Publications

2025

• Basil Barter and Jungnam Cho* (2025) "RNA Methylation in Retrotransposon Control" Trends in Genetics Accepted

2024

• Long-Hai Zou#, Bailiang Zhu#, Yaxin Chen, Yaping Lu, Muthusamy Ramkrishnan, Chao Xu, Xiaohong Zhou, Yiqian Ding, Jungnam Cho* and Mingbing Zhou* (2024) "Genetic and Epigenetic Reprogramming in Response to Internal and External Cues by Induced Transposon Mobilization in Moso Bamboo" New Phytologist 244(5):1916-1930

• Jie Chu*, Josephine Newman and Jungnam Cho* (2024) "Molecular Mimicry of Transposable Elements in Plants" Plant and Cell Physiology Published online

• Keun Pyo Lee#, Kaiwei Liu#, Eun Yu Kim#, Laura Medina-Puche, Haihong Dong, Minghui Di, Rahul Mohan Singh, Mengping Li, Shan Qi, Zhuoling Meng, Jungnam Cho, Heng Zhang, Rosa Lozano-Duran and Chanhong Kim* (2024) "The m6A Reader ECT1 Drives mRNA Sequestration to Dampen Salicylic Acid-dependent Stress Responses in Arabidopsis" The Plant Cell 36(3):746-763

• Ling Wang#, Hui Li#, Zhen Lei, Dong-Hoon Jeong and Jungnam Cho* (2024) “The CARBON CATABOLITE REPRESSION 4A-mediated RNA Deadenylation Ppathway Acts on the Transposon RNAs That Are Not Regulated by Small RNAs” New Phytologist 241(4):1636-1645

2023

• Wenwen Fan#, Ling Wang#, Zhen Lei#, Hui Li#, Jie Chu#, Mengxiao Yan, Yuqin Wang, Hongxia Wang, Jun Yang and Jungnam Cho* (2023) "m6A RNA Demethylase AtALKBH9B Promotes Mobilization of a Heat-activated Long Terminal Repeat Retrotransposon in Arabidopsis" Science Advances 9(48):eadf3292

• Yilin Xie#, Songbei Ying#, Zijuan Li#, Yu'e Zhang#, Jiafu Zhu#, Jinyu Zhang, Meiyue Wang, Huishan Diao, Haoyu Wang, Yuyun Zhang, Luhuan Ye, Yili Zhuang, Fei Zhao, Wan Teng, Wenli Zhang, Yiping Tong, Jungnam Cho*, Zhicheng Dong*, Yongbiao Xue* and Yijing Zhang* (2023) "Transposable Element-initiated Enhancer-like Elements Generate the Subgenome-biased Spike Specificity of Polyploid Wheat" Nature Communications 14(1):7465

• Jie Chu, Xiaorui Zhang and Jungnam Cho* (2023) “Visualization of Synthetic Retroelement Integration Reveals Determinants of Permissivity to Retrotransposition” Plant Physiology 193(2):915-918

• Jungnam Cho, Daniel Schubert and Yue Zhou* (2023) “Editorial: Beyond Genetics: Modifications of Nucleic Acid and Chromatin” Frontiers in Plant Science 14:1223443

• Jie Chu, Ling Wang and Jungnam Cho* (2023) “PopRice Extrachromosomal DNA Sponges ABSCISIC ACID-INSENSITIVE 5 in Rice Seed-to-Seedling Transition” Plant Physiology 192(1):56-59

• Anna Brestovitsky, Mayumi Iwasaki, Jungnam Cho, Natthawut Adulyanukosol, Jerzy Paszkowski and Marco Catoni* (2023) “Specific Suppression of Long Terminal Repeat Retrotransposon Mobilization in Plants” Plant Physiology 191(4):2245-2255

2022

• Ling Wang#, Haiyan Zhuang#, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang* and Jungnam Cho* (2022) “m6A RNA Methylation Impairs Gene Expression Variability and Reproductive Thermotolerance in Arabidopsis” Genome Biology 23(1):244

• Hyunjin Koo, Soomin Kim, Hyun-Seung Park, Sang-Ji Lee, Nam-Chon Paek, Jungnam Cho and Tae-Jin Yang* (2022) “Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin” Mobile DNA 13:18

• So Young Park, Jungnam Cho and Dong-Hoon Jeong* (2022) “Small Regulatory RNAs in Rice Epigenetic Regulation” Biochemical Society Transactions BST20210336

• Wenwen Fan#, Ling Wang#, Jie Chu#, Hui Li#, Eun Yu Kim* and Jungnam Cho* (2022) “Tracing Mobile DNAs: from Molecular to Population Scales” Frontiers in Plant Science 13:837378

• Eun Yu Kim*, Kyung Do Kim* and Jungnam Cho* (2022) “Harnessing Epigenetic Variability for Crop Improvement: Current Status and Future Prospects” Genes and Genomics 44(3):259-266

