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Park ME, Yun JY, Kim HU. C-to-G Base Editing Enhances Oleic Acid Production by Generating Novel Alleles of FATTY ACID DESATURASE 2 in Plants. Front Plant Sci 2021; 12:748529. [PMID: 34764970 PMCID: PMC8576475 DOI: 10.3389/fpls.2021.748529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/30/2021] [Indexed: 06/01/2023]
Abstract
The demand for vegetable oil, which is mainly used for dietary purposes and cooking, is steadily increasing worldwide. It is often desirable to reduce unsaturation levels of fatty acids in order to increase storage stability and reduce trans-fat generation during cooking. Functional disruption of FATTY ACID DESATURASE 2 (FAD2) prevents the conversion of monounsaturated oleic acid to polyunsaturated linoleic acid, thereby enhancing the production of the desirable oleic acid. However, FAD2 null alleles, due to growth defects under stress conditions, are impractical for agronomical purposes. Here, we aimed to attenuate FAD2 activity in planta while avoiding adverse growth effects by introducing amino-acid substitutions using CRISPR base editors. In Arabidopsis, we applied the adenine base editor (ABE) and cytosine base editor (CBE) to induce semi-random base substitutions within several selected FAD2 coding regions. Isolation of base-edited fad2 alleles with higher oleic acid revealed that the CBE application induced C-to-T and/or C-to-G base substitutions within the targeted sequences, resulting in an alteration of the FAD2 enzyme activities; for example, fad2-144 with multiple C-to-G base substitutions showed less growth defects but with a significant increase in oleic acids by 3-fold higher than wild type. Our "proof-of-concept" approach suggests that equivalent alleles may be generated in vegetable oil crops via precision genome editing for practical cultivation. Our targeted semi-random strategy may serve as a new complementary platform for planta engineering of useful agronomic traits.
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Affiliation(s)
- Mid-Eum Park
- Department of Molecular Biology, Graduate School, Sejong University, Seoul, South Korea
| | - Jae-Young Yun
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | - Hyun Uk Kim
- Department of Molecular Biology, Graduate School, Sejong University, Seoul, South Korea
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
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Hu J, Cai J, Park SJ, Lee K, Li Y, Chen Y, Yun JY, Xu T, Kang H. N 6 -Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant J 2021; 106:1759-1775. [PMID: 33843075 DOI: 10.1111/tpj.15270] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 05/16/2023]
Abstract
As the most abundant internal modification of mRNA, N6 -methyladenosine (m6 A) methylation of RNA is emerging as a new layer of epitranscriptomic gene regulation in cellular processes, including embryo development, flowering-time control, microspore generation and fruit ripening, in plants. However, the cellular role of m6 A in plant responses to environmental stimuli remains largely unexplored. In this study, we show that m6 A methylation plays an important role in salt stress tolerance in Arabidopsis. All mutants of m6 A writer components, including MTA, MTB, VIRILIZER (VIR) and HAKAI, displayed salt-sensitive phenotypes in an m6 A-dependent manner. The vir mutant, in which the level of m6 A was most highly reduced, exhibited salt-hypersensitive phenotypes. Analysis of the m6 A methylome in the vir mutant revealed a transcriptome-wide loss of m6 A modification in the 3' untranslated region (3'-UTR). We demonstrated further that VIR-mediated m6 A methylation modulates reactive oxygen species homeostasis by negatively regulating the mRNA stability of several salt stress negative regulators, including ATAF1, GI and GSTU17, through affecting 3'-UTR lengthening linked to alternative polyadenylation. Our results highlight the important role played by epitranscriptomic mRNA methylation in the salt stress response of Arabidopsis and indicate a strong link between m6 A methylation and 3'-UTR length and mRNA stability during stress adaptation.
