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Shin H, Park JE, Park HR, Choi WL, Yu SH, Koh W, Kim S, Soh HY, Waminal NE, Belandres HR, Lim JY, Yi G, Ahn JH, Kim J, Kim Y, Koo N, Kim K, Perumal S, Kang T, Kim J, Jang H, Kang DH, Kim YS, Jeong H, Yang J, Song S, Park S, Kim JA, Lim YP, Park B, Hsieh T, Yang T, Choi D, Kim HH, Lee S, Huh JH. Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae. New Phytol 2022; 235:743-758. [PMID: 35403705 PMCID: PMC9320894 DOI: 10.1111/nph.18155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/25/2021] [Accepted: 03/28/2022] [Indexed: 05/15/2023]
Abstract
Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Jeong Eun Park
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hye Rang Park
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Woo Lee Choi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Seung Hwa Yu
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Wonjun Koh
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Seungill Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Department of Environmental HorticultureUniversity of SeoulSeoul02504South Korea
| | - Hye Yeon Soh
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Nomar Espinosa Waminal
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Hadassah Roa Belandres
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Joo Young Lim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Gibum Yi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Jong Hwa Ahn
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - June‐Sik Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Yong‐Min Kim
- Korea Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141South Korea
| | - Namjin Koo
- Korea Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141South Korea
| | - Kyunghee Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Sampath Perumal
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Taegu Kang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Junghyo Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Hosung Jang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Dong Hyun Kang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Ye Seul Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hyeon‐Min Jeong
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Junwoo Yang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Somin Song
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Suhyoung Park
- Department of Horticultural Crop ResearchNational Institute of Horticultural and Herbal ScienceRural Development AdministrationWanjuJeollabuk‐do55365South Korea
| | - Jin A. Kim
- Department of Agricultural BiotechnologyNational Academy of Agricultural ScienceRural Development AdministrationJeonjuJeollabuk‐do54874South Korea
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeon34134South Korea
| | | | - Tzung‐Fu Hsieh
- Plants for Human Health InstituteNorth Carolina State UniversityNorth Carolina Research CampusKannapolisNC27695USA
| | - Tae‐Jin Yang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Doil Choi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hyun Hee Kim
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Soo‐Seong Lee
- BioBreeding InstituteAnseongGyeonggi‐do17544South Korea
| | - Jin Hoe Huh
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
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Shin H, Choi WL, Lim JY, Huh JH. Epigenome editing: targeted manipulation of epigenetic modifications in plants. Genes Genomics 2022; 44:307-315. [PMID: 35000141 DOI: 10.1007/s13258-021-01199-5] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Epigenetic modifications play important roles in diverse cellular processes such as X chromosome inactivation, cell differentiation, development and senescence. DNA methylation and histone modifications are major epigenetic modifications that regulate chromatin structure and gene expression without DNA sequence changes. Epigenetic alterations may induce phenotypic changes stable enough for mitotic or meiotic inheritance. Moreover, the reversibility of epigenetic marks makes the manipulation of chromatin and epigenetic signature an attractive strategy for therapeutic and breeding purposes. Targeted epigenetic manipulation, or epigenome editing, at the gene of interest commonly utilizes specific epigenetic modifiers fused with a targeting module of the conventional genome editing system. OBJECTIVE This review aims to summarize essential epigenetic components and introduce currently available epigenetic mutants and the corresponding epialleles in plants. Furthermore, advances in epigenome editing technology are discussed while proposing its potential application to plant breeding. CONCLUSIONS Epimutations associated with useful traits may provide a valuable resource for crop development. It is important to explore epimutations in a variety of crop species while understanding the fundamental aspects of epigenetic regulation of agronomically important traits such as yield, quality, disease resistance and stress tolerance. In the end, plant breeding programs through epigenome editing may help not only to expand the use of limited genetic resources but also to alleviate consumers' concerns about genetically manipulated crops.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea
| | - Woo Lee Choi
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea
| | - Joo Young Lim
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea
| | - Jin Hoe Huh
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea. .,Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.
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Shim S, Lee HG, Park OS, Shin H, Lee K, Lee H, Huh JH, Seo PJ. Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis. Epigenetics 2022; 17:41-58. [PMID: 33406971 PMCID: PMC8812807 DOI: 10.1080/15592294.2021.1872927] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Plant somatic cells can be reprogrammed into pluripotent cell mass, called callus, through a two-step in vitro tissue culture method. Incubation on callus-inducing medium triggers active cell proliferation to form a pluripotent callus. Notably, DNA methylation is implicated during callus formation, but a detailed molecular process regulated by DNA methylation remains to be fully elucidated. Here, we compared genome-wide DNA methylation profiles between leaf and callus tissues in Arabidopsis using whole-genome bisulphite-sequencing. Global distribution of DNA methylation showed that CHG methylation was increased, whereas CHH methylation was reduced especially around transposable element (TE) regions during the leaf-to-callus transition. We further analysed differentially expressed genes around differentially methylated TEs (DMTEs) during the leaf-to-callus transition and found that genes involved in cell cycle regulation were enriched and also constituted a coexpression gene network along with pluripotency regulators. In addition, a conserved DNA sequence analysis for upstream cis-elements led us to find a putative transcription factor associated with cell fate transition. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) was newly identified as a regulator of plant regeneration, and consistently, the cca1lhy mutant displayed altered phenotypes in callus proliferation. Overall, these results suggest that DNA methylation coordinates cell cycle regulation during callus formation, and CCA1 may act as a key upstream coordinator at least in part in the processes.
