35 results on '"Cho, Jungnam"'
Search Results
2. Harnessing epigenetic variability for crop improvement: current status and future prospects
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Kim, Eun Yu, Kim, Kyung Do, and Cho, Jungnam
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- 2022
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3. Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin
- Author
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Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, and Yang, Tae-Jin
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- 2022
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4. m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis
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Wang, Ling, Zhuang, Haiyan, Fan, Wenwen, Zhang, Xia, Dong, Haihong, Yang, Hongxing, and Cho, Jungnam
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- 2022
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5. Recent advancement of NGS technologies to detect active transposable elements in plants
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Satheesh, Viswanathan, Fan, Wenwen, Chu, Jie, and Cho, Jungnam
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- 2021
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6. Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons
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Kim, Eun Yu, Wang, Ling, Lei, Zhen, Li, Hui, Fan, Wenwen, and Cho, Jungnam
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- 2021
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7. The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid–dependent stress responses in Arabidopsis.
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Lee, Keun Pyo, Liu, Kaiwei, Kim, Eun Yu, Medina-Puche, Laura, Dong, Haihong, Di, Minghui, Singh, Rahul Mohan, Li, Mengping, Qi, Shan, Meng, Zhuoling, Cho, Jungnam, Zhang, Heng, Lozano-Duran, Rosa, and Kim, Chanhong
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- 2024
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8. The CARBON CATABOLITE REPRESSION 4A‐mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs.
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Wang, Ling, Li, Hui, Lei, Zhen, Jeong, Dong‐Hoon, and Cho, Jungnam
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TRANSPOSONS ,NON-coding RNA ,CATABOLITE repression ,RNA replicase ,MOBILE genetic elements ,RNA - Abstract
Summary: Transposable elements (TEs) are mobile genetic elements that can impair the host genome stability and integrity. It has been well documented that activated transposons in plants are suppressed by small interfering (si) RNAs. However, transposon repression by the cytoplasmic RNA surveillance system is unknown.Here, we show that mRNA deadenylation is critical for controlling transposons in Arabidopsis. Trimming of poly(A) tail is a rate‐limiting step that precedes the RNA decay and is primarily mediated by the CARBON CATABOLITE REPRESSION 4 (CCR4)‐NEGATIVE ON TATA‐LESS (NOT) complex.We found that the loss of CCR4a leads to strong derepression and mobilization of TEs in Arabidopsis. Intriguingly, CCR4a regulates a largely distinct set of TEs from those controlled by RNA‐dependent RNA Polymerase 6 (RDR6), a key enzyme that produces cytoplasmic siRNAs. This indicates that the cytoplasmic RNA quality control mechanism targets the TEs that are poorly recognized by the previously well‐characterized RDR6‐mediated pathway, and thereby augments the host genome stability.Our study suggests a hitherto unknown mechanism for transposon repression mediated by RNA deadenylation and unveils a complex nature of the host's strategy to maintain the genome integrity. [ABSTRACT FROM AUTHOR]
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- 2024
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9. Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants
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Cho, Jungnam, Benoit, Matthias, Catoni, Marco, Drost, Hajk-Georg, Brestovitsky, Anna, Oosterbeek, Matthijs, and Paszkowski, Jerzy
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- 2019
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10. The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice
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Choi, Jeongmin, Lee, Tak, Cho, Jungnam, Servante, Emily K., Pucker, Boas, Summers, William, Bowden, Sarah, Rahimi, Mehran, An, Kyungsook, An, Gynheung, Bouwmeester, Harro J., Wallington, Emma J., Oldroyd, Giles, and Paszkowski, Uta.
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- 2020
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11. m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis.
