study, we tested the RNAi response to siRNA (PTGS pathway) by using a plasmid containing an enhanced green fluorescent protein (eGFP) gene as a target as well as a plasmid creates siRNA transcript, in a form of a hairpin, against eGFP gene. To investigate TGS pathway via RNAi, we also used a plasmid creates hairpin siRNA transcript against pgk-1 promoter. The data presented here indicated long-lasting inhibition in expression of eGFP and puromycin genes, both under the control of the murine Pgk-1 promoter. However, Southern blot analysis showed no methylation in pgk-1 promoter.
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Affiliation(s)
- Fariba Esmaeili
- Department of Biology, Faculty of Basic Sciences, Shahr-e-kord University, Shahr-e-kord, Iran.
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Borejsza-Wysocka E, Norelli JL, Aldwinckle HS, Malnoy M. Stable expression and phenotypic impact of attacin E transgene in orchard grown apple trees over a 12 year period. BMC Biotechnol 2010; 10:41. [PMID: 20525262 PMCID: PMC2910661 DOI: 10.1186/1472-6750-10-41] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 06/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background Transgenic trees currently are being produced by Agrobacterium-mediated transformation and biolistics. The future use of transformed trees on a commercial basis depends upon thorough evaluation of the potential environmental and public health risk of the modified plants, transgene stability over a prolonged period of time and the effect of the gene on tree and fruit characteristics. We studied the stability of expression and the effect on resistance to the fire blight disease of the lytic protein gene, attacin E, in the apple cultivar 'Galaxy' grown in the field for 12 years. Results Using Southern and western blot analysis, we compared transgene copy number and observed stability of expression of this gene in the leaves and fruit in several transformed lines during a 12 year period. No silenced transgenic plant was detected. Also the expression of this gene resulted in an increase in resistance to fire blight throughout 12 years of orchard trial and did not affect fruit shape, size, acidity, firmness, weight or sugar level, tree morphology, leaf shape or flower morphology or color compared to the control. Conclusion Overall, these results suggest that transgene expression in perennial species, such as fruit trees, remains stable in time and space, over extended periods and in different organs. This report shows that it is possible to improve a desirable trait in apple, such as the resistance to a pathogen, through genetic engineering, without adverse alteration of fruit characteristics and tree shape.
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Choi HW, Yu XH, Lemaux PG, Cho MJ. Stability and inheritance of endosperm-specific expression of two transgenes in progeny from crossing independently transformed barley plants. PLANT CELL REPORTS 2009; 28:1265-1272. [PMID: 19529943 PMCID: PMC2717377 DOI: 10.1007/s00299-009-0726-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 05/11/2009] [Accepted: 05/27/2009] [Indexed: 05/27/2023]
Abstract
To study stability and inheritance of two different transgenes in barley, we crossed a homozygous T(8) plant, having uidA (or gus) driven by the barley endosperm-specific B(1)-hordein promoter (localized in the near centromeric region of chromosome 7H) with a second homozygous T(4) plant, having sgfp(S65T) driven by the barley endosperm-specific D-hordein promoter (localized on the subtelomeric region of chromosome 2H). Both lines stably expressed the two transgenes in the generations prior to the cross. Three independently crossed F(1) progeny were analyzed by PCR for both uidA and sgfp(S65T) in each plant and functional expression of GUS and GFP in F(2) seeds followed a 3:1 Mendelian segregation ratio and transgenes were localized by FISH to the same location as in the parental plants. FISH was used to screen F(2) plants for homozygosity of both transgenes; four homozygous plants were identified from the two crossed lines tested. FISH results showing presence of transgenes were consistent with segregation ratios of expression of both transgenes, indicating that the two transgenes were expressed without transgene silencing in homozygous progeny advanced to the F(3) and F(4) generations. Thus, even after crossing independently transformed, homozygous parental plants containing a single, stably expressed transgene, progeny were obtained that continued to express multiple transgenes through generation advance. Such stability of transgenes, following outcrossing, is an important attribute for trait modification and for gene flow studies.