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Affiliation(s)
- Sangrea Shim
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Ok-Sun Park
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
| | - Hosub Shin
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, Korea
| | - Kyounghee Lee
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Jin Hoe Huh
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
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Shin H, Park HR, Park JE, Yu SH, Yi G, Kim JH, Koh W, Kim HH, Lee SS, Huh JH. Reduced fertility caused by meiotic defects and micronuclei formation during microsporogenesis in xBrassicoraphanus. Genes Genomics 2021; 43:251-258. [PMID: 33555504 PMCID: PMC7966196 DOI: 10.1007/s13258-021-01050-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 01/12/2023]
Abstract
Background Hybridization and polyploidization events are important driving forces in plant evolution. Allopolyploids formed between different species can be naturally or artificially created but often suffer from genetic instability and infertility in successive generations. xBrassicoraphanus is an intergeneric allopolyploid obtained from a cross between Brassica rapa and Raphanus sativus, providing a useful resource for genetic and genomic study in hybrid species. Objective The current study aims to understand the cause of hybrid sterility and pollen abnormality in different lines of synthetic xBrassicoraphanus from the cytogenetic perspective. Methods Alexander staining was used to assess the pollen viability. Cytogenetic analysis was employed to monitor meiotic chromosome behaviors in pollen mother cells (PMCs). Origins of parental chromosomes in xBrassicoraphanus meiocytes were determined by genome in situ hybridization analysis. Results The xBrassicoraphanus lines BB#4 and BB#6 showed high rates of seed abortion and pollen deformation. Abnormal chromosome behaviors were observed in their PMCs, frequently forming univalents and inter-chromosomal bridges during meiosis. A positive correlation also exists between meiotic defects and the formation of micronuclei, which is conceivably responsible for unbalanced gamete production and pollen sterility. Conclusion These results suggest that unequal segregation of meiotic chromosomes, due in part to non-homologous interactions, is responsible for micronuclei and unbalanced gamete formation, eventually leading to pollen degeneration and inferior fertility in unstable xBrassicoraphanus lines.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Hye Rang Park
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Jeong Eun Park
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Seung Hwa Yu
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gibum Yi
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea
| | - Jung Hyo Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Wonjun Koh
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
| | | | - Jin Hoe Huh
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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Park HR, Park JE, Kim JH, Shin H, Yu SH, Son S, Yi G, Lee SS, Kim HH, Huh JH. Meiotic Chromosome Stability and Suppression of Crossover Between Non-homologous Chromosomes in x Brassicoraphanus, an Intergeneric Allotetraploid Derived From a Cross Between Brassica rapa and Raphanus sativus. Front Plant Sci 2020; 11:851. [PMID: 32612629 PMCID: PMC7309133 DOI: 10.3389/fpls.2020.00851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
Hybridization and polyploidization are major driving forces in plant evolution. Allopolyploids can be occasionally formed from a cross between distantly related species but often suffer from chromosome instability and infertility. xBrassicoraphanus is an intergeneric allotetraploid (AARR; 2n = 38) derived from a cross between Brassica rapa (AA; 2n = 20) and Raphanus sativus (RR; 2n = 18). xBrassicoraphanus is fertile and genetically stable, while retaining complete sets of both B. rapa and R. sativus chromosomes. Precise control of meiotic recombination is essential for the production of balanced gametes, and crossovers (COs) must occur exclusively between homologous chromosomes. Many interspecific hybrids have problems with meiotic division at early generations, in which interactions between non-homologous chromosomes often bring about aneuploidy and unbalanced gamete formation. We analyzed meiotic chromosome behaviors in pollen mother cells (PMCs) of allotetraploid and allodiploid F1 individuals of newly synthesized xBrassicoraphanus. Allotetraploid xBrassicoraphanus PMCs showed a normal diploid-like meiotic behavior. By contrast, allodiploid xBrassicoraphanus PMCs displayed abnormal segregation of chromosomes mainly due to the absence of homologous pairs. Notably, during early stages of meiosis I many of allodiploid xBrassicoraphanus chromosomes behave independently with few interactions between B. rapa and R. sativus chromosomes, forming many univalent chromosomes before segregation. Chromosomes were randomly assorted at later stages of meiosis, and tetrads with unequal numbers of chromosomes were formed at completion of meiosis. Immunolocalization of HEI10 protein mediating meiotic recombination revealed that COs were more frequent in synthetic allotetraploid xBrassicoraphanus than in allodiploid, but less than in the stabilized line. These findings suggest that structural dissimilarity between B. rapa and R. sativus chromosomes prevents non-homologous interactions between the parental chromosomes in allotetraploid xBrassicoraphanus, allowing normal diploid-like meiosis when homologous pairing partners are present. This study also suggests that CO suppression between non-homologous chromosomes is required for correct meiotic progression in newly synthesized allopolyploids, which is important for the formation of viable gametes and reproductive success in the hybrid progeny.
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Affiliation(s)
- Hye Rang Park
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Jung Hyo Kim
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Seung Hwa Yu
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Sehyeok Son
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Gibum Yi
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | | | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Yi G, Shin H, Park HR, Park JE, Ahn JH, Lim S, Lee JG, Lee EJ, Huh JH. Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis. BMC Plant Biol 2020; 20:252. [PMID: 32493222 PMCID: PMC7268423 DOI: 10.1186/s12870-020-02470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/27/2019] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. RESULTS The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved. CONCLUSION The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.
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Affiliation(s)
- Gibum Yi
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Department of Central Area Crop Science, National Institute of Crop Science, RDA, Suwon, 16429 Republic of Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Hye Rang Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jong Hwa Ahn
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Illumina Korea, Yeongdeungpo-gu, Seoul, 07325 South Korea
| | - Sooyeon Lim
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
- National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jeollabuk-do 55365 South Korea
| | - Jeong Gu Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Eun Jin Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
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Lee SK, Kim H, Cho JI, Nguyen CD, Moon S, Park JE, Park HR, Huh JH, Jung KH, Guiderdoni E, Jeon JS. Deficiency of rice hexokinase HXK5 impairs synthesis and utilization of starch in pollen grains and causes male sterility. J Exp Bot 2020; 71:116-125. [PMID: 31671177 DOI: 10.1093/jxb/erz436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 08/20/2019] [Accepted: 10/10/2019] [Indexed: 05/28/2023]
Abstract
There is little known about the function of rice hexokinases (HXKs) in planta. We characterized hxk5-1, a Tos17 mutant of OsHXK5 that is up-regulated in maturing pollen, a stage when starch accumulates. Progeny analysis of self-pollinated heterozygotes of hxk5-1 and reciprocal crosses between the wild-type and heterozygotes revealed that loss of HXK5 causes male sterility. Homozygous hxk5-1, produced via anther culture, and additional homozygous hxk5-2, hxk5-3 and hxk5-4 lines created by CRISPR/Cas9 confirmed the male-sterile phenotype. In vitro pollen germination ability and in vivo pollen tube growth rate were significantly reduced in the hxk5 mutant pollen. Biochemical analysis of anthers with the mutant pollen revealed significantly reduced hexokinase activity and starch content, although they were sufficient to produce some viable seed. However, the mutant pollen was unable to compete successfully against wild-type pollen. Expression of the catalytically inactive OsHXK5-G113D did not rescue the hxk5 male-sterile phenotype, indicating that its catalytic function was responsible for pollen fertility, rather than its role in sugar sensing and signaling. Our results demonstrate that OsHXK5 contributes to a large portion of the hexokinase activity necessary for the starch utilization pathway during pollen germination and tube growth, as well as for starch biosynthesis during pollen maturation.
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Affiliation(s)
- Sang-Kyu Lee
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Hyunbi Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Jung-Il Cho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Cong Danh Nguyen
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hye Rang Park
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier, France
- Université de Montpellier, CIRAD INRA Montpellier SupAgro, Montpellier, France
| | - Jong-Seong Jeon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
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Kim JS, Lim JY, Shin H, Kim BG, Yoo SD, Kim WT, Huh JH. ROS1-Dependent DNA Demethylation Is Required for ABA-Inducible NIC3 Expression. Plant Physiol 2019; 179:1810-1821. [PMID: 30692220 PMCID: PMC6446795 DOI: 10.1104/pp.18.01471] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/14/2019] [Indexed: 05/15/2023]
Abstract
DNA methylation plays an important role in diverse developmental processes in many eukaryotes, including the response to environmental stress. Abscisic acid (ABA) is a plant hormone that is up-regulated under stress. The involvement of DNA methylation in the ABA response has been reported but is poorly understood. DNA demethylation is a reverse process of DNA methylation and often induces structural changes of chromatin leading to transcriptional activation. In Arabidopsis (Arabidopsis thaliana), active DNA demethylation depends on the activity of REPRESSOR OF SILENCING 1 (ROS1), which directly excises 5-methylcytosine from DNA. Here we showed that ros1 mutants were hypersensitive to ABA during early seedling development and root elongation. Expression levels of some ABA-inducible genes were decreased in ros1 mutants, and more than 60% of their proximal regions became hypermethylated, indicating that a subset of ABA-inducible genes are under the regulation of ROS1-dependent DNA demethylation. Notable among them is NICOTINAMIDASE 3 (NIC3) that encodes an enzyme that converts nicotinamide to nicotinic acid in the NAD+ salvage pathway. Many enzymes in this pathway are known to be involved in stress responses. The nic3 mutants display hypersensitivity to ABA, whereas overexpression of NIC3 restores normal ABA responses. Our data suggest that NIC3 is responsive to ABA but requires ROS1-mediated DNA demethylation at the promoter as a prerequisite to transcriptional activation. These findings suggest that ROS1-induced active DNA demethylation maintains the active state of NIC3 transcription in response to ABA.
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Affiliation(s)
- June-Sik Kim
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Joo Young Lim
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Hosub Shin
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54875, Korea
| | - Sang-Dong Yoo
- Division of Life Sciences, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea
| | - Woo Taek Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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9
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Yi G, Kim JS, Park JE, Shin H, Yu SH, Park S, Huh JH. MYB1 transcription factor is a candidate responsible for red root skin in radish (Raphanus sativus L.). PLoS One 2018; 13:e0204241. [PMID: 30240413 PMCID: PMC6150496 DOI: 10.1371/journal.pone.0204241] [Citation(s) in RCA: 16] [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: 03/07/2018] [Accepted: 09/04/2018] [Indexed: 12/30/2022] Open
Abstract
Root skin color is one of the economically important traits in radish (Raphanus sativus), and the pigmentation in red skin varieties is largely attributable to anthocyanin accumulation. Pelargonidin was found as a major anthocyanin pigment accumulated in the sub-epidermal layer of red radish roots. In the 20 F2 population generated from the F1 with red root skins, root skins with red and white colors segregated in a 3:1 ratio. Additionally, a test cross between a red F3 individual and a white skin individual gave rise to 1:1 segregation of red and white, indicating that the root skin color of radish is determined by a single locus and red color is dominant over white. We performed association mapping for root skin color using SNPs obtained from RNA-seq analysis. Segregation analysis on the 152 F3 test-cross population revealed an RsMyb1 transcription factor as a candidate gene to determine root skin color. A PCR marker based on the polymorphism within 2 kb of RsMyb1 was developed and tested on 12 and 152 individuals from F2 and F3 test cross populations, respectively, and red and white root skin colors were completely distinguished corresponding to the genotypes. Expression levels of RsMyb1 in red or purple root cultivars were significantly higher than in white root cultivars. These findings suggest that RsMyb1 is a crucial determinant for anthocyanin biosynthesis in radish roots, and the molecular marker developed in this study will be useful for marker-assisted selection for red skin individuals at early seedling stages.
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Affiliation(s)
- Gibum Yi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - June-Sik Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jeong Eun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hosub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Seung Hwa Yu
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Suhyung Park
- Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
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10
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So KK, Ko YH, Chun J, Bal J, Jeon J, Kim JM, Choi J, Lee YH, Huh JH, Kim DH. Global DNA Methylation in the Chestnut Blight Fungus Cryphonectria parasitica and Genome-Wide Changes in DNA Methylation Accompanied with Sectorization. Front Plant Sci 2018; 9:103. [PMID: 29456549 PMCID: PMC5801561 DOI: 10.3389/fpls.2018.00103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Mutation in CpBck1, an ortholog of the cell wall integrity mitogen-activated protein kinase kinase kinase (MAPKKK) of Saccharomyces cerevisiae, in the chestnut blight fungus Cryphonectria parasitica resulted in a sporadic sectorization as culture proceeded. The progeny from the sectored area maintained the characteristics of the sector, showing a massive morphogenetic change, including robust mycelial growth without differentiation. Epigenetic changes were investigated as the genetic mechanism underlying this sectorization. Quantification of DNA methylation and whole-genome bisulfite sequencing revealed genome-wide DNA methylation of the wild-type at each nucleotide level and changes in DNA methylation of the sectored progeny. Compared to the wild-type, the sectored progeny exhibited marked genome-wide DNA hypomethylation but increased methylation sites. Expression analysis of two DNA methyltransferases, including two representative types of DNA methyltransferase (DNMTase), demonstrated that both were significantly down-regulated in the sectored progeny. However, functional analysis using mutant phenotypes of corresponding DNMTases demonstrated that a mutant of CpDmt1, an ortholog of RID of Neurospora crassa, resulted in the sectored phenotype but the CpDmt2 mutant did not, suggesting that the genetic basis of fungal sectorization is more complex. The present study revealed that a mutation in a signaling pathway component resulted in sectorization accompanied with changes in genome-wide DNA methylation, which suggests that this signal transduction pathway is important for epigenetic control of sectorization via regulation of genes involved in DNA methylation.
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Affiliation(s)
- Kum-Kang So
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, South Korea
| | - Yo-Han Ko
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, South Korea
| | - Jeesun Chun
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, South Korea
| | - Jyotiranjan Bal
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, South Korea
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jung-Mi Kim
- Department of Bio-Environmental Chemistry, Wonkwang University, Iksan, South Korea
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, South Korea
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11
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Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee J, Lee SC, Kwon JK, Lee HY, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 2017; 18:210. [PMID: 29089032 PMCID: PMC5664825 DOI: 10.1186/s13059-017-1341-9] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/06/2017] [Indexed: 01/08/2023] Open
Abstract
Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jieun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Myung-Shin Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Ho-Sub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Hyun-Ah Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Youngsill Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Soohyun Oh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joo Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhye Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunbi Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Eui Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - JunKi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Yunji Hong
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Ryan W Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Won-Hee Kang
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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12
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Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee J, Lee SC, Kwon JK, Lee HY, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 2017; 18:210. [PMID: 29089032 DOI: 10.1007/s13580-019-00157-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/19/2019] [Accepted: 10/06/2017] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. RESULTS We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. CONCLUSIONS Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.