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Affiliation(s)
- Jianzhong Hu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Kwanuk Lee
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Yuxia Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yao Chen
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Jae-Young Yun
- Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang, 25354, Korea
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Hunseung Kang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
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Choi M, Yun JY, Kim JH, Kim JS, Kim ST. The efficacy of CRISPR-mediated cytosine base editing with the RPS5a promoter in Arabidopsis thaliana. Sci Rep 2021; 11:8087. [PMID: 33850267 PMCID: PMC8044221 DOI: 10.1038/s41598-021-87669-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
CRISPR/Cas9-mediated genome editing is an important and versatile technology in modern biological research. Recent advancements include base-editing CRISPR tools that enable targeted nucleotide substitutions using a fusion protein comprising a nickase variant of Cas9 and a base deaminase. Improvements in base editing efficiencies and inheritable of edited loci need to be made to make CRISPR a viable system in plants. Here, we report efficiency of cytosine base editors (CBEs) in Arabidopsis thaliana by applying the strong endogenous RPS5a promoter to drive the expression of nickase Cas9 and either rAPOBEC1 from rat (BE3) or the PmCDA1 activation-induced cytidine deaminase from sea lamprey (AIDv2). Compared with the strong heterologous CaMV35S promoter of viral origin, the RPS5a promoter improved CBE efficiency by 32% points with the number of T1 plants showing over 50% conversion ratio when the LFY gene was targeted. CBE induced nonsense mutations in LFY via C-to-T conversion, which resulted in loss-of-function lfy phenotypes; defects in LFY function were associated with the targeted base substitutions. Our data suggest that optimal promoter choice for CBE expression may affect base-editing efficiencies in plants. The results provide a strategy to optimize low-efficiency base editors and demonstrate their applicability for functional assays and trait development in crop research.
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Affiliation(s)
- Minkyung Choi
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Jae-Young Yun
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea.,Institute of Green Bioscience & Technology, Seoul National University, Pyeongchang, Republic of Korea
| | - Jun-Hyuk Kim
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea.
| | - Sang-Tae Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea. .,Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
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Yun JY, Kim ST, Kim SG, Kim JS. A zero-background CRISPR binary vector system for construction of sgRNA libraries in plant functional genomics applications. Plant Biotechnol Rep 2019; 13:543-551. [DOI: 10.1007/s11816-019-00567-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/17/2019] [Indexed: 08/30/2023]
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Zhang J, Eswaran G, Alonso-Serra J, Kucukoglu M, Xiang J, Yang W, Elo A, Nieminen K, Damén T, Joung JG, Yun JY, Lee JH, Ragni L, Barbier de Reuille P, Ahnert SE, Lee JY, Mähönen AP, Helariutta Y. Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nat Plants 2019; 5:1033-1042. [PMID: 31595065 PMCID: PMC6795544 DOI: 10.1038/s41477-019-0522-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/19/2019] [Indexed: 05/18/2023]
Abstract
Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.
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Affiliation(s)
- Jing Zhang
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Gugan Eswaran
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Juan Alonso-Serra
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Melis Kucukoglu
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jiale Xiang
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Weibing Yang
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Annakaisa Elo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Teddy Damén
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Jae-Young Yun
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Jung-Hun Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Laura Ragni
- ZMBP-Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | | | - Sebastian E Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ji-Young Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea.
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - Ykä Helariutta
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
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Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, Choi M, Woo JW, Kim JS. Author Correction: Precision genome engineering through adenine base editing in plants. Nat Plants 2018; 4:730. [PMID: 30139955 DOI: 10.1038/s41477-018-0251-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In Supplementary Fig. 1b originally published with this Brief Communication, the DNA sequence of nickase Cas9 was incorrect; this has now been amended.
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Affiliation(s)
- Beum-Chang Kang
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- IBS School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Young Yun
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Sang-Tae Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - YouJin Shin
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jahee Ryu
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Minkyung Choi
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Je Wook Woo
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
- IBS School, University of Science and Technology, Daejeon, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
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7
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Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, Choi M, Woo JW, Kim JS. Precision genome engineering through adenine base editing in plants. Nat Plants 2018; 4:427-431. [PMID: 29867128 DOI: 10.1038/s41477-018-0178-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/16/2018] [Indexed: 05/19/2023]
Abstract
The recent development of adenine base editors (ABEs) has enabled efficient and precise A-to-G base conversions in higher eukaryotic cells. Here, we show that plant-compatible ABE systems can be successfully applied to protoplasts of Arabidopsis thaliana and Brassica napus through transient transfection, and to individual plants through Agrobacterium-mediated transformation to obtain organisms with desired phenotypes. Targeted, precise A-to-G substitutions generated a single amino acid change in the FT protein or mis-splicing of the PDS3 RNA transcript, and we could thereby obtain transgenic plants with late-flowering and albino phenotypes, respectively. Our results provide 'proof of concept' for in planta ABE applications that can lead to induced neo-functionalization or altered mRNA splicing, opening up new avenues for plant genome engineering and biotechnology.