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Affiliation(s)
- Hae-Woon Choi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- School of Bioscience and Biotechnology, Chungnam National University, Daejeon, 305-764 Korea
| | - Xiao-Hong Yu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973 USA
| | - Peggy G. Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Myeong-Je Cho
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- RWC Research Campus, Pioneer Hi-Bred International, Inc., 700A Bay Road, Redwood City, CA 94063 USA
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Zhang C, Gai Y, Wang W, Zhu Y, Chen X, Jiang X. Construction and analysis of a plant transformation binary vector pBDGG harboring a bi-directional promoter fusing dual visible reporter genes. J Genet Genomics 2009; 35:245-9. [PMID: 18439982 DOI: 10.1016/s1673-8527(08)60034-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 11/27/2007] [Accepted: 12/07/2007] [Indexed: 11/28/2022]
Abstract
The constitutive promoter of cauliflower mosaic virus 35S (CaMV 35S) is a polar unidirectional promoter and is widely used in plant genetic engineering. In the present study, the unidirectional CaMV 35S promoter has been modified to a bi-directional promoter by fusing its minimal promoter element to the 5' end of CaMV 35S promoter in the opposite orientation. To qualitatively and quantitatively estimate its bi-directional transcriptional function and activity, two visible reporter genes, gusA (beta-glucuronidase, GUS) and gfp (green fluorescent protein, GFP), were fused to the two ends of the promoter in bi-orientations ending with NOS terminator sequences, respectively. Stable expression of gusA and gfp genes in transgenic tobacco (Nicotiana tabacum L.) was visualized by histochemically staining for GUS and fluorescence microscopic observation under UV for GFP in transgenic plants. The expression of two reporter genes showed that the constructed bi-directional promoter did have the bi-directional transcriptional function in both expected orientations. The quantitative estimation of GUS and GFP were determined on a HITACHI F1000 Fluorescence Spectrophotometer with various wavelengths of excitation and emission. The GUS activity varied from 8 to 250 pmol 4-MU/min/mg protein and the GFP content varied from 0.9 to 1.8 microg/mg protein in various lines of transgenic tobacco plants. Higher GUS activity generally coupled with lower GFP content, and vice versa.
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Affiliation(s)
- Chunxiao Zhang
- College of Bioscience and Bioengineering, Hebei University of Science & Technology, Shijiazhuang 050018, China
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Dalla Costa L, Vaccari I, Mandolini M, Martinelli L. Elaboration of a reliable strategy based on real-time PCR to characterize genetically modified plantlets and to evaluate the efficiency of a marker gene removal in grape (Vitis spp.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:2668-77. [PMID: 19265380 DOI: 10.1021/jf802740m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We have developed an effective strategy based on real-time PCR assay for the molecular characterization of genetically modified grape and to quantify the efficiency of a marker gene removal. This research has been implemented in Vitis vinifera cv. Brachetto plantlets where exogenes were inserted during cocultures of embryogenic calli with Agrobacterium tumefaciens carrying the chemically inducible site-specific cre/loxP pX6 vector where the expression of the cre recombinase is regulated by 17-beta-estradiol. The neomycin phosphotransferase gene (nptII) for the kanamycin resistance trait was inserted as part of the gene transfer protocol, and this exogene was employed as a case study for carrying out our research. The 9-cis-epoxycarotenoid dioxygenase (nced2) and chalcone isomerase (chi) genes coding for two enzymes, involved respectively in abscisic acid and flavonoid biosynthesis, proved to be valuable reference endogenes for real-time PCR assays. Two types of duplo-target plasmids were exploited for building the standard curves: in one type (p-nptII/nced2) the nptII sequence is linked to the nced2 sequence; in the other (p-nptII/chi) it is linked to the chi. These calibrators were intended to simulate an ideal genetically modified plant carrying a homozygous single-copy exogene insertion. The repeatability test confirmed the suitability of both plasmid calibrators. Foreign gene stability can be monitored during long-term plant preservation, and the method proved to be suitable for quantifying the efficiency of nptII gene removal induced by 17-beta-estradiol.
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Affiliation(s)
- Lorenza Dalla Costa
- Fondazione Edmund Mach-IASMA Research and Innovation Centre, Genomics and Crop Biology Area, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
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Lee SW, Padmanabhan P, Ray P, Gambhir SS, Doyle T, Contag C, Goodman SB, Biswal S. Stem cell-mediated accelerated bone healing observed with in vivo molecular and small animal imaging technologies in a model of skeletal injury. J Orthop Res 2009; 27:295-302. [PMID: 18752273 PMCID: PMC4154812 DOI: 10.1002/jor.20736] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 06/05/2008] [Indexed: 02/04/2023]
Abstract
Adult stem cells are promising therapeutic reagents for skeletal regeneration. We hope to validate by molecular imaging technologies the in vivo life cycle of adipose-derived multipotent cells (ADMCs) in an animal model of skeletal injury. Primary ADMCs were lentivirally transfected with a fusion reporter gene and injected intravenously into mice with bone injury or sham operation. Bioluminescence imaging (BLI), [(18)F]FHBG (9-(fluoro-hydroxy-methyl-butyl-guanine)-micro-PET, [(18)F]Fluoride ion micro-PET and micro-CT were performed to monitor stem cells and their effect. Bioluminescence microscopy and immunohistochemistry were done for histological confirmation. BLI showed ADMC's traffic from the lungs then to the injury site. BLI microscopy and immunohistochemistry confirmed the ADMCs in the bone defect. Micro-CT measurements showed increased bone healing in the cell-injected group compared to the noninjected group at postoperative day 7 (p < 0.05). Systemically administered ADMC's traffic to the site of skeletal injury and facilitate bone healing, as demonstrated by molecular and small animal imaging. Molecular imaging technologies can validate the usage of adult adipose tissue-derived multipotent cells to promote fracture healing. Imaging can in the future help establish therapeutic strategies including dosage and administration route.