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Affiliation(s)
- Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jieun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Myung-Shin Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Ho-Sub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Hyun-Ah Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Youngsill Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Soohyun Oh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joo Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhye Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunbi Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Eui Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - JunKi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Yunji Hong
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Ryan W Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Won-Hee Kang
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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13
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Kim HM, Lee BR, Lee ES, Kwon MH, Huh JH, Kwon BE, Park EK, Chang SY, Kweon MN, Kim PH, Ko HJ, Chung CH. iNKT cells prevent obesity-induced hepatic steatosis in mice in a C-C chemokine receptor 7-dependent manner. Int J Obes (Lond) 2017; 42:270-279. [PMID: 28811651 PMCID: PMC5803573 DOI: 10.1038/ijo.2017.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/19/2017] [Accepted: 07/21/2017] [Indexed: 02/08/2023]
Abstract
Non-alcoholic fatty liver disease and non-alcoholic steatohepatitis are characterized by an increase in hepatic triglyceride content with infiltration of immune cells, which can cause steatohepatitis and hepatic insulin resistance. C-C chemokine receptor 7 (CCR7) is primarily expressed in immune cells, and CCR7 deficiency leads to the development of multi-organ autoimmunity, chronic renal disease and autoimmune diabetes. Here, we investigated the effect of CCR7 on hepatic steatosis in a mouse model and its underlying mechanism. Our results demonstrated that body and liver weights were higher in the CCR7−/− mice than in the wild-type (WT) mice when they were fed a high-fat diet. Further, glucose tolerance and insulin sensitivity were markedly diminished in CCR7−/− mice. The number of invariant natural killer T (iNKT) cells was reduced in the livers of the CCR7−/− mice. Moreover, liver inflammation was detected in obese CCR7−/− mice, which was ameliorated by the adoptive transfer of hepatic mononuclear cells from WT mice, but not through the transfer of hepatic mononuclear cells from CD1d−/− or interleukin-10-deficient (IL-10−/−) mice. Overall, these results suggest that CCR7+ mononuclear cells in the liver could regulate obesity-induced hepatic steatosis via induction of IL-10-expressing iNKT cells.
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Affiliation(s)
- H M Kim
- Department of Global Medical Science, Yonsei University Wonju College of Medicine, Wonju, Korea.,Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - B R Lee
- Laboratory of Microbiology and Immunology, College of Pharmacy, Kangwon National University, Chuncheon, Korea
| | - E S Lee
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - M H Kwon
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - J H Huh
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - B-E Kwon
- Laboratory of Microbiology and Immunology, College of Pharmacy, Kangwon National University, Chuncheon, Korea
| | - E-K Park
- Laboratory of Microbiology and Immunology, College of Pharmacy, Kangwon National University, Chuncheon, Korea
| | - S-Y Chang
- College of Pharmacy, Ajou University, Suwon, Korea
| | - M-N Kweon
- Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Korea
| | - P-H Kim
- Department of Molecular Bioscience, School of Biomedical Science, Kangwon National University, Chuncheon, Korea
| | - H-J Ko
- Laboratory of Microbiology and Immunology, College of Pharmacy, Kangwon National University, Chuncheon, Korea
| | - C H Chung
- Department of Global Medical Science, Yonsei University Wonju College of Medicine, Wonju, Korea.,Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
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Yi G, Lim S, Chae WB, Park JE, Park HR, Lee EJ, Huh JH. Root Glucosinolate Profiles for Screening of Radish (Raphanus sativus L.) Genetic Resources. J Agric Food Chem 2016; 64:61-70. [PMID: 26672790 DOI: 10.1021/acs.jafc.5b04575] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Radish (Raphanus sativus L.), a root vegetable, is rich in glucosinolates (GLs), which are beneficial secondary metabolites for human health. To investigate the genetic variations in GL content in radish roots and the relationship with other root phenotypes, we analyzed 71 accessions from 23 different countries for GLs using HPLC. The most abundant GL in radish roots was glucoraphasatin, a GL with four-carbon aliphatic side chain. The content of glucoraphasatin represented at least 84.5% of the total GL content. Indolyl GL represented only 3.1% of the total GL at its maximum. The principal component analysis of GL profiles with various root phenotypes showed that four different genotypes exist in the 71 accessions. Although no strong correlation with GL content and root phenotype was observed, the varied GL content levels demonstrate the genetic diversity of GL content, and the amount that GLs could be potentially improved by breeding in radishes.
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Affiliation(s)
| | | | - Won Byoung Chae
- Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration , Wanju-gun, Jeollabuk-do 55365, Korea
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15
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Ahn JH, Kim JS, Kim S, Soh HY, Shin H, Jang H, Ryu JH, Kim A, Yun KY, Kim S, Kim KS, Choi D, Huh JH. Correction: De Novo Transcriptome Analysis to Identify Anthocyanin Biosynthesis Genes Responsible for Tissue-Specific Pigmentation in Zoysiagrass (Zoysia japonica Steud.). PLoS One 2015; 10:e0137943. [PMID: 26340448 PMCID: PMC4560375 DOI: 10.1371/journal.pone.0137943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Ahn JH, Kim JS, Kim S, Soh HY, Shin H, Jang H, Ryu JH, Kim A, Yun KY, Kim S, Kim KS, Choi D, Huh JH. De Novo Transcriptome Analysis to Identify Anthocyanin Biosynthesis Genes Responsible for Tissue-Specific Pigmentation in Zoysiagrass (Zoysia japonica Steud.). PLoS One 2015; 10:e0124497. [PMID: 25905914 PMCID: PMC4408010 DOI: 10.1371/journal.pone.0124497] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 10/07/2014] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Zoysiagrass (Zoysia japonica Steud.) is commonly found in temperate climate regions and widely used for lawns, in part, owing to its uniform green color. However, some zoysiagrass cultivars accumulate red to purple pigments in their spike and stolon tissues, thereby decreasing the aesthetic value. Here we analyzed the anthocyanin contents of two zoysiagrass cultivars 'Anyang-jungji' (AJ) and 'Greenzoa' (GZ) that produce spikes and stolons with purple and green colors, respectively, and revealed that cyanidin and petunidin were primarily accumulated in the pigmented tissues. In parallel, we performed a de novo transcriptome assembly and identified differentially expressed genes between the two cultivars. We found that two anthocyanin biosynthesis genes encoding anthocyanidin synthase (ANS) and dihydroflavonol 4-reductase (DFR) were preferentially upregulated in the purple AJ spike upon pigmentation. Both ANS and DFR genes were also highly expressed in other zoysiagrass cultivars with purple spikes and stolons, but their expression levels were significantly low in the cultivars with green tissues. We observed that recombinant ZjDFR1 and ZjANS1 proteins successfully catalyze the conversions of dihydroflavonols into leucoanthocyanidins and leucoanthocyanidins into anthocyanidins, respectively. These findings strongly suggest that upregulation of ANS and DFR is responsible for tissue-specific anthocyanin biosynthesis and differential pigmentation in zoysiagrass. The present study also demonstrates the feasibility of a de novo transcriptome analysis to identify the key genes associated with specific traits, even in the absence of reference genome information.