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Affiliation(s)
- Beum-Chang Kang
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- IBS School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Young Yun
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Sang-Tae Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - YouJin Shin
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jahee Ryu
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Minkyung Choi
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Je Wook Woo
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
- IBS School, University of Science and Technology, Daejeon, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
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Shin SE, Lim JM, Koh HG, Kim EK, Kang NK, Jeon S, Kwon S, Shin WS, Lee B, Hwangbo K, Kim J, Ye SH, Yun JY, Seo H, Oh HM, Kim KJ, Kim JS, Jeong WJ, Chang YK, Jeong BR. CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii. Sci Rep 2016; 6:27810. [PMID: 27291619 PMCID: PMC4904240 DOI: 10.1038/srep27810] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/25/2016] [Indexed: 01/20/2023] Open
Abstract
Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicity and off-targeting associated with vector-driven expression of Cas9. We obtained CRISPR/Cas9-induced mutations at three loci including MAA7, CpSRP43 and ChlM, and targeted mutagenic efficiency was improved up to 100 fold compared to the first report of transgenic Cas9-induced mutagenesis. Interestingly, we found that unrelated vectors used for the selection purpose were predominantly integrated at the Cas9 cut site, indicative of NHEJ-mediated knock-in events. As expected with Cas9 RNPs, no off-targeting was found in one of the mutagenic screens. In conclusion, we improved the knockout efficiency by using Cas9 RNPs, which opens great opportunities not only for biological research but also industrial applications in Chlamydomonas and other microalgae. Findings of the NHEJ-mediated knock-in events will allow applications of the CRISPR/Cas9 system in microalgae, including "safe harboring" techniques shown in other organisms.
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Affiliation(s)
- Sung-Eun Shin
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jong-Min Lim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyun Gi Koh
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Eun Kyung Kim
- Advanced Biomass R&D Center (ABC), KAIST, Daejeon 34141, Republic of Korea
| | - Nam Kyu Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seungjib Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sohee Kwon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Won-Sub Shin
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Bongsoo Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kwon Hwangbo
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biological Science, Chungnam National University (CNU), Daejeon 34134, Republic of Korea
| | - Jungeun Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- Department of Chemistry, Seoul National University (SNU), Seoul 08826, Republic of Korea
| | - Sung Hyeok Ye
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- Basic science, IBS school, Korea University of Science and Technology (UST), Seoul 08826, Republic of Korea
| | - Jae-Young Yun
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University (KNU), Daegu 41566, Republic of Korea
| | - Hee-Mock Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University (KNU), Daegu 41566, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- Department of Chemistry, Seoul National University (SNU), Seoul 08826, Republic of Korea
| | - Won-Joong Jeong
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, Daejeon 34141, Republic of Korea
| | - Byeong-ryool Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Yun JY, Tamada Y, Kang YE, Amasino RM. Arabidopsis trithorax-related3/SET domain GROUP2 is required for the winter-annual habit of Arabidopsis thaliana. Plant Cell Physiol 2012; 53:834-46. [PMID: 22378382 PMCID: PMC3345368 DOI: 10.1093/pcp/pcs021] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/21/2012] [Indexed: 05/18/2023]
Abstract
The winter-annual habit of Arabidopsis thaliana requires active alleles of flowering locus C (FLC), which encodes a potent flowering repressor, and FRIGIDA (FRI), an activator of FLC. FLC activation by FRI is accompanied by an increase in specific histone modifications, such as tri-methylation of histone H3 at lysine 4 (H3K4me3), and requires three H3K4 methyltransferases, the Drosophila Trithorax-class Arabidopsis trithorax1 (ATX1) and ATX2, and yeast Set1-class ATX-related7/set domain group25 (ATXR7/SDG25). However, lesions in all of these genes failed to suppress the enhanced FLC expression caused by FRI completely, suggesting that another H3K4 methyltransferase may participate in the FLC activation. Here, we show that ATXR3/SDG2, which is a member of a novel class of H3K4 methyltransferases, also contributes to FLC activation. An ATXR3 lesion suppressed the enhanced FLC expression and delayed flowering caused by an active allele of FRI in non-vernalized plants. The decrease in FLC expression in atxr3 mutants was accompanied by reduced H3K4me3 levels at FLC chromatin. We also found that the rapid flowering of atxr3 was epistatic to that of atxr7, suggesting that ATXR3 functions in FLC activation in sequence with ATXR7. Our results indicate that the novel-class H3K4 methyltransferase, ATXR3, is a transcriptional activator that plays a role in the FLC activation and establishing the winter-annual habit. In addition, ATXR3 also contributes to the activation of other FLC clade members, such as flowering locus M/MADS affecting flowering1 (FLM/MAF1) and MAF5, at least partially explaining the ATXR3 function in delayed flowering caused by non-inductive photoperiods.