2021

• Zhen Lei, Eun Yu Kim and Jungnam Cho* (2021) “Enrichment of Cytoplasmic RNA Granules from Arabidopsis Seedlings” Bio-protocol 11(21):e4212

• Zhen Lei#, Ling Wang#, Eun Yu Kim and Jungnam Cho* (2021) “Phase Separation of Chromatin and Small RNA Pathways in Plants” The Plant Journal 108(5):1256-1265

• Eun Yu Kim#, Ling Wang#, Zhen Lei#, Hui Li, Wenwen Fan and Jungnam Cho* (2021) “Ribosome Stalling and SGS3 Phase Separation Prime the Epigenetic Silencing of Transposons” Nature Plants 7(3):303-309

• Viswanathan Satheesh#, Wenwen Fan#, Jie Chu and Jungnam Cho* (2021) “Recent Advancement of NGS Technologies to Detect Active Transposable Elements in Plants” Genes and Genomics 43(3):289-294

• Wenwen Fan and Jungnam Cho* (2021) “Quantitative Measurement of Transposon Copy Number Using the Droplet Digital PCR” Methods in Molecular Biology 2250:171-176

• Eun Yu Kim, Wenwen Fan and Jungnam Cho* (2021) “Determination of TE Insertion Positions Using Transposon Display” Methods in Molecular Biology 2250:115-121

• Ling Wang, Jungnam Cho* and Viswanathan Satheesh* (2021) “Bioinformatics Analysis Guides to LTR Retrotransposon-derived Extrachromosomal Linear DNAs Identified by ALE-seq” Methods in Molecular Biology 2250:111-114

• Ling Wang, Eun Yu Kim and Jungnam Cho* (2021) “High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq” Methods in Molecular Biology 2250:103-110

• Jungnam Cho* (2021) “Plant Transposable Elements: Methods and Protocols” Methods in Molecular Biology 2250

2020

• Gui-Yun Tao#, Muthusamy Ramakrishnan#, Kunnummal Kurungara Vinod, Kim Yrjala, Viswanathan Satheesh, Jungnam Cho, Ying Fu* and Mingbing Zhou* (2020) “Multi-omics Analysis of Cellular Pathways Involved in Different Rapid Growth Stages of Moso Bamboo” Tree Physiology 40(11):1487-1508

• Muthusamy Ramakrishnan, Kim Yrjala, Kunnummal Kurungara Vinod, Anket Sharma, Jungnam Cho, Viswanathan Satheesh and Mingbing Zhou* (2020) “Genetics and Genomics of Moso Bamboo (Phyllostachys edulis): Current Status, Future Challenges and Biotechnological Opportunities Towards a Sustainable Bamboo Industry” Food and Energy Security 2020;00:e229

• Jeongmin Choi*, Tak Lee, Jungnam Cho, Emily Servante, Boas Pucker, William Summers, Sarah Bowden, Mehran Rahimi, Kyungsook An, Gynheung An, Harro Bouwmeester, Emma Wallington, Giles Oldroyd and Uta Paszkowski* (2020) “The Negative Regulator SMAX1 Controls Mycorrhizal Symbiosis and Strigolactone Biosynthesis in Rice” Nature Communications 11:2114

2019

• Jungnam Cho*, Matthias Benoit, Marco Catoni, Hajk-Georg Drost, Anna Brestovitsky, Matthijs Oosterbeek and Jerzy Paszkowski* (2019) “Sensitive Detection of Pre-integration Intermediates of Long Terminal Repeat Retrotransposons in Crop Plants” Nature Plants 5(1):26-33

2018

• Jungnam Cho* (2018) “Transposon-derived Non-coding RNAs and Their Function” Frontiers in Plant Science 9:600

2017

• Jungnam Cho* and Jerzy Paszkowski* (2017) “Regulation of Rice Root Development by a Retrotransposon Acting as a miRNA Sponge” Elife 6:e30038

Before 2016

• Min-Young Kang, Soo-Cheul Yoo, Hye-Young Kwon, Byoung-Doo Lee, Jung-Nam Cho, Yoo-Sun Noh and Nam-Chon Paek* (2015) “Negative Regulatory Roles of DE-ETIOLATED1 in Flowering Time in Arabidopsis” Scientific Reports 5:9728

• Jung-Nam Cho, Jee-Youn Ryu, Young-Min Jeong, Jihye Park, Ji-Joon Song, Richard M. Amasino, Bosl Noh* and Yoo-Sun Noh* (2012) “Control of Seed Germination by Light-induced Histone Arginine Demethylation Activity” Developmental Cell 22(4):736-748

• Hae-Ryong Song, Ju-Dong Song, Jung-Nam Cho, Richard M. Amasino, Bosl Noh* and Yoo-Sun Noh* (2009) “The RNA Binding Protein ELF9 Directly Reduces SUPPRESSOR OF OVEREXPRESSION OF CO Transcript Levels in Arabidopsis, Possibly via Nonsense-Mediated mRNA Decay” The Plant Cell 21:1195-1211