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Affiliation(s)
- Sheen-Woo Lee
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
| | - Parasuraman Padmanabhan
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
| | - Pritha Ray
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
| | - Sanjiv Sam Gambhir
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
| | - Timothy Doyle
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Christopher Contag
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Stuart B. Goodman
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Sandip Biswal
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, 300 Pasteur Drive S-062B, Stanford, California 94304
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Abstract
Using a methylated-DNA enrichment technique (methylated CpG island recovery assay, MIRA) in combination with whole-genome tiling arrays, we have characterized by MIRA-chip the entire B cell "methylome" of an individual human at 100-bp resolution. We find that at the chromosome level high CpG methylation density is correlated with subtelomeric regions and Giemsa-light bands (R bands). The majority of the most highly methylated regions that could be identified on the tiling arrays were associated with genes. Approximately 10% of all promoters in B cells were found to be methylated, and this methylation correlates with low gene expression. Notably, apparent exceptions to this correlation were the result of transcription from previously unidentified, unmethylated transcription start sites, suggesting that methylation may control alternate promoter usage. Methylation of intragenic (gene body) sequences was found to correlate with increased, not decreased, transcription, and a methylated region near the 3' end was found in approximately 12% of all genes. The majority of broad regions (10-44 kb) of high methylation were at segmental duplications. Our data provide a valuable resource for the analysis of CpG methylation patterns in a differentiated human cell type and provide new clues regarding the function of mammalian DNA methylation.
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Chan AP, Melake-Berhan A, O'Brien K, Buckley S, Quan H, Chen D, Lewis M, Banks JA, Rabinowicz PD. The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii. BMC Genomics 2008; 9:282. [PMID: 18549478 PMCID: PMC2442089 DOI: 10.1186/1471-2164-9-282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 06/12/2008] [Indexed: 11/28/2022] Open
Abstract
Background The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be produced, little is known about basic aspects of its molecular biology. In order to provide the first glimpse to the epigenetic landscape of this early divergent vascular plant, we used the methylation filtration technique. Methylation filtration genomic libraries select unmethylated DNA clones due to the presence of the methylation-dependent restriction endonuclease McrBC in the bacterial host. Results We conducted a characterization of the DNA methylation patterns of the S. moellendorffii genome by sequencing a set of S. moellendorffii shotgun genomic clones, along with a set of methylation filtered clones. Chloroplast DNA, which is typically unmethylated, was enriched in the filtered library relative to the shotgun library, showing that there is DNA methylation in the extremely small S. moellendorffii genome. The filtered library also showed enrichment in expressed and gene-like sequences, while the highest-copy repeats were largely under-represented in this library. These results show that genes and repeats are differentially methylated in the S. moellendorffii genome, as occurs in other plants studied. Conclusion Our results shed light on the genome methylation pattern in a member of a relatively unexplored plant lineage. The DNA methylation data reported here will help understanding the involvement of this epigenetic mark in fundamental biological processes, as well as the evolutionary aspects of epigenetics in land plants.
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Affiliation(s)
- Agnes P Chan
- J. Craig Venter Institute, Rockville, MD 20850, USA.
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Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 2008; 177:1975-85. [PMID: 18073417 DOI: 10.1534/genetics.107.080234] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) represent approximately 45% of the human genome and 50-90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown that retrotransposons can influence the expression of adjacent host genes. In this study, the methylation patterns of TEs and their flanking sequences in different tissues were undertaken using a novel technique called transposon methylation display (TMD). TMD was successfully applied on a highly copied (approximately 1000 copies), newly amplified LTR retrotransposon family in rice called Dasheng. We determined that the methylation status of a subset of LTRs varies in leaves vs. roots. In addition, we determined that tissue-specific LTR methylation correlated with tissue-specific expression of the flanking rice gene. Genes showing tissue-specific expression were in opposite orientation relative to the LTR. Antisense transcripts were detected in the tissue where the sense transcripts from that gene were not detected. Comparative analysis of Dasheng LTR methylation in the two subspecies, japonica vs. indica revealed LTR-mediated differences in subspecies gene expression. Subspecies-specific expression was due either to polymorphic Dasheng insertion sites between the two subspecies or to subspecies-specific methylation of LTRs at the same locus accounted for observed differences in the expression of adjacent genes.
