PSDL PUBLICATIONS

2025

    # First Author | * Corresponding Author

  • EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer

    • Hanbyeol Kim#, Do-Gyun Kim#, Seongyun Ha, Jun-Young Jang, Francisca N. de L. Vitorino, Joanna M. Gongora, Woochul Kim, Yoonji Oh, Gyeongsik Park, Hyeji Kang, Soo-Hyun Im, Chan Kwon Jung, Seon-Young Kim, Inkyung Jung, Jae-Kyung Won, Benjamin A. Garcia, Su-Jin Kim, Kyu Eun Lee, Je-Kyung Ryu*, Chul-Hwan Lee*. EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer. bioRxiv (2025).

    DOI

  • MORC2 phosphorylation fine tunes its DNA compaction activity

    • Winnie Tan#, Jeong Veen Park, Hariprasad Venugopal, Jie Qiong Lou, Prabavi Shayana Dias, Pedro L. Baldoni, Toby Dite, Kyoung-Wook Moon, Christine R. Keenan, Alexandra D. Gurzau, Andrew Leis, Jumana Yousef, Vineet Vaibhav, Laura F. Dagley, Ching-Seng Ang, Laura Corso, Chen Davidovich, Stephin J. Vervoort, Gordon K. Smyth, Marnie E. Blewitt, Rhys S. Allan, Elizabeth Hinde, Sheena D'Arcy, Je-Kyung Ryu*, Shabih Shakeel*. MORC2 phosphorylation fine tunes its DNA compaction activity. Nature Communications (2025).

    DOI- Nature Communications

2024

  • HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization

    • Lucy Brennan#, Hyeong-Ku Kim, Serafin Colmenares, Tatum Ego, Amit Kumar, Sam Safran, Je-Kyung Ryu, Gary Karpen*. HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization. bioRxiv (2024).

    DOI

  • Anisotropic scrunching of SMC with a baton-pass mechanism

    • Kyoung-Wook Moon#, Do-Gyun Kim, Je-Kyung Ryu*. Anisotropic scrunching of SMC with a baton-pass mechanism. Commun Biol 7, 881 (2024).

    DOI- Communications Biology

  • Mechanism of phase condensation for chromosome architecture and function

    • Jeong Veen Park#, Jeong Jun Kim & Je-Kyung Ryu*. Mechanism of phase condensation for chromosome architecture and function. Exp Mol Med (2024).

    DOI- Experimental & Molecular Medicine

2023

  • Molecular basis for SOX2-dependent regulation of super-enhancer activity

    • Wanki Yoo#, Yi Wei Song, Jihyun Kim, Jihye Ahn, Jaehoon Kim, Yongdae Shin, Je-Kyung Ryu, Kyeong Kyu Kim*. Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Research (2023).

    DOI- Nucleic Acids Research

  • Spontaneous Unidirectional Loop Extrusion Emerges from Symmetry Breaking of SMC Extension

    • Bonato Andrea#, Jae-Won Jang, Kyoung-Wook Moon, Do-Gyun Kim, Michieletto Davide*, Je-Kyung Ryu*. Spontaneous Unidirectional Loop Extrusion Emerges from Symmetry Breaking of SMC Extension. arXiv preprint (2023).

    DOI

  • Current working models of SMC-driven DNA-loop extrusion

    • Kyoung-Wook Moon#, Je-Kyung Ryu*. Current working models of SMC-driven DNA-loop extrusion. Biochem Soc Trans (2023).

    DOI- Biochemical Society Transactions

  • Requirement of Cholesterol for Calcium-Dependent Vesicle Fusion by Strengthening Synaptotagmin-1-Induced Membrane Bending

    • Houda Yasmine Ali Moussa, Kyung Chul Shin, Janarthanan Ponraj, Soo Jin Kim, Je-Kyung Ryu, Said Mansour, Yongsoo Park. Requirement of Cholesterol for Calcium-Dependent Vesicle Fusion by Strengthening Synaptotagmin-1-Induced Membrane Bending. Advanced Science 10, 15 (2023).

    DOI- Advanced Science

2022

  • Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

    • Je-Kyung Ryu#, Sang-Hyun Rah#, Richard Janissen#, Jacob W. Karppenmakers#, and Cees Dekker*, “Condensin extrudes DNA loops in steps upto hundreds of base pairs that are generated by ATP binding events”. Nucleic Acids Research (Impact factor 16.971), gkab1268 (2022).

    DOI- Nucleic Acids Research

  • SMC complexes can traverse physical roadblocks bigger than their ring size

    • Biswajit Pradhan#, Roman Barth, Eugene Kim, Iain F. Davidson, Benedikt Bauer, Theo van Laar, Wayne Wang, Je-Kyung Ryu, Jaco van der Torre, Jan-Michael Peters, and Cees Dekker*. “SMC complexes can traverse physical roadblocks bigger than their ring size”. Cell Reports 41(3), 111491 (2022).