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Affiliation(s)
- Jae-Young Yun
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
- These authors contributed equally to this work
| | - Yosuke Tamada
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
- National Institute for Basic Biology, Okazaki, Aichi, 444-8585 Japan
- School of Life Science, Graduate University of Advanced Studies, Okazaki, Aichi, 444-8585 Japan
- These authors contributed equally to this work
| | - Ye Eun Kang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
- *Corresponding author: E-mail, ; Fax, +1-608-262-3453
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Lim BC, Ki CS, Cho A, Hwang H, Kim KJ, Hwang YS, Kim YE, Yun JY, Jeon BS, Lim YH, Paek SH, Chae JH. Pantothenate kinase-associated neurodegeneration in Korea: recurrent R440P mutation in PANK2 and outcome of deep brain stimulation. Eur J Neurol 2011; 19:556-61. [PMID: 22103354 DOI: 10.1111/j.1468-1331.2011.03589.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND PURPOSE The purpose of this study was to evaluate the mutation status of PANK2 among Korean patients with pantothenate kinase-associated neurodegeneration (PKAN) and to document the outcome of pallidal deep brain stimulation (DBS). METHODS Direct sequencing and deletion/duplication analysis of PANK2 were conducted in 12 patients (11 unrelated) with PKAN, diagnosed on the basis of extrapyramidal dysfunction and the 'eye-of-the-tiger sign' on brain magnetic resonance imaging (MRI). Pallidal DBS was conducted in four patients, and the outcomes were measured using the Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS). RESULTS A PANK2 mutation was identified in both alleles in all patients. The most prevalent mutation was c.1319G>C (p.R440P) in 8/22 mutated alleles (36%). An intragenic deletion ranging from exons 2 to 4 was found in one allele (1/22, 4.5%) using deletion/duplication analysis. The outcome of pallidal DBS was favorable in two patients with atypical PKAN and moderate severity of dystonia. However, two patients with typical PKAN and relatively severe symptoms showed variable responses. CONCLUSIONS The c.1319G>C (p.R440P) mutation appears to be a founder genotype among Korean patients with PKAN. Furthermore, this study provides additional data for the recent international effort to evaluate the efficacy of pallidal DBS in the treatment of patients with PKAN.
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Affiliation(s)
- B C Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Korea.
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Jean Finnegan E, Bond DM, Buzas DM, Goodrich J, Helliwell CA, Tamada Y, Yun JY, Amasino RM, Dennis ES. Polycomb proteins regulate the quantitative induction of VERNALIZATION INSENSITIVE 3 in response to low temperatures. Plant J 2011; 65:382-91. [PMID: 21265892 DOI: 10.1111/j.1365-313x.2010.04428.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Vernalization, the promotion of flowering in response to low temperatures, is one of the best characterized examples of epigenetic regulation in plants. The promotion of flowering is proportional to the duration of the cold period, but the mechanism by which plants measure time at low temperatures has been a long-standing mystery. We show that the quantitative induction of the first gene in the Arabidopsis vernalization pathway, VERNALIZATION INSENSITIVE 3 (VIN3), is regulated by the components of Polycomb Response Complex 2, which trimethylates histone H3 lysine 27 (H3K27me3). In differentiated animal cells, H3K27me3 is mostly associated with long-term gene repression, whereas, in pluripotent embyonic stem cells, many cell lineage-specific genes are inactive but exist in bivalent chromatin that carries both active (H3K4me3) and repressive (H3K27me3) marks on the same molecule. During differentiation, bivalent domains are generally resolved to an active or silent state. We found that H3K27me3 maintains VIN3 in a repressed state prior to cold exposure; this mark is not removed during VIN3 induction. Instead, active VIN3 is associated with bivalently marked chromatin. The continued presence of H3K27me3 ensures that induction of VIN3 is proportional to the duration of the cold, and that plants require prolonged cold to promote the transition to flowering. The observation that Polycomb proteins control VIN3 activity defines a new role for Polycomb proteins in regulating the rate of gene induction.