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Friedman AR, Baker BJ. The evolution of resistance genes in multi-protein plant resistance systems. Curr Opin Genet Dev 2007; 17:493-9. [DOI: 10.1016/j.gde.2007.08.014] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 08/31/2007] [Indexed: 11/26/2022]
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Affiliation(s)
- Pablo D Rabinowicz
- J. C. Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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Latha AM, Rao KV, Reddy TP, Reddy VD. Development of transgenic pearl millet (Pennisetum glaucum (L.) R. Br.) plants resistant to downy mildew. PLANT CELL REPORTS 2006; 25:927-35. [PMID: 16607531 DOI: 10.1007/s00299-006-0141-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 02/02/2006] [Accepted: 02/07/2006] [Indexed: 05/08/2023]
Abstract
Transgenic pearl millet lines expressing pin gene--exhibiting high resistance to downy mildew pathogen, Sclerospora graminicola--were produced using particle-inflow-gun (PIG) method. Shoot-tip-derived embryogenic calli were co-bombarded with plasmids containing pin and bar genes driven by CaMV 35S promoter. Bombarded calli were cultured on MS medium with phosphinothricin as a selection agent. Primary transformants 1T(0), 2T(0), and 3T(0) showed the presence of both bar and pin coding sequences as evidenced by PCR and Southern blot analysis, respectively. T(1) progenies of three primary transformants, when evaluated for downy mildew resistance, segregated into resistant and susceptible phenotypes. T(1) plants resistant to downy mildew invariably exhibited tolerance to Basta suggesting co-segregation of pin and bar genes. Further, the downy mildew resistant 1T(1) plants were found positive for pin gene in Southern and Northern analyses thereby confirming stable integration, expression, and transmission of pin gene. 1T(2) progenies of 1T(0) conformed to dihybrid segregation of 15 resistant:1 susceptible plants.
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Affiliation(s)
- A Madhavi Latha
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007 Andhra Pradesh, India
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McGinnis KM, Springer C, Lin Y, Carey CC, Chandler V. Transcriptionally silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics 2006; 173:1637-47. [PMID: 16702420 PMCID: PMC1526669 DOI: 10.1534/genetics.106.058669] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 05/09/2006] [Indexed: 11/18/2022] Open
Abstract
Plants with mutations in one of three maize genes, mop1, rmr1, and rmr2, are defective in paramutation, an allele-specific interaction that leads to meiotically heritable chromatin changes. Experiments reported here demonstrate that these genes are required to maintain the transcriptional silencing of two different transgenes, suggesting that paramutation and transcriptional silencing of transgenes share mechanisms. We hypothesize that the transgenes are silenced through an RNA-directed chromatin mechanism, because mop1 encodes an RNA-dependent RNA polymerase. In all the mutants, DNA methylation was reduced in the active transgenes relative to the silent transgenes at all of the CNG sites monitored within the transgene promoter. However, asymmetrical methylation persisted at one site within the reactivated transgene in the rmr1-1 mutant. With that one mutant, rmr1-1, the transgene was efficiently resilenced upon outcrossing to reintroduce the wild-type protein. In contrast, with the mop1-1 and rmr2-1 mutants, the transgene remained active in a subset of progeny even after the wild-type proteins were reintroduced by outcrossing. Interestingly, this immunity to silencing increased as the generations progressed, consistent with a heritable chromatin state being formed at the transgene in plants carrying the mop1-1 and rmr2-1 mutations that becomes more resistant to silencing in subsequent generations.
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Affiliation(s)
- Karen M McGinnis
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
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Maghuly F, Leopold S, da Câmara Machado A, Borroto Fernandez E, Ali Khan M, Gambino G, Gribaudo I, Schartl A, Laimer M. Molecular characterization of grapevine plants transformed with GFLV resistance genes: II. PLANT CELL REPORTS 2006; 25:546-53. [PMID: 16408176 DOI: 10.1007/s00299-005-0087-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 10/18/2005] [Accepted: 10/26/2005] [Indexed: 05/06/2023]
Abstract
A collection of 127 putatively transgenic individuals of Vitis vinifera cv. Russalka was characterized by PCR and Southern hybridization. Six different constructs containing the neomycin phosphotransferase (nptII) marker gene and sequences of the Grapevine Fanleaf Virus Coat Protein (GFLV CP) gene including non-translatable and truncated forms were transferred via Agrobacterium-mediated transformation. Detection of transgenic sequences by PCR was positive in all lines. Southern blot analysis revealed that the number of inserted T-DNA copies ranged from 1 to 6. More than 46% of the tested transgenic lines contain one copy of the inserted T-DNA, qualifying them as interesting candidates for further breeding programs. Southern data of one line indicate the presence of an incomplete copy of the T-DNA, thus confirming previous PCR results. Since many putative transgenic lines shared identical hybridization patterns, they were clustered into 39 lines and considered as having originated from independent transformation events. The detection of the tetracycline (TET) resistance genes in 15% of the lines shows that an integration of plasmid backbone sequences beyond the T-DNA borders occurred. Enzyme-linked immunosorbent assay (ELISA) performed on leaf tissue did not show any accumulation of the GFLV CP in the 39 transgenic lines analyzed. Reverse transcription polymerase chain reaction (RT-PCR) and Northern blot were carried out; RT-PCR analyses showed that the GFLV CP mRNA was expressed at variable levels.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Biotechnology Unit, Institute of Applied Microbiology BOKU, Nussdorfer Lände 11, A-1190 Vienna, Austria
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Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O'Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA. Differential methylation of genes and repeats in land plants. Genome Res 2006; 15:1431-40. [PMID: 16204196 PMCID: PMC1240086 DOI: 10.1101/gr.4100405] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration (MF). Therefore, MF has been used as a gene enrichment technology in sorghum and maize, where gene enrichment was proportional to genome size. Here we apply MF to a broad variety of plant species spanning a wide range of genome sizes. Differential methylation of genic and non-genic sequences was observed in all species tested, from non-vascular to vascular plants, but in some cases, such as wheat and pine, a lower than expected level of enrichment was observed. Remarkably, hexaploid wheat and pine show a dramatically large number of gene-like sequences relative to other plants. In hexaploid wheat, this apparent excess of genes may reflect an abundance of methylated pseudogenes, which may thus be more prevalent in recent polyploids.
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Influence of the Nature of the T-DNA Insertion Region on Transgene Expression in Arabidopsis thaliana. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-006-0002-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Neves N, Delgado M, Silva M, Caperta A, Morais-Cecílio L, Viegas W. Ribosomal DNA heterochromatin in plants. Cytogenet Genome Res 2005; 109:104-11. [PMID: 15753565 DOI: 10.1159/000082388] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 02/19/2004] [Indexed: 11/19/2022] Open
Abstract
The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.
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Affiliation(s)
- N Neves
- Secção de Genética, Centro de Botânica Aplicada à Agricultura, Instituto Superior de Agronomia, Lisboa, Portugal
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Ma XF, Gustafson JP. Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 2005; 109:236-49. [PMID: 15753583 DOI: 10.1159/000082406] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 03/09/2004] [Indexed: 11/19/2022] Open
Abstract
Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F1 hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.
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Affiliation(s)
- X-F Ma
- Department of Agronomy, University of Missouri-Columbia, MO 65211, USA
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41
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Makvandi-Nejad S, McLean MD, Hirama T, Almquist KC, Mackenzie CR, Hall JC. Transgenic tobacco plants expressing a dimeric single-chain variable fragment (scfv) antibody against Salmonella enterica serotype Paratyphi B. Transgenic Res 2005; 14:785-92. [PMID: 16245169 DOI: 10.1007/s11248-005-7461-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Accepted: 05/17/2005] [Indexed: 10/25/2022]
Abstract
Transgenic tobacco plants were produced that express an anti-Salmonella enterica single-chain variable fragment (scFv) antibody that binds to the lipopolysaccharide (LPS) of S. enterica Paratyphi B. The coding sequence of this scFv was optimized for expression in tobacco, synthesized and subsequently placed behind three different promoters: an enhanced tobacco constitutive ubiquitous promoter (EntCUP4), and single- and double-enhancer versions of the Cauliflower Mosaic Virus 35S promoter (CaMV 35S). These chimeric genes were introduced into Nicotiana tabacum cv. 81V9 by Agrobacterium-mediated transformation and 50 primary transgenic (T(0)) plants per construct were produced. Among these plants, 23 were selected for the ability to express active scFv as determined by enzyme-linked immunosorbent assay (ELISA) using S. enterica LPS as antigen. Expanded bed adsorption-immobilized metal affinity chromatography (EBA-IMAC) was used to purify 41.7 mug of scFv/g from leaf tissue. Gel filtration and surface plasmon resonance (SPR) analyses demonstrated that the purified scFv was active as a dimer or higher-order multimer. In order to identify T(1) plants suitable for development of homozygous lines with heritable scFv expression, kanamycin-resistance segregation analyses were performed to determine the number of T-DNA loci in each T(0) plant, and quantitative ELISA and immunoblot analyses were used to compare expression of active and total anti-Salmonella scFv, respectively, in the T(1) generation. As S. enterica causes millions of enteric fevers and hundreds of thousands of deaths worldwide each year, large-scale production and purification of this scFv will have potential for uses in diagnosis and detection, as a therapeutic agent, and in applications such as water system purification.
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Affiliation(s)
- Shokouh Makvandi-Nejad
- Department of Environmental Biology, University of Guelph, Bovey Building, 50 Stone Rd. E, NIG 2W1 Guelph, Ontario, Canada
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Qu LQ, Yoshihara T, Ooyama A, Goto F, Takaiwa F. Iron accumulation does not parallel the high expression level of ferritin in transgenic rice seeds. PLANTA 2005; 222:225-33. [PMID: 15821927 DOI: 10.1007/s00425-005-1530-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Accepted: 02/22/2005] [Indexed: 05/03/2023]
Abstract
To answer the question whether iron accumulation in transgenic rice seeds depends on the expression level of exogenous soybean ferritin, we generated two kinds of ferritin hyper-expressing rice lines by introducing soybean ferritin SoyferH-1 gene under the control of the rice seed storage glutelin gene promoter, GluB-1 and the rice seed storage globulin gene promoter, Glb-1, (GluB-1/SoyferH-1 and Glb-1/SoyferH-1, DF lines), and by introducing the SoyferH-1 gene under the control of Glb-1 promoter alone (Glb-1/SoyferH-1, OF lines). Ferritin expression was restricted to the endosperm in both lines and protein levels determined by western blot analysis were up to 13-fold higher than in a construct previously reported FK22 (GluB-1/SoyferH-1, in genetically Kitaake background); [corrected] however, the maximum iron concentrations in seeds of both of the new lines were only about 30% higher than FK22. The maximum iron concentration in the OF and DF lines was about threefold higher than in the non-transformant. The mean Fe concentration in leaves of ferritin over-expressing lines decreased to less than half of the non-transformant while that the plant biomasses and seed yields of the ferritin-transformed lines were not significantly different from those of the non-transformant, suggesting that accumulation of Fe in seeds of hyper-expression ferritin rice did not always depend on the expression level of exogenous ferritin but may have been limited by Fe uptake and transport. No obvious differences were observed for other divalent-metal concentrations (Ca, Cd, Cu, Mg, Mn and Zn) in the seeds among all experimental lines and non-transformant.
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Affiliation(s)
- Le Qing Qu
- Laboratory of Genetic Engineering, Department of Plant Biotechnology, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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Engineer CB, Fitzsimmons KC, Schmuke JJ, Dotson SB, Kranz RG. Development and evaluation of a Gal4-mediated LUC/GFP/GUS enhancer trap system in Arabidopsis. BMC PLANT BIOLOGY 2005; 5:9. [PMID: 15941484 PMCID: PMC1164422 DOI: 10.1186/1471-2229-5-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 06/07/2005] [Indexed: 05/02/2023]
Abstract
BACKGROUND Gal4 enhancer trap systems driving expression of LacZ and GFP reporters have been characterized and widely used in Drosophila. However, a Gal4 enhancer trap system in Arabidopsis has not been described in the primary literature. In Drosophila, the reporters possess a Gal4 upstream activation sequence (UAS) as five repeats (5XUAS) and lines that express Gal4 from tissue specific enhancers have also been used for the ectopic expression of any transgene (driven by a 5XUAS). While Gal4 transactivation has been demonstrated in Arabidopsis, wide use of a trap has not emerged in part because of the lack of detailed analysis, which is the purpose of the present study. RESULTS A key feature of this study is the use of luciferase (LUC) as the primary reporter and rsGFP-GUS as secondary reporters. Reporters driven by a 5XUAS are better suited in Arabidopsis than those containing a 1X or 2X UAS. A 5XUAS-LUC reporter is expressed at high levels in Arabidopsis lines transformed with Gal4 driven by the full, enhanced 35S promoter. In contrast, a minimum 35S (containing the TATA region) upstream of Gal4 acts as an enhancer trap system. Luciferase expression in trap lines of the T1, T2, and T3 generations are generally stable but by the T4 generation approximately 25% of the lines are significantly silenced. This silencing is reversed by growing plants on media containing 5-aza-2'-deoxycytidine. Quantitative multiplex RT-PCR on the Gal4 and LUC mRNA indicate that this silencing can occur at the level of Gal4 or LUC transcription. Production of a 10,000 event library and observations on screening, along with the potential for a Gal4 driver system in other plant species are discussed. CONCLUSION The Gal4 trap system described here uses the 5XUAS-LUC and 5XUAS rsGFP-GUS as reporters and allows for in planta quantitative screening, including the rapid monitoring for silencing. We conclude that in about 75% of the cases silencing is at the level of transcription of the Gal4 transgene and is at an acceptable frequency to make the Gal4 trap system in Arabidopsis of value. This system will be useful for the isolation and comprehensive characterization of specific reporter and driver lines.
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Affiliation(s)
- Cawas B Engineer
- Washington University, Department of Biology Campus Box 1137, 1 Brookings Drive St. Louis, MO 63130, USA
| | - Karen C Fitzsimmons
- Washington University, Department of Biology Campus Box 1137, 1 Brookings Drive St. Louis, MO 63130, USA
| | | | | | - Robert G Kranz
- Washington University, Department of Biology Campus Box 1137, 1 Brookings Drive St. Louis, MO 63130, USA
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Yang L, Ding J, Zhang C, Jia J, Weng H, Liu W, Zhang D. Estimating the copy number of transgenes in transformed rice by real-time quantitative PCR. PLANT CELL REPORTS 2005; 23:759-63. [PMID: 15459795 DOI: 10.1007/s00299-004-0881-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 08/20/2004] [Accepted: 08/21/2004] [Indexed: 05/24/2023]
Abstract
In transgenic plants, transgene copy number can greatly influence the expression level and genetic stability of the target gene, making estimation of transgene copy number an important area of genetically modified (GM) crop research. Transgene copy numbers are currently estimated by Southern analysis, which is laborious and time-consuming, requires relatively large amounts of plant materials and may involve hazardous radioisotopes. We report here the development of a sensitive, high-throughput real-time (RT)-PCR technique for estimating transgene copy number in GM rice. This system uses TaqMan quantitative RT-PCR and comparison to a novel rice endogenous reference gene coding for sucrose phosphate synthase (SPS) to determine the copy numbers of the exogenous beta-glucuronidase (GUS) and hygromycin phosphotransferase (HPT) genes in transgenic rice. The copy numbers of the GUS and HPT in primary rice transformants (T0) were calculated by comparing quantitative PCR results of the GUS and HPT genes with those of the internal standard, SPS. With optimized PCR conditions, we achieved significantly accurate estimates of one, two, three and four transgene copies in the T0 transformants. Furthermore, our copy number estimations of both the GUS reporter gene and the HPT selective marker gene showed that rearrangements of the T-DNA occurred more frequently than is generally believed in transgenic rice.
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Affiliation(s)
- Litao Yang
- School of life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
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Breault JE, Shiina H, Igawa M, Ribeiro-Filho LA, Deguchi M, Enokida H, Urakami S, Terashima M, Nakagawa M, Kane CJ, Carroll PR, Dahiya R. Methylation of the γ -Catenin Gene Is Associated With Poor Prognosis of Renal Cell Carcinoma. Clin Cancer Res 2005. [DOI: 10.1158/1078-0432.557.11.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: γ-Catenin is a cell adhesion protein, and its functional loss is associated with tumor invasion and metastasis. We hypothesize that (1) promoter CpG methylation regulates the expression and function of the γ-catenin gene in renal cell carcinoma (RCC) and (2) methylation of the γ-catenin gene is associated with poor prognosis of RCC. To test these hypotheses, we analyzed the CpG methylation status of the γ-catenin gene and its correlation with clinical outcome in RCC.
Experimental Design: Genomic DNA and total RNA were extracted from three renal cancer cell lines (A498, Caki-1, and Caki-2) and 54 RCC tissue samples with their corresponding normal kidney tissue samples. Expression of γ-catenin gene was analyzed by reverse transcription-PCR and immunostaining. Promoter methylation was analyzed by two different methylation-specific PCR (MSP-A and MSP-B), and the results were verified by DNA sequencing.
Results: The demethylating agent (5-aza-2′-deoxycytidine) increased levels of mRNA transcript of the γ-catenin gene in three renal cancer cell lines. γ-Catenin mRNA and protein expression were significantly reduced in RCC samples compared with normal kidney samples, respectively (P < 0.05). MSP-A and MSP-B bands were detected in 45 of 54 (83.3%) and 49 of 54 (90.7%) RCC samples, respectively. In normal kidney, weak products of MSP-A and MSP-B were detected in 5 of 54 (9.3%) and 6 of 54 (11.1%) samples, respectively. Likewise, both MSP-A and MSP-B ratios were significantly higher in RCC samples compared with normal kidney samples, respectively (P < 0.01). Multivariate analysis revealed that the MSP-B ratio was a powerful and independent predictor superior to nuclear grade and Robson stage with respect to survival and disease progression (P = 0.029 and 0.0071, respectively). No mutations in the NH2-terminal region of γ-catenin were found in this study.
Conclusion: Expression of γ-catenin is regulated by promoter CpG methylation, and the balance between methylated and unmethylated RCC cell populations could determine its functional role. Because the conventional nuclear grade and/or staging system have some limitations to predict precise clinical outcome, this is the first report demonstrating that promoter CpG methylation of γ-catenin can be an independent and superior predictor for survival and disease progression.
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Affiliation(s)
- Julia E. Breault
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | - Hiroaki Shiina
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | | | - Leopoldo A. Ribeiro-Filho
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | - Masao Deguchi
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | - Hideki Enokida
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | - Shinji Urakami
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | | | - Masayuki Nakagawa
- 4Department of Urology, Kagoshima University Faculty of Medicine, Kagoshima, Japan
| | - Christopher J. Kane
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | - Peter R. Carroll
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
| | - Rajvir Dahiya
- 1Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California; Departments of
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Braithwaite KS, Geijskes RJ, Smith GR. A variable region of the sugarcane bacilliform virus (SCBV) genome can be used to generate promoters for transgene expression in sugarcane. PLANT CELL REPORTS 2004; 23:319-26. [PMID: 15309498 DOI: 10.1007/s00299-004-0817-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2004] [Revised: 05/01/2004] [Accepted: 05/04/2004] [Indexed: 05/03/2023]
Abstract
Four promoters derived from sugarcane bacilliform virus (SCBV) were compared and characterised. Three were obtained by PCR amplification of purified virion DNA extracted from three sugarcane cultivars. The fourth promoter was obtained by subcloning from an almost genome-length clone of SCBV. All promoters were able to drive stable expression of beta-glucuronidase in sugarcane. The PCR-derived promoter sequences shared more DNA homology with banana streak virus than to the subcloned SCBV. The subcloned promoter was the strongest expressing and was able to drive reporter gene expression in vitro and in the leaves, meristems and roots of glasshouse-grown sugarcane. Expression levels were at least equal to or higher than those measured for the maize polyubiquitin promoter.
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Affiliation(s)
- K S Braithwaite
- David North Plant Research Centre, BSES Limited, P.O. Box 86, Indooroopilly, Queensland, 4068, Australia.