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Wang, Ling, Zhuang, Haiyan, Fan, Wenwen, Zhang, Xia, Dong, Haihong, Yang, Hongxing, and Cho, Jungnam
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- 2022
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12. Genetics and genomics of moso bamboo (Phyllostachys edulis) : Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry
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Ramakrishnan, Muthusamy, Yrjälä, Kim, Vinod, Kunnummal Kurungara, Sharma, Anket, Cho, Jungnam, Satheesh, Viswanathan, Zhou, Mingbing, Helsinki Institute of Sustainability Science (HELSUS), and Department of Forest Sciences
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CROSS-SPECIES AMPLIFICATION ,4112 Forestry ,sustainable development ,BAMBUSA-EDULIS ,FUNCTIONAL-ANALYSIS ,bamboo industry ,transposons ,MICROSATELLITE MARKERS ,SSR MARKERS ,WIDE IDENTIFICATION ,TRANSCRIPTION FACTORS ,PHYLOGENETIC-RELATIONSHIPS ,POACEAE BAMBUSOIDEAE ,moso bamboo ,genomics ,TRANSPOSABLE ELEMENTS ,Phyllostachys edulis ,bioeconomy ,biotechnology - Abstract
Sustainable goals for contemporary world seek viable solutions for interconnected challenges, particularly in the fields of food and energy security and climate change. We present bamboo, one of the versatile plant species on earth, as an ideal candidate for bioeconomy for meeting some of these challenges. With its potential realized, particularly in the industrial sector, countries such as China are going extensive with bamboo development and cultivation to support a myriad of industrial uses. These include timber, fiber, biofuel, paper, food, and medicinal industries. Bamboo is an ecologically viable choice, having better adaptation to wider environments than do other grasses, and can help to restore degraded lands and mitigate climate change. Bamboo, as a crop species, has not become amenable to genetic improvement, due to its long breeding cycle, perennial nature, and monocarpic behavior. One of the commonly used species, moso bamboo (Phyllostachys edulis) is a potential candidate that qualifies as industrial bamboo. With its whole-genome information released, genetic manipulations of moso bamboo offer tremendous potential to meet the industrial expectations either in quality or in quantity. Further, bamboo cultivation can expect several natural hindrances through biotic and abiotic stresses, which needs viable solutions such as genetic resistance. Taking a pragmatic view of these future requirements, we have compiled the present status of bamboo physiology, genetics, genomics, and biotechnology, particularly of moso bamboo, to drive various implications in meeting industrial and cultivation requirements. We also discuss challenges underway, caveats, and contextual opportunities concerning sustainable development.
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- 2020
13. Tracing Mobile DNAs: From Molecular to Population Scales.
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Fan, Wenwen, Wang, Ling, Chu, Jie, Li, Hui, Kim, Eun Yu, and Cho, Jungnam
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MOBILE genetic elements ,TRANSPOSONS ,PLANT epigenetics ,BOTANY ,EUKARYOTIC genomes ,PLANT genomes - Abstract
Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile nature of transposon has been also actively exploited in plant science research by generating genetic mutants in non-model plant systems. On the other hand, transposon mobilization can bring about detrimental effects to host genomes and they are therefore mostly silenced by the epigenetic mechanisms. TEs have been studied as major silencing targets and acted a main feature in the remarkable growth of the plant epigenetics field. Despite the importance of transposon in plant biology and biotechnology, their mobilization and the underlying mechanisms are largely left unanswered. This is mainly because of the sequence repetitiveness of transposons, which makes their detection and analyses difficult and complicated. Recently, some attempts have been made to develop new experimental methods detecting active transposons and their mobilization behavior. These techniques reveal TE mobility in various levels, including the molecular, cellular, organismal and population scales. In this review, we will highlight the novel technical approaches in the study of mobile genetic elements and discuss how these techniques impacted on the advancement of transposon research and broadened our understanding of plant genome plasticity. [ABSTRACT FROM AUTHOR]
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- 2022
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14. Phase separation of chromatin and small RNA pathways in plants.
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Lei, Zhen, Wang, Ling, Kim, Eun Yu, and Cho, Jungnam
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NON-coding RNA ,PHASE separation ,PLANT RNA ,CHROMATIN ,SMALL interfering RNA - Abstract
SUMMARY: Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid–liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self‐assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants. Significance Statement: Biomolecular condensate formation is mediated by liquid–liquid phase separation and is critical for various biological processes in both plants and animals. We review phase separation occurring in plants with a specific focus on the chromatin and small RNA pathways. [ABSTRACT FROM AUTHOR]
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- 2021
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15. Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo.
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Tao, Gui-Yun, Ramakrishnan, Muthusamy, Vinod, Kunnummal Kurungara, Yrjälä, Kim, Satheesh, Viswanathan, Cho, Jungnam, Fu, Ying, and Zhou, Mingbing
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CELL analysis ,ORGANELLE formation ,DNA synthesis ,DNA replication ,CARBOHYDRATE metabolism - Abstract
Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein–protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway. [ABSTRACT FROM AUTHOR]
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- 2020
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16. Transposon-Derived Non-coding RNAs and Their Function in Plants.
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Cho, Jungnam
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TRANSPOSONS ,NON-coding RNA ,PLANT genomes ,PLANTS - Abstract
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted. [ABSTRACT FROM AUTHOR]
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- 2018
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17. Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo.
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Zou, Long‐Hai, Zhu, Bailiang, Chen, Yaxin, Lu, Yaping, Ramkrishnan, Muthusamy, Xu, Chao, Zhou, Xiaohong, Ding, Yiqian, Cho, Jungnam, and Zhou, Mingbing
- Subjects
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DNA methylation , *CROPS , *GENETIC regulation , *PHYLLOSTACHYS ,DEVELOPING countries - Abstract
Summary Long terminal repeat retroelements (LTR‐REs) have profound effects on DNA methylation and gene regulation. Despite the vast abundance of LTR‐REs in the genome of Moso bamboo (Phyllostachys edulis), an industrial crop in underdeveloped countries, their precise implication of the LTR‐RE mobility in stress response and development remains unknown. We investigated the RNA and DNA products of LTR‐REs in Moso bamboo under various developmental stages and stressful conditions. Surprisingly, our analyses identified thousands of active LTR‐REs, particularly those located near genes involved in stress response and developmental regulation. These genes adjacent to active LTR‐REs exhibited an increased expression under stress and are associated with reduced DNA methylation that is likely affected by the induced LTR‐REs. Moreover, the analyses of simultaneous mapping of insertions and DNA methylation showed that the LTR‐REs effectively alter the epigenetic status of the genomic regions where they inserted, and concomitantly their transcriptional competence which might impact the stress resilience and growth of the host. Our work unveils the unusually strong LTR‐RE mobility in Moso bamboo and its close association with (epi)genetic changes, which supports the co‐evolution of the parasitic DNAs and host genome in attaining stress tolerance and developmental robustness. [ABSTRACT FROM AUTHOR]
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- 2024
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18. Detecting Signatures of TE Polymorphisms in Short-Read Sequencing Data
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Anne C. Roulin, Christoph Stritt, University of Zurich, Cho, Jungnam, and Roulin, Anne C
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Polymorphism Detection ,Computer science ,Sequencing data ,Single-nucleotide polymorphism ,Computational biology ,580 Plants (Botany) ,Short read ,Genome ,Population genomics ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,10126 Department of Plant and Microbial Biology ,1311 Genetics ,1312 Molecular Biology ,10211 Zurich-Basel Plant Science Center ,Functional genomics ,Reference genome - Abstract
Transposable elements (TEs) are an important cause of evolutionary change and functional diversity, yet they are routinely discarded in the first steps of many analyses. In this chapter we show how, given a reference genome, TEs can be incorporated fairly easily into functional and evolutionary studies. We offer a glimpse into a program which detects TE insertion polymorphisms and discuss practical issues arising from the diversity of TEs and genome architectures. Detecting TE polymorphisms relies on a series of ad hoc criteria because, in contrast to single nucleotide polymorphisms, there is no general way to model TE activity. Signatures of TE polymorphisms in reference-aligned reads depend on the type of TE as well as on the complexity of the genomic background. As a consequence, a basic understanding of the limitations imposed by the data and of what the algorithm is doing is important to obtain reliable results. Here, we hope to convey such a basic understanding and help researchers to avoid some of the common pitfalls of TE polymorphism detection.
