All Outputs (29)

Molecular Mimicry of Transposable Elements in Plants (2024)
Journal Article
Chu, J., Newman, J., & Cho, J. (2024). Molecular Mimicry of Transposable Elements in Plants. Plant & Cell Physiology, https://doi.org/10.1093/pcp/pcae058

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 ess... Read More about Molecular Mimicry of Transposable Elements in Plants.

The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid–dependent stress responses in Arabidopsis (2023)
Journal Article
Lee, K. P., Liu, K., Kim, E. Y., Medina-Puche, L., Dong, H., Di, M., Singh, R. M., Li, M., Qi, S., Meng, Z., Cho, J., Zhang, H., Lozano-Duran, R., & Kim, C. (online). The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid–dependent stress responses in Arabidopsis. The Plant Cell, https://doi.org/10.1093/plcell/koad300

m6A RNA demethylase AtALKBH9B promotes mobilization of a heat-activated long terminal repeat retrotransposon in Arabidopsis (2023)
Journal Article
Fan, W., Wang, L., Lei, Z., Li, H., Chu, J., Yan, M., …Cho, J. (2023). m6A RNA demethylase AtALKBH9B promotes mobilization of a heat-activated long terminal repeat retrotransposon in Arabidopsis. Science Advances, 9(48), Article eadf3292. https://doi.org/10.1126/sciadv.adf3292

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 le... Read More about m6A RNA demethylase AtALKBH9B promotes mobilization of a heat-activated long terminal repeat retrotransposon in Arabidopsis.

The CARBON CATABOLITE REPRESSION 4A ‐mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs (2023)
Journal Article
Wang, L., Li, H., Lei, Z., Jeong, D., & Cho, J. (online). The CARBON CATABOLITE REPRESSION 4A ‐mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs. New Phytologist, https://doi.org/10.1111/nph.19435

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, transpo... Read More about The CARBON CATABOLITE REPRESSION 4A ‐mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs.

Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat (2023)
Journal Article
Xie, Y., Ying, S., Li, Z., Zhang, Y., Zhu, J., Zhang, J., …Zhang, Y. (2023). Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat. Nature Communications, 14(1), Article 7465. https://doi.org/10.1038/s41467-023-42771-9

Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analys... Read More about Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat.

Visualization of synthetic retroelement integration reveals determinants of permissivity to retrotransposition (2023)
Journal Article
Chu, J., Zhang, X., & Cho, J. (2023). Visualization of synthetic retroelement integration reveals determinants of permissivity to retrotransposition. Plant Physiology, 193(2), 915-918. https://doi.org/10.1093/plphys/kiad396

PopRice extrachromosomal DNA sponges ABSCISIC ACID-INSENSITIVE 5 in rice seed-to-seedling transition (2023)
Journal Article
Chu, J., Wang, L., & Cho, J. (2023). PopRice extrachromosomal DNA sponges ABSCISIC ACID-INSENSITIVE 5 in rice seed-to-seedling transition. Plant Physiology, 192(1), 56-59. https://doi.org/10.1093/plphys/kiad071

Specific suppression of long terminal repeat retrotransposon mobilization in plants (2022)
Journal Article
Brestovitsky, A., Iwasaki, M., Cho, J., Adulyanukosol, N., Paszkowski, J., & Catoni, M. (2023). Specific suppression of long terminal repeat retrotransposon mobilization in plants. Plant Physiology, 191(4), 2245-2255. https://doi.org/10.1093/plphys/kiac605

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 mob... Read More about Specific suppression of long terminal repeat retrotransposon mobilization in plants.

m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis (2022)
Journal Article
Wang, L., Zhuang, H., Fan, W., Zhang, X., Dong, H., Yang, H., & Cho, J. (2022). m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis. Genome Biology, 23(1), Article 244. https://doi.org/10.1186/s13059-022-02814-8

Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin (2022)
Journal Article
Koo, H., Kim, S., Park, H., Lee, S., Paek, N., Cho, J., & Yang, T. (2022). Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin. Mobile DNA, 13(1), Article 18. https://doi.org/10.1186/s13100-022-00274-2

Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active... Read More about Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin.

Small regulatory RNAs in rice epigenetic regulation (2022)
Journal Article
Park, S. Y., Cho, J., & Jeong, D. (2022). Small regulatory RNAs in rice epigenetic regulation. Biochemical Society Transactions, 50(3), 1215-1225. https://doi.org/10.1042/bst20210336

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-directe... Read More about Small regulatory RNAs in rice epigenetic regulation.

Tracing Mobile DNAs: From Molecular to Population Scales (2022)
Journal Article
Fan, W., Wang, L., Chu, J., Li, H., Kim, E. Y., & Cho, J. (2022). Tracing Mobile DNAs: From Molecular to Population Scales. Frontiers in Plant Science, 13, Article 837378. https://doi.org/10.3389/fpls.2022.837378

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 mob... Read More about Tracing Mobile DNAs: From Molecular to Population Scales.

Plant Transposable Elements: Methods and Protocols (2021)
Book
Cho, J. (2021). J. Cho (Ed.). Plant Transposable Elements: Methods and Protocols. Springer US. https://doi.org/10.1007/978-1-0716-1134-0

Harnessing epigenetic variability for crop improvement: current status and future prospects (2021)
Journal Article
Kim, E. Y., Kim, K. D., & Cho, J. (2022). Harnessing epigenetic variability for crop improvement: current status and future prospects. Genes & Genomics, 44(3), 259-266. https://doi.org/10.1007/s13258-021-01189-7

Background The epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that suppl... Read More about Harnessing epigenetic variability for crop improvement: current status and future prospects.

Phase separation of chromatin and small RNA pathways in plants (2021)
Journal Article
Lei, Z., Wang, L., Kim, E. Y., & Cho, J. (2021). Phase separation of chromatin and small RNA pathways in plants. The Plant Journal, 108(5), 1256-1265. https://doi.org/10.1111/tpj.15517

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... Read More about Phase separation of chromatin and small RNA pathways in plants.

Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq (2021)
Book Chapter
Wang, L., Cho, J., & Satheesh, V. (2021). Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq. . Springer US. https://doi.org/10.1007/978-1-0716-1134-0_10

High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq (2021)
Book Chapter
Wang, L., Kim, E. Y., & Cho, J. (2021). High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq. . Springer US. https://doi.org/10.1007/978-1-0716-1134-0_9

Determination of TE Insertion Positions Using Transposon Display (2021)
Book Chapter
Kim, E. Y., Fan, W., & Cho, J. (2021). Determination of TE Insertion Positions Using Transposon Display. . Springer US. https://doi.org/10.1007/978-1-0716-1134-0_11

Quantitative Measurement of Transposon Copy Number Using the Droplet Digital PCR (2021)
Book Chapter
Fan, W., & Cho, J. (2021). Quantitative Measurement of Transposon Copy Number Using the Droplet Digital PCR. . Springer US. https://doi.org/10.1007/978-1-0716-1134-0_16

Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons (2021)
Journal Article
Kim, E. Y., Wang, L., Lei, Z., Li, H., Fan, W., & Cho, J. (2021). Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons. Nature Plants, 7(3), 303-309. https://doi.org/10.1038/s41477-021-00867-4

Transposable elements (TEs, transposons) are mobile DNAs that can cause fatal mutations1. To suppress their activity, host genomes deploy small interfering RNAs (siRNAs) that trigger and maintain their epigenetic silencing2,3. Whereas 24-nucleotide (... Read More about Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons.