9 results on '"Cho, Jungnam"'
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2. Recent advancement of NGS technologies to detect active transposable elements in plants.
- Author
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Satheesh V, Fan W, Chu J, and Cho J
- Subjects
- High-Throughput Nucleotide Sequencing trends, Terminal Repeat Sequences, Plants genetics, Retroelements, Sequence Analysis, DNA trends
- Abstract
Background: Unlike peoples' belief that transposable elements (TEs) are "junk DNAs" or "genomic parasites", TEs are essential genomic elements that bring about genetic diversity and enable evolution of a species. In fact, transposons are major constituent of chromosome in crop genomes, particularly in major cereal crops, the primary type of which is long terminal repeat (LTR) retrotransposon. Since TE mobilization can be controlled by specific environmental stimulation and as the result can generate novel genetic variations, it has been suggested that controlled mobilization of TEs can be a plausible method for crop breeding. To achieve this goal, series of sequencing techniques have been recently established to identify TEs that are active in mobility. These methods target and detect extrachromosomal DNAs (ecDNAs), which are final products of integration. The newly identified TEs by these methods exhibit strong transpositional activity which can generate novel genetic diversity and provide useful breeding resources., Conclusions: In this mini review, we summarize and introduce ALE-seq, mobilome-seq, and VLP DNA-seq techniques employed to detect active TEs in plants.
- Published
- 2021
- Full Text
- View/download PDF
3. Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons.
- Author
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Kim EY, Wang L, Lei Z, Li H, Fan W, and Cho J
- Subjects
- Codon, RNA, Plant metabolism, RNA, Small Interfering metabolism, Arabidopsis genetics, Epigenesis, Genetic, Gene Expression Regulation, Plant, Gene Silencing, Retroelements genetics, Ribosomes metabolism
- Abstract
Transposable elements (TEs, transposons) are mobile DNAs that can cause fatal mutations
1 . To suppress their activity, host genomes deploy small interfering RNAs (siRNAs) that trigger and maintain their epigenetic silencing2,3 . Whereas 24-nucleotide (nt) siRNAs mediate RNA-directed DNA methylation (RdDM) to reinforce the silent state of TEs3 , activated or naive TEs give rise to 21- or 22-nt siRNAs by the RNA-DEPENDENT RNA POLYMERASE 6 (RDR6)-mediated pathway, triggering both RNAi and de novo DNA methylation4,5 . This process, which is called RDR6-RdDM, is critical for the initiation of epigenetic silencing of active TEs; however, their specific recognition and the selective processing of siRNAs remain elusive. Here, we suggest that plant transposon RNAs undergo frequent ribosome stalling caused by their unfavourable codon usage. Ribosome stalling subsequently induces RNA truncation and localization to cytoplasmic siRNA bodies, both of which are essential prerequisites for RDR6 targeting6,7 . In addition, SUPPRESSOR OF GENE SILENCING 3 (SGS3), the RDR6-interacting protein7 , exhibits phase separation both in vitro and in vivo through its prion-like domains, implicating the role of liquid-liquid phase separation in siRNA body formation. Our study provides insight into the host recognition of active TEs, which is important for the maintenance of genome integrity.- Published
- 2021
- Full Text
- View/download PDF
4. 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
5. 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
6. 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
7. Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants.
- Author
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Cho J, Benoit M, Catoni M, Drost HG, Brestovitsky A, Oosterbeek M, and Paszkowski J
- Subjects
- Arabidopsis genetics, Computational Biology methods, Gene Expression Regulation, Plant, Heat-Shock Response genetics, Solanum lycopersicum genetics, Oryza genetics, Crops, Agricultural genetics, Retroelements genetics, Sequence Analysis, DNA methods, Terminal Repeat Sequences
- Abstract
Retrotransposons have played an important role in the evolution of host genomes
1,2 . Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2 . Such studies provide important 'snapshots' reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis3 . However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5' LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.- Published
- 2019
- Full Text
- View/download PDF
8. 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
9. Regulation of rice root development by a retrotransposon acting as a microRNA sponge
- Author
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Jungnam Cho, Jerzy Paszkowski, Cho, Jungnam [0000-0002-4078-7763], and Apollo - University of Cambridge Repository
- Subjects
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
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