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Affiliation(s)
- Jong Hwa Ahn
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
| | - June-Sik Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Seungill Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 151-921, Korea
| | - Hye Yeon Soh
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 151-921, Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
| | - Hosung Jang
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
| | - Ju Hyun Ryu
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
| | | | | | - Shinje Kim
- FnP Co., Ltd, Jeungpyeong, 368-811, Korea
| | - Ki Sun Kim
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Doil Choi
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 151-921, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 151-921, Korea
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Lee J, Jang H, Shin H, Choi WL, Mok YG, Huh JH. AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis. Nucleic Acids Res 2014; 42:11408-18. [PMID: 25228464 PMCID: PMC4191409 DOI: 10.1093/nar/gku834] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a primary epigenetic modification regulating gene expression and chromatin structure in many eukaryotes. Plants have a unique DNA demethylation system in that 5-methylcytosine (5mC) is directly removed by DNA demethylases, such as DME/ROS1 family proteins, but little is known about the downstream events. During 5mC excision, DME produces 3′-phosphor-α, β-unsaturated aldehyde and 3′-phosphate by successive β- and δ-eliminations, respectively. The kinetic studies revealed that these 3′-blocking lesions persist for a significant amount of time and at least two different enzyme activities are required to immediately process them. We demonstrate that Arabidopsis AP endonucleases APE1L, APE2 and ARP have distinct functions to process such harmful lesions to allow nucleotide extension. DME expression is toxic to E. coli due to excessive 5mC excision, but expression of APE1L or ARP significantly reduces DME-induced cytotoxicity. Finally, we propose a model of base excision repair and DNA demethylation pathway unique to plants.
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Affiliation(s)
- Jiyoon Lee
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Hosung Jang
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Hosub Shin
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Woo Lee Choi
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Young Geun Mok
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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Kim JE, Lee YH, Huh JH, Kang DR, Rhee Y, Lim SK. Early-stage chronic kidney disease, insulin resistance, and osteoporosis as risk factors of sarcopenia in aged population: the fourth Korea National Health and Nutrition Examination Survey (KNHANES IV), 2008-2009. Osteoporos Int 2014; 25:2189-98. [PMID: 24846317 DOI: 10.1007/s00198-014-2745-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 05/07/2014] [Indexed: 12/17/2022]
Abstract
UNLABELLED Sarcopenia means the progressive loss of skeletal muscle mass and strength with aging. In this study, we found that insulin resistance, chronic kidney disease stage 3, and osteoporosis at the femur neck were closely associated with sarcopenia in elderly men. These conditions modified to slow down the progression of sarcopenia. INTRODUCTION Sarcopenia is known to have multiple contributing factors; however, its modifiable risk factors have not yet been determined. The aim of this study was to identify the most influential and modifiable risk factors for sarcopenia in elderly. METHODS This was a population-based, cross-sectional study using data from the Fourth Korea National Health and Nutrition Examination Survey (KNHANES IV), 2008-2009. This study included 940 men and 1,324 women aged 65 years and older who completed a body composition analysis using dual-energy X-ray absorptiometry. Sarcopenia was defined as an appendicular skeletal muscle mass divided by height(2) of less than 1 standard deviation below the sex-specific mean for a younger reference group. RESULTS Using univariate analysis, age, body mass index (BMI), homeostasis model assessment for insulin resistance (HOMA-IR), limitations in daily activities, regular exercise, high-risk drinking, family income, osteoporosis, daily energy, and protein intake were associated with sarcopenia in men; age, BMI, limitations in daily activities, regular exercise, occupation, osteoporosis at the total hip, and daily energy intake were associated with sarcopenia in women. In the multivariate logistic regression analysis, HOMA-IR ≥2.5 (odds ratio [OR] for sarcopenia, 2.27; 95 % confidence interval [CI], 1.21-4.25), chronic kidney disease stage 3 (OR, 3.13; 95 % CI, 1.14-8.61), and osteoporosis at the femur neck (OR, 6.83; 95 % CI, 1.08-43.41) were identified as risk factors for sarcopenia in men. CONCLUSIONS Insulin resistance, chronic kidney disease, and osteoporosis at the femur neck should be modified to prevent the acceleration of skeletal muscle loss in elderly men.
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Affiliation(s)
- J E Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-752, Republic of Korea,
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Abstract
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Methylation of cytosine to 5-methylcytosine
(5mC) is important
for gene expression, gene imprinting, X-chromosome inactivation, and
transposon silencing. Active demethylation in animals is believed
to proceed by DNA glycosylase removal of deaminated or oxidized 5mC.
In plants, 5mC is removed from the genome directly by the DEMETER
(DME) family of DNA glycosylases. Arabidopsis thaliana DME excises 5mC to activate expression of maternally imprinted genes.
Although the related Repressor of Silencing 1 (ROS1) enzyme has been
characterized, the molecular basis for 5mC recognition by DME has
not been investigated. Here, we present a structure–function
analysis of DME and the related DME-like 3 (DML3) glycosylases for
5mC and its oxidized derivatives. Relative to 5mC, DME and DML3 exhibited
robust activity toward 5-hydroxymethylcytosine, limited activity for
5-carboxylcytosine, and no activity for 5-formylcytosine. We used
homology modeling and mutational analysis of base excision and DNA
binding to identify residues important for recognition of 5mC within
the context of DNA and inside the enzyme active site. Our results
indicate that the 5mC binding pocket is composed of residues from
discrete domains and is responsible for discrimination against 5mC
derivatives, and suggest that DME, ROS1, and DML3 utilize subtly different
mechanisms to probe the DNA duplex for cytosine modifications.