    DOI- Cell Reports

PSDL

AFTER PSDL

BEFORE PSDL

2021

  • Current Understanding of Molecular Phase Separation in Chromosomes

    • Je-Kyung Ryu#*, Da-Eun Hwang, and Jeong-Mo Choi*, “Current understandings of molecular phase separation in chromosome”, Int. J. Mol. Sci. 22(19), 10736 (2021).

    DOI- International Journal of Molecular Sciences

  • Extreme parsimony in ATP consumption by 20S complexes in the global disassembly of single SNARE complexes

    • Changwon Kim#, Min Ju Shon#, Sung Hyun Kim, Gee Sung Eun, Je-Kyung Ryu, Changbong Hyeon, ReinhardJahn and Tae-Young Yoon*. Extreme parsimony in ATP consumption by 20S complexes in the global disassembly of single SNARE complexes. Nature Communications 12, 3206 (2021).

    DOI- Nature Communications

  • Structure-function relationships of SMC protein complexes for DNA loop extrusion

    • Hansol Lee#, Haemin Noh, and Je-Kyung Ryu*, “Structure-function relationships of SMC proteinsfor DNAloop extrusion”, Biodesign 9(1), 1-13 (2021).

    DOI- Biodesign

  • Bridging-induced phase separation induced by cohesin SMC protein complexes

    • Je-Kyung Ryu#, Celine Bouchoux, Hon Wing Liu, Eugene Kim, Masashi Minamino, Ralph de Groot, AllardKatan, Andrea Bonato, Davide Marenduzzo, Davide Michieletto, Frank Uhlmann*, and Cees Dekker*. “Bridging-induced phase separation induced by cohesin SMC protein complexes”. Science Advances 7(7), abe5905 (2021).

    DOI- Science Advances

2020

  • The condensin holocomplex cycles dynamically between open and collapsed states

    • Je-Kyung Ryu#, Allard Katan, Eli van der Sluis, Thomas Wisse, Jaco van der Torre, Ralph de Groot, Christian Haering, and Cees Dekker*. “The condensin holocomplex cycles dynamically between open and collapsed states”. Nature Structural & Molecular Biology 27(12), 1134-1141 (2020).

    DOI- Nature Structural & Molecular Biology

2018

  • Models of synaptotagmin-1 to trigger Ca2+-dependent vesicle fusion

    • Yongsoo Park* and Je-Kyung Ryu*. “Models of synaptotagmin-1 to trigger Ca2+-dependent vesicle fusion”. FEBS Letters 592(21), 3480-3492 (2018).
    Invited review: Special Issue on “Exocytosis and Endocytosis”, edited by Wilhelm Just

    DOI- FEBS Letters

2017

  • Reconstruction of LPS transfer cascade reveals structural determinants within LBP, CD14 and TLR4-MD2 for efficient LPS recognition and transfer

    • Je-Kyung Ryu#, Soo Jin Kim#, Sang-Hyun Rah, Ji In Kang, Hi Eun Jung, Heung-Kyu Lee, Jie-Oh Lee, Beom Seok Park, Tae-Young Yoon*, and Ho Min Kim*. “Reconstruction of LPS transfer cascade reveals structural determinants within LBP, CD14 and TLR4-MD2 for efficient LPS recognition and transfer”. Immunity (Impact factor: 31.745) 46(1), 38-50 (2017).
    Recommended by F1000, introduced to the magazine of the Science and Technology of KOFST

    DOI- Immunity

2016

  • Progresses in understanding N-ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes

    • Je-Kyung Ryu#, Reinhard Jahn*and Tae-Young Yoon*. “Progresses in understanding N-ethylmaleimidesensitive factor (NSF) mediated disassembly of SNARE complexes”. Biopolymers 105(8), 518-531 (2016).
    Invited review: Special Issue for GTP and ATP Hydrolysis in Biology, edited by Alfred Wittinghofer.

    DOI- Biopolymers

2015

  • Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover

    • Je-Kyung Ryu#, Duyoung Min#, Sang-Hyun Rah#, Soo Jin Kim, Yongsoo Park, Haesoo Kim, Changbong Hyeon, Ho Min Kim, Reinhard Jahn &Tae-Young Yoon. “Spring-loaded unraveling of a single SNARE complex by NSF inone round of ATP turnover”. Science 347(6229), 1485-1489 (2015).

    DOI- Science

2014

  • Programmed folding of DNA origami structures through single-molecule force control

    • Wooli Bae#, Kipom Kim#, Duyoung Min, Je-Kyung Ryu, Changbong Hyeon& Tae-Young Yoon. “Programmed folding DNA origami structures through single-molecule force control”. Nature Communications 5, 5654 (2014).

    DOI- Nature Communications