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- 2021
19. Identification of Active Transposable Elements in Plants: The Mobilome-Seq Approach
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Michael Thieme, Anne C. Roulin, University of Zurich, Cho, Jungnam, and Roulin, Anne C
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Transposable element ,food and beverages ,Computational biology ,Biology ,580 Plants (Botany) ,Phenotype ,Genome ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,10126 Department of Plant and Microbial Biology ,1311 Genetics ,1312 Molecular Biology ,Gene silencing ,Identification (biology) ,Mobilome ,Epigenetics ,10211 Zurich-Basel Plant Science Center ,Genome size - Abstract
Transposable elements (TEs) are the main component of eukaryotic genomes. Besides their impact on genome size, TEs are also functionally important as they can alter gene expression and influence phenotypic variation. In plants, most top-down studies focus on extremely clear phenotypes such as the shape or the color of individuals and do not explore fully the role of TEs in evolution. Assessing the impact of TEs in a more systematic manner, however, requires identifying active TEs to further study their impact on phenotypes. In this chapter, we describe an in planta approach that consists in activating TEs by interfering with pathways involved in their silencing. It enables to directly investigate the functional impact of single TE families at low cost.
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- 2021
20. The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice
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Uta Paszkowski, Emma J. Wallington, Harro J. Bouwmeester, William Summers, Jeongmin Choi, Mehran Rahimi, Boas Pucker, Kyungsook An, Gynheung An, Giles E. D. Oldroyd, Tak Lee, Emily K. Servante, Jungnam Cho, Sarah Bowden, Lee, Tak [0000-0001-7008-7605], Cho, Jungnam [0000-0002-4078-7763], Pucker, Boas [0000-0002-3321-7471], Summers, William [0000-0002-4835-4743], Bowden, Sarah [0000-0001-5105-076X], Bouwmeester, Harro J. [0000-0003-0907-2732], Wallington, Emma J. [0000-0003-3715-7901], Oldroyd, Giles [0000-0002-5245-6355], Paszkowski, Uta. [0000-0002-7279-7632], Apollo - University of Cambridge Repository, Plant Hormone Biology (SILS, FNWI), Bouwmeester, Harro J [0000-0003-0907-2732], Wallington, Emma J [0000-0003-3715-7901], and Paszkowski, Uta [0000-0002-7279-7632]
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0106 biological sciences ,0301 basic medicine ,Arabidopsis ,General Physics and Astronomy ,01 natural sciences ,Plant Roots ,631/449 ,Lactones ,Gene Expression Regulation, Plant ,Mycorrhizae ,RNA-Seq ,14/19 ,lcsh:Science ,Phylogeny ,Plant Proteins ,Regulation of gene expression ,45/70 ,Multidisciplinary ,Homozygote ,article ,Intracellular Signaling Peptides and Proteins ,food and beverages ,631/449/2676/2061 ,Karrikin ,Cell biology ,Crosstalk (biology) ,Multigene Family ,38/77 ,Signal transduction ,631/449/2676 ,Heterocyclic Compounds, 3-Ring ,Signal Transduction ,Science ,Strigolactone ,Genetics and Molecular Biology ,Germination ,Biology ,General Biochemistry, Genetics and Molecular Biology ,96/95 ,38/91 ,03 medical and health sciences ,Symbiosis ,Furans ,Gene ,Pyrans ,45 ,Arabidopsis Proteins ,fungi ,Oryza ,General Chemistry ,biology.organism_classification ,030104 developmental biology ,General Biochemistry ,lcsh:Q ,010606 plant biology & botany - Abstract
Most plants associate with beneficial arbuscular mycorrhizal (AM) fungi that facilitate soil nutrient acquisition. Prior to contact, partner recognition triggers reciprocal genetic remodelling to enable colonisation. The plant Dwarf14-Like (D14L) receptor conditions pre-symbiotic perception of AM fungi, and also detects the smoke constituent karrikin. D14L-dependent signalling mechanisms, underpinning AM symbiosis are unknown. Here, we present the identification of a negative regulator from rice, which operates downstream of the D14L receptor, corresponding to the homologue of the Arabidopsis thaliana Suppressor of MAX2-1 (AtSMAX1) that functions in karrikin signalling. We demonstrate that rice SMAX1 is a suppressor of AM symbiosis, negatively regulating fungal colonisation and transcription of crucial signalling components and conserved symbiosis genes. Similarly, rice SMAX1 negatively controls strigolactone biosynthesis, demonstrating an unexpected crosstalk between the strigolactone and karrikin signalling pathways. We conclude that removal of SMAX1, resulting from D14L signalling activation, de-represses essential symbiotic programmes and increases strigolactone hormone production.