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Affiliation(s)
- Sonja C Brooks
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
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20
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Jang H, Shin H, Eichman BF, Huh JH. Excision of 5-hydroxymethylcytosine by DEMETER family DNA glycosylases. Biochem Biophys Res Commun 2014; 446:1067-72. [PMID: 24661881 DOI: 10.1016/j.bbrc.2014.03.060] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 03/15/2014] [Indexed: 12/25/2022]
Abstract
In plants and animals, 5-methylcytosine (5mC) serves as an epigenetic mark to repress gene expression, playing critical roles for cellular differentiation and transposon silencing. Mammals also have 5-hydroxymethylcytosine (5hmC), resulting from hydroxylation of 5mC by TET family-enzymes. 5hmC is abundant in mouse Purkinje neurons and embryonic stem cells, and regarded as an important intermediate for active DNA demethylation in mammals. However, the presence of 5hmC in plants has not been clearly demonstrated. In Arabidopsis, the DEMETER (DME) family DNA glycosylases efficiently remove 5mC, which results in DNA demethylation and transcriptional activation of target genes. Here we show that DME and ROS1 have a significant 5hmC excision activity in vitro, although we detected no 5hmC in Arabidopsis, suggesting that it is very unlikely for plants to utilize 5hmC as a DNA demethylation intermediate. Our results indicate that both plants and animals have 5mC in common but DNA demethylation systems have independently evolved with distinct mechanisms.
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Affiliation(s)
- Hosung Jang
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea
| | - Hosub Shin
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Jin Hoe Huh
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea.
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21
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Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sørensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 2014; 46:270-8. [PMID: 24441736 DOI: 10.1038/ng.2877] [Citation(s) in RCA: 534] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/30/2013] [Indexed: 12/12/2022]
Abstract
Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.
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Affiliation(s)
- Seungill Kim
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Minkyu Park
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Seon-In Yeom
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Yong-Min Kim
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Je Min Lee
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Hyun-Ah Lee
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Eunyoung Seo
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyeongchae Cheong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyongyong Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gir-Won Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
| | - Sang-Keun Oh
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Chungyun Bae
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Saet-Byul Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hye-Young Lee
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Shin-Young Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Myung-Shin Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Byoung-Cheorl Kang
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3] Vegetable Breeding Research Center, Seoul National University, Seoul, Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hee-Bum Yang
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hee-Jin Jeong
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Won-Hee Kang
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Jin-Kyung Kwon
- Vegetable Breeding Research Center, Seoul National University, Seoul, Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - June-Sik Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Byung-Dong Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Oded Cohen
- Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel
| | - Ilan Paran
- Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
| | - Saet Buyl Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
| | - Yeon-Ki Kim
- Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Korea
| | | | | | | | - Young Sam Seo
- Ginseng Resources Research Laboratory, Korea Ginseng Corporation, Daejeon, Korea
| | - Suk-Yoon Kwon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun A Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jeong Mee Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
| | - Paul W Bosland
- 1] Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA. [2] Chile Pepper Institute, New Mexico State University, Las Cruces, New Mexico, USA
| | - Gregory Reeves
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA
| | | | | | - Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hee-Seung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Min-Soo Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA
| | - Yang Do Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Beom-Seok Park
- Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea
| | - Allen van Deynze
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Woo Taek Kim
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hee Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Inhwa Yeam
- Department of Horticulture and Breeding, Andong National University, Andong, Korea
| | - James J Giovannoni
- 1] US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, USA. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Sang-Jik Lee
- Biotechnology Institute, Nongwoo Bio, Yeoju, Korea
| | - Ryan W Kim
- Genome Center, University of California, Davis, Davis, California, USA
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Jong-Sung Lim
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Doil Choi
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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Huh JH, Song MK, Park KH, Kim KJ, Kim JE, Rhee YM, Lim SK. Gender-specific pleiotropic bone-muscle relationship in the elderly from a nationwide survey (KNHANES IV). Osteoporos Int 2014; 25:1053-61. [PMID: 24150214 DOI: 10.1007/s00198-013-2531-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 09/25/2013] [Indexed: 12/16/2022]
Abstract
SUMMARY The aim of this study was to examine the gender-specific association between sarcopenia and bone geometry/metabolic parameters. Low muscle mass was associated with greater deterioration of bone than in deterioration of glucose or lipid profiles. This bone-muscle relationship was more prominent in men than in women. INTRODUCTION There are few studies that report on gender differences in the effects of low muscle mass on bone and metabolic parameters in elderly subjects. This study aimed to assess the gender-specific influence of muscle mass on bone and metabolic parameters. METHODS A total of 2,264 participants (940 men and 1,324 women) whose age ranged from 65 to 92 years were analyzed using data from The Fourth Korea National Health and Nutrition Examination Surveys (2008-2009). We measured bone mineral density (BMD) and appendicular muscle mass using the dual-energy X-ray absorptiometry and also measured metabolic profiles. RESULTS The age-related trend in bone and muscle coincided in men but not in women. Femoral neck (FN) and total hip (TH) BMD were highly correlated with muscle mass in both genders. However, in women, this correlation was not significant in the lumbar spine (LS). In addition, this positive correlation was stronger in the FN or TH than in the LS and was stronger in men than in women. Subjects with sarcopenia were at a higher risk for osteoporosis in the FN, TH, and LS in men, and in the TH and FN in women. The degree of association between muscle mass and metabolic profiles was relatively very weak. CONCLUSION Bone-muscle relationship was more prominent in men than in women. The gender differences in bone-muscle relationship may be helpful for the development of gender-specific preventive strategies in the elderly, especially in men.
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Affiliation(s)
- J H Huh
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-752, South Korea
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Huh JH, Kim TH, Kim K, Song JA, Jung YJ, Jeong JY, Lee MJ, Kim YK, Lee DH, An HJ. Dysregulation of miR-106a and miR-591 confers paclitaxel resistance to ovarian cancer. Br J Cancer 2013; 109:452-61. [PMID: 23807165 PMCID: PMC3721386 DOI: 10.1038/bjc.2013.305] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [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: 04/02/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 12/19/2022] Open
Abstract
Background: MicroRNAs are noncoding regulatory RNAs strongly implicated in carcinogenesis, cell survival, and chemosensitivity. Here, microRNAs associated with chemoresistance in ovarian carcinoma, the most lethal of gynaecological malignancies, were identified and their functional effects in chemoresistant ovarian cancer cells were assessed. Methods: MicroRNA expression in paclitaxel (PTX)-resistant SKpac sublines was compared with that of the PTX-sensitive, parental SKOV3 ovarian cancer cell line using microarray and qRT–PCR. The function of differentially expressed microRNAs in chemoresistant ovarian cancer was further evaluated by apoptosis, cell proliferation, and migration assays. Results: Upregulation of miR-106a and downregulation of miR-591 were associated with PTX resistance in ovarian cancer cells and human tumour samples. Transfection with anti-miR-106a or pre-miR-591 resensitized PTX-resistant SKpac cells to PTX by enhancing apoptosis (23 and 42% increase), and inhibited their cell migration (43 and 56% decrease) and proliferation (64 and 65% decrease). Furthermore, ZEB1 was identified as a novel target gene of miR-591, and BCL10 and caspase-7 were target genes of miR-106a, as identified by immunoblotting and luciferase assay. Conclusion: MiR-106a and miR-591 have important roles in conferring PTX resistance to ovarian cancer cells. Modulation of these microRNAs resensitizes PTX-resistant cancer cells by targeting BCL10, caspase-7, and ZEB1.