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Affiliation(s)
- E Jean Finnegan
- CSIRO, Climate Adaptation Flagship, Canberra, ACT 2601, Australia.
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Yun JY, Uhm YK, Kim HJ, Lim SH, Chung JH, Shin MK, Yim SV, Lee MH. Transforming growth factor beta receptor II (TGFBR2) polymorphisms and the association with nonsegmental vitiligo in the Korean population. Int J Immunogenet 2010; 37:289-91. [PMID: 20518838 DOI: 10.1111/j.1744-313x.2010.00923.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The precise cause of vitiligo is unknown. However, autoimmunity is considered the most likely aetiology, especially in nonsegmental vitiligo (NSV). In this study we determined whether or not the transforming growth factor beta receptor II (TGFBR2) gene contributes to susceptibility for NSV in the Korean population. Blood samples were collected from 415 controls and 233 cases. We selected three single nucleotide polymorphisms (SNPs) in the TGFBR2 gene. The genotypes of the SNPs were determined using direct sequencing. All of the SNPs were significantly different between the vitiligo patients and controls (rs2005061, co-dominant, dominant, recessive, P < 0.05; rs3773645, co-dominant, dominant, recessive, P < 0.05; rs3773649, co-dominant, recessive, P < 0.05). In addition, haplotype 1 (CG) and haplotype 2 (GA) of the linkage disequilibrium (LD) block were also associated with a risk of NSV. The present study suggests that TGFBR2 might be related to NSV.
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Affiliation(s)
- J Y Yun
- Department of Clinical Pharmacology, School of Medicine, Kyung Hee University, Seoul, Korea
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Tamada Y, Yun JY, Woo SC, Amasino RM. ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. Plant Cell 2009; 21:3257-69. [PMID: 19855050 PMCID: PMC2782277 DOI: 10.1105/tpc.109.070060] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Revised: 09/04/2009] [Accepted: 09/16/2009] [Indexed: 05/18/2023]
Abstract
In the winter-annual accessions of Arabidopsis thaliana, presence of an active allele of FRIGIDA (FRI) elevates expression of FLOWERING LOCUS C (FLC), a repressor of flowering, and thus confers a vernalization requirement. FLC activation by FRI involves methylation of Lys 4 of histone H3 (H3K4) at FLC chromatin. Many multicellular organisms that have been examined contain two classes of H3K4 methylases, a yeast (Saccharomyces cerevisiae) Set1 class and a class related to Drosophila melanogaster Trithorax. In this work, we demonstrate that ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), a putative Set1 class H3K4 methylase, is required for proper FLC expression. The atxr7 mutation partially suppresses the delayed flowering of a FRI-containing line. The rapid flowering of atxr7 is associated with reduced FLC expression and is accompanied by decreased H3K4 methylation and increased H3K27 methylation at FLC. Thus, ATXR7 is required for the proper levels of these histone modifications that set the level of FLC expression to create a vernalization requirement in winter-annual accessions. Previously, it has been reported that lesions in ATX1, which encodes a Trithorax class H3K4 methylase, partially suppress the delayed flowering of winter-annual Arabidopsis. We show that the flowering phenotype of atx1 atxr7 double mutants is additive relative to those of single mutants. Therefore, both classes of H3K4 methylases appear to be required for proper regulation of FLC expression.