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- 2020
21. Regulation of rice root development by a retrotransposon acting as a microRNA sponge
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Jungnam Cho, Jerzy Paszkowski, Cho, Jungnam [0000-0002-4078-7763], and Apollo - University of Cambridge Repository
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0301 basic medicine ,Transposable element ,Retroelements ,root development ,QH301-705.5 ,Science ,Plant Development ,Plant Biology ,Retrotransposon ,Oryza sativa ,Biology ,Plant Roots ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Gene Expression Regulation, Plant ,microRNA ,Gene expression ,miR171 ,Biology (General) ,Transcription factor ,Gene ,2. Zero hunger ,Genetics ,Regulation of gene expression ,General Immunology and Microbiology ,General Neuroscience ,Gene Expression Profiling ,food and beverages ,Oryza ,General Medicine ,MicroRNAs ,030104 developmental biology ,Medicine ,Trans-acting ,Other ,Research Article - Abstract
It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species., eLife digest An organism’s genome contains all of the DNA the individual needs to survive and grow. Transposons are pieces of DNA that can move around the genome. They make up almost half of human DNA and over 85% of the DNA of major crop plants like maize, barley and wheat. When transposons move they can cause harmful changes in the regions where they insert into the DNA and so cells have mechanisms in place to tightly control the activities of the transposons. However, some transposons cause changes to DNA that are beneficial to the organism. Thus, the relationship between transposons and their host organisms is an example of a delicate but mostly peaceful coexistence. Although the cellular mechanisms controlling transposons are quite well known, the extent to which the transposons affect the ability of organisms to survive, develop and reproduce is poorly understood. A family of proteins known as the SCARECROW-like transcription factors are important for the roots of plants to develop properly. In other organs such as the leaves or flowers these proteins can cause developmental defects, so the plants carefully control where the proteins are made. Thus, plants normally produce a molecule called miR171 in leaves and flowers, but not in roots, that inhibits protein production by binding to and destabilising the RNA molecules that act as templates to make these proteins. Cho and Paszkowski have now identified a transposon that produces an RNA molecule with similarities to the RNA templates used to make the SCARECROW-like transcription factors. The experiments show that this transposon RNA is found in very high amounts in roots and mimics the transcription factor RNA so well that miR171 binds to it. This inactivates miR171 in roots to allow the SCARECROW-like transcription factors to be produced. These findings reveal a new mechanism by which transposons may regulate how plants develop and provide possible new approaches for boosting the growth of rice and other crop plants. Similar regulatory interactions between transposons and their host DNA may also be present in animals and other organisms.