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Affiliation(s)
- J H Huh
- Department of Pathology, College of Medicine, CHA University, 351 Yatap-dong, Seongnam, Gyeonggi-Do, South Korea
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Huh JH, Park MS, Jeon HH. Early development of reflux esophagitis after successful Helicobacter pylori eradication in superficial gastritis. JNMA J Nepal Med Assoc 2011; 51:189-191. [PMID: 22922899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
The relationship between gastroesophageal reflux disease (GERD) and Helicobacter pylori (H. pylori) eradication is still debated. Recently, we had a patient of GERD who had developed it shortly after H. pylori eradication therapy. A 72-year-old man was diagnosed by endoscopy as suffering from severe superficial gastritis in the stomach body. A rapid urease test showed H. pylori infection. He was then started on proton pump inhibitor (PPI) based therapy for two weeks eradicating H.pylori. After completion of H. pylori eradication, he complained of a heart-burn sensation. Follow-up endoscopy showed reflux esophagitis, of grade B according to the Los Angeles classification. Since the patient had developed GERD after completion of the triple therapy, their suggests that H. pylori eradication must have triggered the development of de novo GERD after a short period of time.
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Affiliation(s)
- J H Huh
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
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Kim OR, Cho MC, Kim BD, Huh JH. A splicing mutation in the gene encoding phytoene synthase causes orange coloration in Habanero pepper fruits. Mol Cells 2010; 30:569-74. [PMID: 21120629 DOI: 10.1007/s10059-010-0154-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/10/2010] [Accepted: 09/10/2010] [Indexed: 10/18/2022] Open
Abstract
Peppers (Capsicum spp.) display a variety of fruit colors that are reflected by the composition and amount of diverse carotenoid pigments accumulated in the pericarp. Three independent loci, c1, c2, and y, are known to determine the mature color of pepper fruits by their allelic combinations. We examined the inheritance of fruit color in recombinant inbred lines (RILs) derived from an interspecific cross between C. annuum cv. TF68 (red) and C. chinense cv. Habanero (orange). The c2 gene encodes phytoene synthase (PSY), a rate-limiting enzyme in the carotenoid biosynthesis pathway. TF68 has a dominant c2+ allele whereas Habanero is homozygous for the recessive c2 allele, which determined RIL fruit color. Here we report that the recessive c2 allele has a point mutation in the PSY gene that occurs at a splice acceptor site of the fifth intron leading to both a frame shift and premature translational termination, suggesting that impaired activity of PSY is responsible for orange fruit color. During ripening, PSY is expressed at a significantly high level in orange colored fruits compared to red ones. Interestingly, the PSY gene of red Habanero has a conserved splice acceptor dinucleotide AG. Further analysis suggests that red Habanero is a wild type revertant of the PSY mutant orange Habanero.
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Affiliation(s)
- Ok Rye Kim
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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Choi Y, Huh JH, Gehring M, Hsieh TF, Ibarra C, Silva P, Zilberman D, Fischer RL. S05-02. Regulation of gene imprinting in arabidopsis. Mech Dev 2009. [DOI: 10.1016/j.mod.2009.06.955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
AIMS Claudin 2 (CLDN2) is a family of integral membrane tight junctions. The aim was to determine the influence of CLDN2 expression on tumour behaviour and its role in breast carcinogenesis. METHOD AND RESULTS Thirty-seven invasive breast carcinomas and corresponding normal breast tissues were examined for CLDN2 protein and mRNA expression using Western blotting and semiquantitative reverse transcriptase-polymerase chain reaction. The expression of CLDN2 protein in 118 cases of breast carcinoma was further studied with immunohistochemistry and related to various clinicopathological parameters. CLDN2 protein expression was significantly down-regulated (0.4-fold) in tumours compared with corresponding normal breast tissue (P < 0.0001). Down-regulation of CLDN2 was significantly associated with lymph node metastasis (P = 0.047) by Western blot analysis, and with high clinical stage (P = 0.040) by immunohistochemistry. The expression levels of CLDN2 mRNA in high clinical stages (stages II and III) were lower than those in low clinical stage (stage I) and normal tissue, but not statistically significantly so. CONCLUSIONS These results suggest that CLDN2 is implicated in the progression as well as the development of breast carcinoma, indicating that CLDN2 is a possible tumour suppressor gene product.
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Affiliation(s)
- T H Kim
- Department of Pathology, Bundang CHA Hospital, Gyonggi-do, Korea
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Abstract
Gene imprinting, the differential expression of maternal and paternal alleles, independently evolved in mammals and in flowering plants. A unique feature of flowering plants is a double-fertilization event in which the sperm fertilize not only the egg, which forms the embryo, but also the central cell, which develops into the endosperm (an embryo-supporting tissue). The distinctive mechanisms of gene imprinting in the endosperm, which involve DNA demethylation and histone methylation, begin in the central cell and sperm prior to fertilization. Flowering plants might have coevolved double fertilization and imprinting to prevent parthenogenetic development of the endosperm.
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Affiliation(s)
- Jin Hoe Huh
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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29
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Abstract
Imprinting occurs in the endosperm of flowering plants. Endosperm, produced by fertilization of the central cell in the female gametophyte, is essential for embryo and seed development. Several imprinted genes play an important role in endosperm development. The mechanism of gene imprinting involves DNA methylation and histone modification. DNA methylation is actively removed at the imprinted alleles to be activated. Histone methylation mediated by the Polycomb group complex provides another layer of epigenetic regulation at the silenced alleles. Endosperm gene imprinting can be uncoupled from seed development when fertilization of the central cell is prevented. Imprinting may be a mechanism to ensure fertilization of the central cell thereby preventing parthenogenic development of the endosperm.
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Affiliation(s)
- Jin Hoe Huh
- University of California at Berkeley, Plant & Microbial Biology Department, Berkeley, CA 94720-3102, USA
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30
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Abstract
Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5' and 3' ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.