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Tomita R, Hamada T, Horiguchi G, Iba K, Kodama H. Transgene overexpression with cognate small interfering RNA in tobacco. FEBS Lett 2004; 573:117-20. [PMID: 15327985 DOI: 10.1016/j.febslet.2004.07.063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 07/20/2004] [Accepted: 07/27/2004] [Indexed: 10/26/2022]
Abstract
Small interfering RNAs (siRNAs) are a key component of RNA silencing, including cosuppression. Here, we show an example in which siRNA does not serve in the downregulation of target genes. A tobacco endoplasmic reticulum omega-3 fatty acid desaturase (NtFAD3) catalyzes the formation of alpha-linolenate (18:3). Introduction of the NtFAD3 gene into tobacco plants caused strong reduction of 18:3 content in leaf tissues, which is associated with the production of the NtFAD3 siRNAs. However, this silencing effect was lacking in the root tissues. Both the introduced NtFAD3 and endogenous NtFAD3 genes were expressed successfully, and the roots showed increased 18:3 phenotype. Surprisingly, the NtFAD3 siRNAs were produced even in the root tissues. Expression of a hairpin double-stranded RNA against the NtFAD3 gene caused efficient reduction of 18:3 content in root tissues. Therefore, cosuppression of the NtFAD3 gene in tobacco appears to include an as yet unidentified developmental stage and tissue-specific mechanism of regulation of siRNA function.
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Affiliation(s)
- Rie Tomita
- Department of Bioproduction Science, Faculty of Horticulture, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
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Rudd S, Frisch M, Grote K, Meyers BC, Mayer K, Werner T. Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. PLANT PHYSIOLOGY 2004; 135:715-22. [PMID: 15208419 PMCID: PMC514109 DOI: 10.1104/pp.103.037861] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Revised: 03/26/2004] [Accepted: 03/28/2004] [Indexed: 05/17/2023]
Abstract
We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation of S/MARs inside genes. In cases where S/MARs were predicted within genes, these intragenic S/MARs were preferentially located within the 5'-half, most prominently within introns 1 and 2. Using Arabidopsis whole-genome expression data generated by the massively parallel signature sequencing methodology, we found a negative correlation between S/MAR-containing genes and transcriptional abundance. Expressed sequence tag data correlated the same way with S/MAR-containing genes. Thus, intragenic S/MARs show a negative correlation with transcription level. For various genes it has been shown experimentally that S/MARs can function as transcriptional regulators and that they have an implication in stabilizing expression levels within transgenic plants. On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation.
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Affiliation(s)
- Stephen Rudd
- Munich Information Center for Protein Sequences/Institute for Bioinformatics, GSF-National Research Center for Environment and Health, 85764 Neuherberg, Germany
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Han Y, Griffiths A, Li H, Grierson D. The effect of endogenous mRNA levels on co-suppression in tomato. FEBS Lett 2004; 563:123-8. [PMID: 15063735 DOI: 10.1016/s0014-5793(04)00280-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Revised: 03/08/2004] [Accepted: 03/08/2004] [Indexed: 11/25/2022]
Abstract
Introduction of truncated polygalacturonase (PG) transgenes into tomato plants caused the production of small interfering RNAs (siRNAs) and co-suppression of both the endogenous and PG transgenes in ripening fruits by post-transcriptional gene silencing. In order to test the possible effect on co-suppression of the endogenous PG mRNA level, we transferred the PG transgenes from a PG-silenced line (wild type background) by crossing to two ripening regulatory mutants with reduced PG: Never-ripe (Nr, approximately 10% endogenous PG mRNA compared to wild type) and ripening-inhibitor (rin, approximately 1% endogenous PG mRNA) and to wild type (as a control). The PG transgenes caused strong co-suppression of the transgenes and the endogenous PG gene in cells with high PG mRNA background (wild type) and silencing appeared to be linked with higher transgene copy number and/or a particular transgene locus. In cells with low endogenous PG mRNA accumulation (Nr), the endogenous PG gene was preferentially suppressed compared to the transgenes, whose expression was not reduced significantly. The expression of the transgenes was also not reduced in the very low PG background (rin), in which endogenous PG was barely detectable. In all the analysed lines with all three PG background levels, siRNAs accumulated in leaves and green fruits, in which the endogenous PG gene is not transcribed. The relatively abundant production of siRNAs in most of the lines was linked with a particular transgene insert. These results suggest that a certain threshold level of endogenous PG mRNA is required for the co-suppression of the truncated PG transgenes and the endogenous PG gene or for extensive silencing of the transgenes.
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MESH Headings
- Crosses, Genetic
- Gene Dosage
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Solanum lycopersicum/genetics
- Mutagenesis, Insertional
- Plants, Genetically Modified
- RNA Processing, Post-Transcriptional
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/biosynthesis
- Suppression, Genetic
- Transgenes
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Affiliation(s)
- Yuanhuai Han
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Abstract
RNA-mediated gene silencing has emerged in recent years as an important mechanism for regulating gene expression. Some of the key discoveries have been made in plants
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Affiliation(s)
- Marjori A Matzke
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences in Vienna, Austria.
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