- Published
- 2017
22. Molecular Mimicry of Transposable Elements in Plants.
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Chu J, Newman J, and Cho J
- Abstract
Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species. Thus far, studies have mainly investigated the cis-acting regulatory roles of TEs generated by their insertions nearby or within the host genes. However, the trans-acting effects of TE-derived RNA and DNA remained obscure to date. TEs contain various regulatory elements within their sequences that can accommodate the binding of specific RNAs and proteins. Recently, it was suggested that some of these cellular regulators are shared between TEs and the host genes, and the competition for the common host factors underlies the fine-tuned developmental reprogramming. In this review, we will highlight and discuss the latest discoveries on the biological functions of plant TEs, with a particular focus on their competitive binding with specific developmental regulators., (© The Author(s) 2024. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.)
- Published
- 2024
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23. The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis.
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Lee KP, Liu K, Kim EY, Medina-Puche L, Dong H, Di M, Singh RM, Li M, Qi S, Meng Z, Cho J, Zhang H, Lozano-Duran R, and Kim C
- Subjects
- Salicylic Acid metabolism, RNA, Messenger genetics, RNA, Messenger metabolism, Gene Expression Regulation, Plant, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Adenine analogs & derivatives
- Abstract
N 6-methyladenosine (m6A) is a common epitranscriptional mRNA modification in eukaryotes. Thirteen putative m6A readers, mostly annotated as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins, have been identified in Arabidopsis (Arabidopsis thaliana), but few have been characterized. Here, we show that the Arabidopsis m6A reader ECT1 modulates salicylic acid (SA)-mediated plant stress responses. ECT1 undergoes liquid-liquid phase separation in vitro, and its N-terminal prion-like domain is critical for forming in vivo cytosolic biomolecular condensates in response to SA or bacterial pathogens. Fluorescence-activated particle sorting coupled with quantitative PCR analyses unveiled that ECT1 sequesters SA-induced m6A modification-prone mRNAs through its conserved aromatic cage to facilitate their decay in cytosolic condensates, thereby dampening SA-mediated stress responses. Consistent with this finding, ECT1 overexpression promotes bacterial multiplication in plants. Collectively, our findings unequivocally link ECT1-associated cytosolic condensates to SA-dependent plant stress responses, advancing the current understanding of m6A readers and the SA signaling network., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2024
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24. m 6 A RNA demethylase AtALKBH9B promotes mobilization of a heat-activated long terminal repeat retrotransposon in Arabidopsis .
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Fan W, Wang L, Lei Z, Li H, Chu J, Yan M, Wang Y, Wang H, Yang J, and Cho J
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- Retroelements genetics, RNA, Hot Temperature, DNA Methylation, Terminal Repeat Sequences genetics, Gene Expression Regulation, Plant, Arabidopsis genetics
- Abstract
Transposons are mobile and ubiquitous DNA molecules that can cause vast genomic alterations. In plants, it is well documented that transposon mobilization is strongly repressed by DNA methylation; however, its regulation at the posttranscriptional level remains relatively uninvestigated. Here, we suggest that transposon RNA is marked by m
6 A RNA methylation and can be localized in stress granules (SGs). Intriguingly, SG-localized AtALKBH9B selectively demethylates a heat-activated retroelement, Onsen , and thereby releases it from spatial confinement, allowing for its mobilization. In addition, we show evidence that m6 A RNA methylation contributes to transpositional suppression by inhibiting virus-like particle assembly and extrachromosomal DNA production. In summary, this study unveils a previously unknown role for m6 A in the suppression of transposon mobility and provides insight into how transposons counteract the m6 A-mediated repression mechanism by hitchhiking the RNA demethylase of the host.- Published
- 2023
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25. Visualization of synthetic retroelement integration reveals determinants of permissivity to retrotransposition.
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Chu J, Zhang X, and Cho J
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- Retroelements genetics, Biochemical Phenomena
- Abstract
Competing Interests: Conflict of interest statement. None declared.
- Published
- 2023
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26. Editorial: Beyond genetics: modifications of nucleic acid and chromatin.
