Staff profile

I did my bachelor (2007) and PhD (2013) in Seoul National University and carried out post-doc study in Cambridge University. In 2018, I started my PI career as a group leader in the CAS-JIC Centre of Excellence for Plant and Microbial Sciences and moved to Durham University in 2023 as an Associate Professor.
The main research subject of my lab is transposable element (TE or transposon), a mobile DNA and better known as “jumping gene”. Unlike common belief that transposon is a dangerous or useless junk DNA, it has been a main source of genetic variability and potent driver of genome evolution. Plants serve as a fascinating model to study transposon as they carry massive amount of it in their genomes. Our research is primarily aimed at understanding its biological functions in plants and dissecting the regulatory mechanisms for its mobilization. To tackle this question, we use Arabidopsis and rice as models and apply multi-disciplinary approaches of genetics, biochemistry, molecular biology, and computational biology. Ultimately, our research will help re-gain crop genetic diversity and contribute to global food security.

Research Interests

• Transposable element

• Genome plasticity

• Epigenetics

• Epitranscriptomics

• RNA secondary structure

Chapter in book

• 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
• 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
• 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
• 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

Edited 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

Journal Article

• Zou, L.-H., Zhu, B., Chen, Y., Lu, Y., Ramkrishnan, M., Xu, C., Zhou, X., Ding, Y., Cho, J., & Zhou, M. (online). Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo. New Phytologist, https://doi.org/10.1111/nph.20107
• Chu, J., Newman, J., & Cho, J. (2024). Molecular Mimicry of Transposable Elements in Plants. Plant & Cell Physiology, https://doi.org/10.1093/pcp/pcae058
• Wang, L., Li, H., Lei, Z., Jeong, D., & Cho, J. (2024). The CARBON CATABOLITE REPRESSION 4A ‐mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs. New Phytologist, 241(4), 1636-1645. https://doi.org/10.1111/nph.19435
• 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. (2023). The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid–dependent stress responses in Arabidopsis. The Plant Cell, 36(3), 746-763. https://doi.org/10.1093/plcell/koad300
• Fan, W., Wang, L., Lei, Z., Li, H., Chu, J., Yan, M., Wang, Y., Wang, H., Yang, J., & 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
• 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
• 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
• 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
• Xie, Y., Ying, S., Li, Z., Zhang, Y., Zhu, J., Zhang, J., Wang, M., Diao, H., Wang, H., Zhang, Y., Ye, L., Zhuang, Y., Zhao, F., Teng, W., Zhang, W., Tong, Y., Cho, J., Dong, Z., Xue, Y., & 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
• Park, S. Y., Cho, J., & Jeong, D.-H. (2022). Small regulatory RNAs in rice epigenetic regulation. Biochemical Society Transactions, 50(3), 1215-1225. https://doi.org/10.1042/bst20210336
• 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
• 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
• Koo, H., Kim, S., Park, H.-S., Lee, S.-J., Paek, N.-C., Cho, J., & Yang, T.-J. (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
• 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
• 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
• Satheesh, V., Fan, W., Chu, J., & Cho, J. (2021). Recent advancement of NGS technologies to detect active transposable elements in plants. Genes & Genomics, 43(3), 289-294. https://doi.org/10.1007/s13258-021-01040-z
• 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
• Tao, G.-Y., Ramakrishnan, M., Vinod, K. K., Yrjälä, K., Satheesh, V., Cho, J., Fu, Y., & Zhou, M. (2020). Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo. Tree Physiology, 40(11), 1487-1508. https://doi.org/10.1093/treephys/tpaa090
• Choi, J., Lee, T., Cho, J., Servante, E. K., Pucker, B., Summers, W., Bowden, S., Rahimi, M., An, K., An, G., Bouwmeester, H. J., Wallington, E. J., Oldroyd, G., & Paszkowski, U. (2020). The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. Nature Communications, 11, Article 2114. https://doi.org/10.1038/s41467-020-16021-1
• Cho, J. (2018). Transposon-Derived Non-coding RNAs and Their Function in Plants. Frontiers in Plant Science, 9, https://doi.org/10.3389/fpls.2018.00600
• Cho, J., Benoit, M., Catoni, M., Drost, H.-G., Brestovitsky, A., Oosterbeek, M., & Paszkowski, J. (2018). Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. Nature Plants, 5(1), 26-33. https://doi.org/10.1038/s41477-018-0320-9
• Cho, J., & Paszkowski, J. (2017). Regulation of rice root development by a retrotransposon acting as a microRNA sponge. eLife, 6, Article e30038. https://doi.org/10.7554/elife.30038
• Kang, M.-Y., Yoo, S.-C., Kwon, H.-Y., Lee, B.-D., Cho, J.-N., Noh, Y.-S., & Paek, N.-C. (2015). Negative regulatory roles of DE-ETIOLATED1 in flowering time inArabidopsis. Scientific Reports, 5(1), Article 9728. https://doi.org/10.1038/srep09728
• Cho, J.-N., Ryu, J.-Y., Jeong, Y.-M., Park, J., Song, J.-J., Amasino, R., Noh, B., & Noh, Y.-S. (2012). Control of Seed Germination by Light-Induced Histone Arginine Demethylation Activity. Developmental Cell, 22(4), 736-748. https://doi.org/10.1016/j.devcel.2012.01.024
• Song, H.-R., Song, J.-D., Cho, J.-N., Amasino, R. M., Noh, B., & Noh, Y.-S. (2009). The RNA Binding Protein ELF9 Directly ReducesSUPPRESSOR OF OVEREXPRESSION OF CO1Transcript Levels inArabidopsis, Possibly via Nonsense-Mediated mRNA Decay. The Plant Cell, 21(4), 1195-1211. https://doi.org/10.1105/tpc.108.064774