PSDL PUBLICATIONS

2025

    # First Author | * Corresponding Author

  • Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search

    • Andrea Bonato#*, Jae-Won Jang, Do-Gyun Kim, Kyoung-Wook Moon, Davide Michieletto*, Je-Kyung Ryu*. Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search. Nucleic Acids Research 53, 14 (2025).
    Selected as Breakthrough Article by Nucleic Acids Research서울대 류제경 교수 연구팀, Nucleic Acids Research 선정 ‘돌파구’(Breakthrough) 논문 선정 - 대학지성 In&Out

    DOI- Nucleic Acids Research

  • 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 is a phosphorylation-dependentDNA compaction machine

    • 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).

    서울대, 유전자 활동 조절하는 MORC2 작동원리 밝혀내 - E동아DOI- 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