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Cho J, Schubert D, and Zhou Y
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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- 2023
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27. PopRice extrachromosomal DNA sponges ABSCISIC ACID-INSENSITIVE 5 in rice seed-to-seedling transition.
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Chu J, Wang L, and Cho J
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- Seedlings genetics, Germination genetics, Seeds genetics, DNA, Gene Expression Regulation, Plant, Abscisic Acid pharmacology, Oryza genetics
- Abstract
Competing Interests: Conflict of interest statement. The authors declare that no conflicts of interest exist.
- Published
- 2023
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28. Specific suppression of long terminal repeat retrotransposon mobilization in plants.
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Brestovitsky A, Iwasaki M, Cho J, Adulyanukosol N, Paszkowski J, and Catoni M
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- Retroelements genetics, Genome, Plant genetics, Terminal Repeat Sequences genetics, Tenofovir, Arabidopsis genetics, Oryza genetics
- Abstract
The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.)
- Published
- 2023
- Full Text
- View/download PDF
29. Small regulatory RNAs in rice epigenetic regulation.
- Author
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Park SY, Cho J, and Jeong DH
- Subjects
- DNA Methylation, DNA Transposable Elements genetics, Epigenesis, Genetic, Gene Expression Regulation, Plant, RNA metabolism, RNA, Small Interfering metabolism, Arabidopsis genetics, Oryza genetics
- Abstract
Plant small RNAs (sRNAs) are short non-coding RNAs that are implicated in various regulatory processes involving post-transcriptional gene silencing and epigenetic gene regulation. In epigenetic regulation, sRNAs are primarily involved in RNA-directed DNA methylation (RdDM) pathways. sRNAs in the RdDM pathways play a role not only in the suppression of transposable element (TE) activity but also in gene expression regulation. Although the major components of the RdDM pathways have been well studied in Arabidopsis, recent studies have revealed that the RdDM pathways in rice have important biological functions in stress response and developmental processes. In this review, we summarize and discuss recent literature on sRNA-mediated epigenetic regulation in rice. First, we describe the RdDM mechanisms in plants. We then introduce recent discoveries on the biological roles of rice genes involved in the RdDM pathway and TE-derived sRNAs working at specific genomic loci for epigenetic control in rice., (© 2022 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)
- Published
- 2022
- Full Text
- View/download PDF
30. Enrichment of Cytoplasmic RNA Granules from Arabidopsis Seedlings.
- Author
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Lei Z, Kim EY, and Cho J
- Abstract
RNA granules (RGs) are membraneless intracellular compartments that play important roles in the post-transcriptional control of gene expression. Stress granules (SGs) are a type of RGs that form under environmental challenges and/or internal cellular stresses. Stress treatments lead to strong mRNAs translational inhibition and storage in SGs until the normal growth conditions are restored. Intriguingly, we recently showed that plant stress granules are associated with siRNA bodies, where the RDR6-mediated and transposon-derived siRNA biogenesis occurs ( Kim et al. , 2021 ). This protocol provides a technical workflow for the enrichment of cytoplasmic RGs from Arabidopsis seedlings. We used the DNA methylation-deficient ddm1 mutant in our study, but the method can be applied to any other plant samples with strong RG formation. The resulting RG fractions can be further tested for either RNAs or proteins using RNA-seq and mass spectrometry-based proteomics., Competing Interests: Competing interestsThe authors declare no conflicts of interest., (Copyright © 2021 The Authors; exclusive licensee Bio-protocol LLC.)