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Choi J, Hyun Y, Kang MJ, In Yun H, Yun JY, Lister C, Dean C, Amasino RM, Noh B, Noh YS, Choi Y. Resetting and regulation of Flowering Locus C expression during Arabidopsis reproductive development. Plant J 2009; 57:918-31. [PMID: 19121105 DOI: 10.1111/j.1365-313x.2008.03776.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The epigenetic regulation of the floral repressor Flowering Locus C (FLC) is one of the critical factors that determine flowering time in Arabidopsis thaliana. Although many FLC regulators, and their effects on FLC chromatin, have been extensively studied, the epigenetic resetting of FLC has not yet been thoroughly characterized. Here, we investigate the FLC expression during gametogenesis and embryogenesis using FLC::GUS transgenic plants and RNA analysis. Regardless of the epigenetic state in adult plants, FLC expression disappeared in gametophytes. Subsequently, FLC expression was reactivated after fertilization in embryos, but not in the endosperm. Both parental alleles contributed equally to the expression of FLC in embryos. Surprisingly, the reactivation of FLC in early embryos was independent of FRIGIDA (FRI) and SUPPRESSOR OF FRIGIDA 4 (SUF4) activities. Instead, FRI, SUF4 and autonomous-pathway genes determined the level of FLC expression only in late embryogenesis. Many FLC regulators exhibited expression patterns similar to that of FLC, indicating potential roles in FLC reprogramming. An FVE mutation caused ectopic expression of FLC in the endosperm. A mutation in PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1 caused defects in FLC reactivation in early embryogenesis, and maintenance of full FLC expression in late embryogenesis. We also show that the polycomb group complex components, Fertilization-Independent endosperm and MEDEA, which mediate epigenetic regulation in seeds, are not relevant for FLC reprogramming. Based on our results, we propose that FLC reprogramming is composed of three phases: (i) repression in gametogenesis, (ii) reactivation in early embryogenesis and (iii) maintenance in late embryogenesis.
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Affiliation(s)
- Jean Choi
- Department of Biological Sciences, Seoul National University, Seoul, 151-742, Korea
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Park JH, Chang BU, Kim YJ, Seo JS, Choi SW, Yun JY. Determination of low (137)Cs concentration in seawater using ammonium 12-molybdophosphate adsorption and chemical separation method. J Environ Radioact 2008; 99:1815-1818. [PMID: 18799246 DOI: 10.1016/j.jenvrad.2008.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 04/23/2008] [Accepted: 07/23/2008] [Indexed: 05/26/2023]
Abstract
A new method has been developed for analyzing (137)Cs in a small volume of seawater. Ammonium 12-molybdophosphate (AMP) was used two times during pretreatment procedure. The first step was to adsorb (137)Cs in seawater samples into AMP in order to reduce sample volume, and the second was to remove (87)Rb, interference nuclide for beta counting. The AMP adsorbing (137)Cs was dissolved by sodium hydroxide solution, and then (137)Cs was finally formed to be cesium chloroplatinate precipitate by adding 10% hexachloroplatinic acid. The beta rays emitted from (137)Cs were measured with a low background gas-proportional alpha/beta counter. This method was applied to several seawater samples taken in the East Sea of Korea. Compared to the routinely used gamma-spectrometry method, this new AMP method was reliable and suitable for analyzing (137)Cs in deep seawater.
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Affiliation(s)
- J H Park
- Korea Institute of Nuclear Safety, Yuseong-gu, Daejeon, Republic of Korea.
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Abstract
The floral regulatory gene SUPERMAN (SUP) encodes a C2H2 type zinc finger protein that is required for maintaining boundaries between floral organs in Arabidopsis. It has been proposed that the main function of SUP is to balance cell proliferation in the third and fourth whorl of developing flowers, thereby maintaining the boundaries between the two whorls. To gain further insight into the function of SUP, we have ectopically expressed SUP using the promoter of APETALA1 (AP1), a gene that is initially expressed throughout floral meristems and later becomes restricted to the first and second whorls. Flowers of AP1::SUP plants have fewer floral organs, consistent with an effect of SUP on cell proliferation. In addition, the AP1::SUP transgene caused the conversion of petals to sepals and suppressed the development of stamens. The expression of the B function homeotic gene APETALA3 (AP3) and its regulator UNUSUAL FLORAL ORGANS (UFO) were delayed and reduced in AP1::SUP flowers. However, SUP does not act merely through UFO, as constitutive expression of UFO did not rescue the defects in petal and stamen development in AP1::SUP flowers. Together, these results suggest that SUP has both indirect and direct effects on the expression of B function homeotic genes.