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Affiliation(s)
- Jon Penterman
- *Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720; and
| | | | - Jin Hoe Huh
- *Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720; and
| | - Tracy Ballinger
- Basic Sciences Division and
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Steven Henikoff
- Basic Sciences Division and
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- To whom correspondence may be addressed. E-mail: or
| | - Robert L. Fischer
- *Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720; and
- To whom correspondence may be addressed. E-mail: or
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Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 2006; 124:495-506. [PMID: 16469697 PMCID: PMC4106368 DOI: 10.1016/j.cell.2005.12.034] [Citation(s) in RCA: 494] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 11/25/2005] [Accepted: 12/09/2005] [Indexed: 11/24/2022]
Abstract
MEDEA (MEA) is an Arabidopsis Polycomb group gene that is imprinted in the endosperm. The maternal allele is expressed and the paternal allele is silent. MEA is controlled by DEMETER (DME), a DNA glycosylase required to activate MEA expression, and METHYLTRANSFERASE I (MET1), which maintains CG methylation at the MEA locus. Here we show that DME is responsible for endosperm maternal-allele-specific hypomethylation at the MEA gene. DME can excise 5-methylcytosine in vitro and when expressed in E. coli. Abasic sites opposite 5-methylcytosine inhibit DME activity and might prevent DME from generating double-stranded DNA breaks. Unexpectedly, paternal-allele silencing is not controlled by DNA methylation. Rather, Polycomb group proteins that are expressed from the maternal genome, including MEA, control paternal MEA silencing. Thus, DME establishes MEA imprinting by removing 5-methylcytosine to activate the maternal allele. MEA imprinting is subsequently maintained in the endosperm by maternal MEA silencing the paternal allele.
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Affiliation(s)
- Mary Gehring
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jin Hoe Huh
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jon Penterman
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yeonhee Choi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - John J. Harada
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Robert B. Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Contact:
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Abstract
In all eukaryotes, multisubunit histone acetyltransferase (HAT) complexes acetylate the highly conserved lysine residues in the amino-terminal tails of core histones to regulate chromatin structure and gene expression. One such complex in yeast, NuA4, specifically acetylates nucleosome-associated histone H4. Recent studies have revealed that NuA4 comprises at least 11 subunits, including Yng2p, a yeast homolog of the candidate human tumor suppressor gene, ING1. Consistent with prior data, we find that cells lacking Yng2p are deficient for NuA4 activity and are temperature-sensitive. Furthermore, we show that the NuA4 complex is present in the absence of Yng2p, suggesting that Yng2p functions to maintain or activate NuA4 HAT activity. Sporulation of diploid yng2 mutant cells reveals a defect in meiotic progression, whereas synchronized yng2 mutant cells display a mitotic delay. Surprisingly, genome-wide expression analysis revealed little change from wild type. Nocodazole arrest and release relieves the mitotic defects, suggesting that Yng2p may have a critical function prior to or during metaphase. Rather than a uniform decrease in acetylated forms of histone H4, we find striking cell-to-cell heterogeneity in the loss of acetylated histone H4 in yng2 mutant cells. Treating yng2 mutants with the histone deacetylase inhibitor trichostatin A suppressed the mitotic delay and restored global histone H4 acetylation, arguing that reduced H4 acetylation may underlie the cell cycle delay.
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Affiliation(s)
- J S Choy
- Center for Molecular Oncology, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
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Abstract
BACKGROUND The extended operative time needed for surgery with complicated atrial incisions may preclude application of the Cox-Maze III procedure (CM-III) as a concomitant operation. And after the CM-III, left atrial (LA) contraction has been reported to recover in reduced magnitude compared with right atrial (RA) contraction. METHODS To decrease operative time, we have modified the CM-III (modification I) by: obliterating the LA appendage instead of excising it; cryoablating the bridge between the LA appendage and margin of the pulmonary vein encircling incision; extending the lateral incision of RA onto the RA appendage without excising it, and extending the incision more inferiorly toward the inferior vena cava; and omitting the T-incision of RA. We compared the clinical results of the conventional CM-III (group 1, n = 18) with those of the modified CM-III group (group 2, n = 23) performed in patients with rheumatic mitral valve (MV) disease. To enlarge the contractile area of the LA, we modified the CM-III to encircle the right and left pulmonary veins separately (modification II), and compared the LA contractilities of the conventional CM-III (group A, n = 15) with those of the second modification (group B, n = 9). RESULTS Modification I: Mean aortic cross-clamp (ACC) times (135 +/- 29 versus 104 +/- 18 minutes, p < 0.005) and cardiopulmonary bypass (CPB) times (240 +/- 33 versus 185 +/- 42 minutes, p < 0.001) were significantly decreased in group 2 compared with those in group 1. In group 1, sinus rhythm was restored in 16 patients (88.9%). RA contractility was demonstrated in 100% of patients with sinus rhythm (16 of 16) and LA contractility in 75% (12 of 16) in the latest follow-up echocardiography. In group 2, sinus rhythm was restored in 21 patients (91.3%). RA contractility was demonstrated in 100% of patients with sinus rhythm (21 of 22) and LA contractility in 76.2% (16 of 21). Modification II: Mean ACC times were increased in group B compared with group A (133 +/- 32 versus 172 +/- 39 minutes, p = 0.02). The A velocities at LA contraction and the ratio of atrial contraction to peak early diastolic filling velocity (A/E ratio) of the trans-mitral flow were 0.14 +/- 0.20 m/sec and 0.23 +/- 0.11 in group A, and 0.58 +/- 0.33 m/sec and 0.47 +/- 0.19 in group B, respectively, both showing a significant increase in group B compared with group A (p < 0.05). CONCLUSIONS Our first modification of the CM-III showed comparable sinus conversion rates and incidence of atrial contractility restoration with significantly shorter ACC and CPB times than the conventional CM-III. The second modification of the CM-III significantly increased the LA contractility when compared with the conventional CM-III, although the second modification required a longer ACC time.
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Affiliation(s)
- K B Kim
- Department of Thoracic and Cardiovascular Surgery, College of Medicine, Seoul National University, Korea.
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Abstract
To investigate the pathogenesis of accelerated graft atherosclerosis after cardiac transplantation, a genetically well-defined and reproducible animal model is required. We performed heterotopic intraabdominal heart transplantation between the two inbred strains of mice. Forty hearts from B10.A mice were transplanted into B10.BR mice. Recipients were sacrificed at 1, 3, 5, 7, 14, 28, and 42 days after implantation. The specimens from both donor and recipient were examined with fluorescent immunohistochemistry and the serial histopathologic changes were evaluated. In the donor hearts, ICAM-1 and VCAM-1 expressions were minimal at day 1 and they gradually increased, reaching their peaks on day 5 or 7 and remained unchanged by day 42. However, there were very little expressions in the recipients' hearts. Mean percent areas of intima in the donor coronaries revealed progressive increase by day 42. However, those in the recipients occupied consistently less than 5% of the lumen. In conclusion, we demonstrated that a heterotopic murine heart transplantation model was a useful tool to produce transplantation coronary artery disease and that adhesion molecules on the cardiac allografts were activated very early and remained elevated at all time-points, nonetheless the arterial lesion was detected after day 28 and its progression was accelerated thereafter.
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Affiliation(s)
- J R Lee
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Children's Hospital, Seoul National University College of Medicine, Korea.
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