- Published
- 2021
- Full Text
- View/download PDF
31. Quantitative Measurement of Transposon Copy Number Using the Droplet Digital PCR.
- Author
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Fan W and Cho J
- Subjects
- DNA, Plant genetics, Fluorescence, Real-Time Polymerase Chain Reaction, Arabidopsis genetics, DNA Copy Number Variations, DNA Transposable Elements
- Abstract
Spontaneous proliferation of transposable elements contributes to genetic diversity at varying levels such as somatic mosaicism, genetic divergence in population, and genome evolution. Such genetic diversity is essential for plants' adaptation to changing environment and serves as a valuable resource for crop improvement. Therefore, measuring the copy number variation of transposable elements with precision and efficiency is important to understand the extent of their proliferation. Droplet Digital PCR (ddPCR) is an accurate and sensitive technique that allows measurement of copy number variation of a transposon. Briefly, genomic DNA is extracted, digested, and partitioned into thousands of nanoliter-scale droplets. The TaqMan real-time PCR followed by the end-point fluorescence detection enables the quantitative measurement of copy number of template DNAs. Here in this chapter, we describe the step-by-step procedure of ddPCR using EVADE retrotransposon of Arabidopsis as an example.
- Published
- 2021
- Full Text
- View/download PDF
32. High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq.
- Author
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Wang L, Kim EY, and Cho J
- Subjects
- Evolution, Molecular, Genome, Plant, High-Throughput Nucleotide Sequencing, Reverse Transcription, Plants genetics, Retroelements, Sequence Analysis, DNA methods, Terminal Repeat Sequences
- Abstract
Extrachromosomal linear DNA (eclDNA) is the reverse-transcribed cDNA intermediate derived from long terminal repeat (LTR) transposable elements (TEs) (Cho et al., Nat Plants 5:26-33, 2018). Given that the eclDNAs are the final intermediate of LTR-TE life cycle prior to integration to the host chromosomes, their presence is considered a strong indication of active LTR retrotransposons (Cho et al., Nat Plants 5:26-33, 2018; Lanciano et al., PLoS Genet 13:e1006630, 2017). Here, we describe a method of amplification of LTR extrachromosomal DNA followed by sequencing (ALE-seq) which determines the 5' LTR sequences of eclDNAs. Briefly, ALE-seq consists of two steps of amplification, in vitro transcription of adaptor-ligated eclDNAs and subsequent reverse transcription to cDNAs primed at the conserved primer binding site (PBS) (Cho et al., Nat Plants 5:26-33, 2018). ALE-seq allows the high-throughput identification of novel LTR-TEs which are active in plants that could be potentially useful for crop biotechnology.
- Published
- 2021
- Full Text
- View/download PDF
33. Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq.
- Author
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Wang L, Cho J, and Satheesh V
- Subjects
- Sequence Analysis, DNA methods, Software, Computational Biology methods, Retroelements, Terminal Repeat Sequences
- Abstract
ALE-seq is a method devised to identify pre-integration intermediates of LTR retrotransposons called extrachromosomal linear DNA, which can be used to predict retrotransposition activity. We describe here a bioinformatic methodology to process reads obtained from the ALE-seq protocol for the effective annotation of novel and active retroelements.
- Published
- 2021
- Full Text
- View/download PDF
34. Determination of TE Insertion Positions Using Transposon Display.
- Author
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Kim EY, Fan W, and Cho J
- Subjects
- Chromosome Mapping, DNA, Plant genetics, Arabidopsis genetics, Mutagenesis, Insertional methods, Retroelements
- Abstract
Mapping the genomic location to which transposons jumped is of greatest interest to transposon biologists. Transposon display (TD) is the technique of choice that is easy and fast in determining the neo-insertion positions of a target transposon. Essentially, tagging of transposon is performed by digesting genomic DNA, ligating adaptors to digested DNA ends and PCR amplifying genomic regions flanking the transposon of interest. In this chapter, the experimental procedure of TD is described using Onsen retrotransposon of Arabidopsis as an example.
- Published
- 2021
- Full Text
- View/download PDF
35. Regulation of rice root development by a retrotransposon acting as a microRNA sponge.
- Author
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Cho J and Paszkowski J
- Subjects
- Gene Expression Profiling, Gene Expression Regulation, Plant, MicroRNAs metabolism, Oryza growth & development, Plant Development, Plant Roots growth & development, Retroelements
- Abstract
It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.
- Published
- 2017
- Full Text
- View/download PDF
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