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Affiliation(s)
- Jae-Young Yun
- School of Biological Sciences, Seoul National University, Seoul, 151-742 Korea
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Kim HS, Shin JY, Yun JY, Ahn DK, Le JY. Immortalization of human embryonic fibroblasts by overexpression of c-myc and simian virus 40 large T antigen. Exp Mol Med 2001; 33:293-8. [PMID: 11795494 DOI: 10.1038/emm.2001.47] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
SV40 large T antigen, a viral oncoprotein, is known to immortalize human diploid fibroblast by soaking up cellular RB and p53, but its frequency is extremely low. Additional genetic alteration is necessary for single-step immortalization. We attempted to find out what this alteration is by overexpressing cellular signal mediator genes; c-myc and cyclin D frequently amplified in many cancer cells. Overexpression of cyclin D did not affect the immortalization, but, overexpression of c-myc along with T antigen could immortalize normal human diploid fibroblast. Several cellular markers tested during immortalization process showed that p21, a cyclin-dependent kinase inhibitor and a marker of cellular senescence, disappeared in the life span-extended cells by T antigen and in the immortalized cells by c-myc. p21 was, however, elevated in the senescent cells and in the cells of crisis. Interestingly, p16 was upregulated whenever T antigen is overexpressed. Telomerase activity was also activated only in the immortalized cells. These results suggest that overexpression of c-myc contributes to immortalization of human diploid fibroblast by activating telomerase activity and suppressing p21 activity.
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Affiliation(s)
- H S Kim
- Department of Biochemistry, College of Medicine, Hallym University, Chunchon, Kangwon-do, Korea
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Moon IS, Kim YG, Park JH, Kim YS, Kim JC, Yun JY, Bang BK, Koh YB. Influence of donor kidney size on immediate renal function (1 month) in kidney transplantation. Transplant Proc 1998; 30:3666. [PMID: 9838608 DOI: 10.1016/s0041-1345(98)01184-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- I S Moon
- Department of Surgery, Urology, Internal Medicine, Kangnam St. Mary's Hospital, Catholic University Medical College, Seoul, Korea
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Park KD, Lee WK, Yun JY, Han DK, Kim SH, Kim YH, Kim HM, Kim KT. Novel anti-calcification treatment of biological tissues by grafting of sulphonated poly(ethylene oxide). Biomaterials 1997; 18:47-51. [PMID: 9003896 DOI: 10.1016/s0142-9612(96)00096-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Biological porcine tissue was modified by the direct coupling of sulphonated poly(ethylene oxide) (PEO-SO3) containing amino acid end groups after glutaraldehyde fixation. The calcification of the modified tissue [bioprosthetic tissue (BT)-PEO-SO3] and control (BT control) was investigated by in vivo rate subdermal, canine aorta-illiac shunt and right ventricle-pulmonary artery shunt implantation models. Less calcium deposition of BT-PEO-SP3 than of BT control was observed in in vivo tests. Such a reduced calcification of BT-PEO-SO3 can be explained by decreases of residual glutaraldehyde groups, a space filling effect and, therefore, improved biostability and synergistic blood-compatible effects of PEO and SO3 groups after the covalent binding of PEO-SO3 to tissue. This simple method can be a useful anti-calcification treatment for implantable tissue valves.
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Affiliation(s)
- K D Park
- Polymer Chemistry Laboratory, Korea Institute of Science and Technology, Seoul, Korea
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Abstract
Biologic porcine tissue was modified by coupling sulfonated polyethyl-eneoxide (PEO-SO3) and the effect of modification on calcification was evaluated in vitro and in vivo. The modification process involves grafting PEO-SO3 to porcine valve leaflet either by carbodiimide (EDC) activation or by direct coupling using glutaraldehyde. Thermal property, measured by differential scanning calorimetry, showed that the shrinkage temperature of modified tissue increased compared with control tissue and fresh tissue, suggesting increased thermal stability. Resistance to collagenase digestion revealed that modified tissues have greater resistance to enzyme digestion than do control tissues. In vitro calcification showed that modified tissues have less calcium deposition than do control tissues. In vivo calcification, using a rat subcutaneous implantation model, also showed less calcification of modified tissue than that of control. The resistance of modified tissue to collagenase, higher shrinkage temperature, and reduced calcification, when compared with control tissue, attest to the usefulness of this chemical modification for implantable biologic tissue.
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Affiliation(s)
- K D Park
- Polymer Chemistry Laboratory, Korea Institute of Science and Technology, Seoul, Korea
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