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Frontiers in 3D Genomics | K4DN 2025 Symposium

The K4DN 2025 conference is more than just an academic gathering—it is a unique platform for researchers from physics, chemistry, biology, and computational sciences to explore the intricate three-dimensional genome structure, nuclear body formation, and their dynamic interactions.

Contact Info

Frontiers in 3D Genomics: Architecture, Dynamics, and Disease

  • Nov 10(Mon) - 14(Fri), 2025
  • Academic Cultural Complex (E9) 5F Chung Kunmo Conference Hall, John Hannah Hall, KAIST, Daejeon, South Korea
Day 1 Timeline

MONDAY, NOVEMBER 10, 2025

Chung Kunmo Conference Hall

  • Registration 10:00–16:00 (Foyer, Chung Kunmo Conference Hall)
  • Educational Workshop: DNA MERFISH and single-cell 3D genomics [Chairperson: Minhee Park (Korea Advanced Institute of Science and Technology)]
    • 10:00-10:40 Quan Zhu / Bogdan Bintu (University of California San Diego)
      Applying spatially resolved single-cell transcriptomics to study human health and disease
    • 10:40-11:20 Dong Xing (Peking University)
      Mapping 3D genome in single cells
  • Lunch 11:20–13:30
  • Opening 13:30-13:40
  • Session 1: Mechanobiology within the Nucleus [Chairperson: Yoori Kim (Daegu Gyeongbuk Institute of Science and Technology)]
    • 13:40-14:10 [20'+10'] Song Li (University of California, Los Angeles)
      Viscoelasticity regulation of cell reprogramming
    • 14:10-14:30 [13'+7'] Dong-Hwee Kim (Korea University)
      Attenuated nuclear tension regulates nuclear wrinkling and chromatin remodeling
    • 14:30-14:55 [15’+10’] Jung-Whan Lee (Dankook University)
      Understanding nuclear mechanobiology for tissue regeneration
    • 14:55-15:25 [20’+10’] Su Chin Heo (University of Pennsylvania)
      Nuclear mechanobiology for enhanced musculoskeletal tissue regeneration
  • Break 15:25–15:45
  • Session 2: CTCF, Cohesin and 3D Chromatin Architecture [Chairperson: Dohwan Lim (Soongsil University)]
    • 15:45-16:10 [15'+10'] Chunliang Li (St. Jude Children's Research Hospital)
      Decoding three-dimensional chromatin architecture and transcriptional control through auxin inducible protein degradation system
    • 16:10-16:15 [10'+5'] Taehyun Kim (Seoul National University)
      The nuclear density landscape governs macromolecular flux and function
    • 16:15-16:30 [10’+5’] Cheuk Yin Cheng (The Hong Kong University of Science & Technology)
      Multi-omic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potentials
    • 16:30-16:45 [10'+5'] Guang Yu (Tsinghua University)
      Establishment of chromatin architecture interplays with embryo hypertranscription
  • Break 16:45–17:10
  • Session 3: Condensates and Chromatin regulation [Chairperson: Yekaterina A Miroshnikova (Max Planck Institute)]
    • 17:10-17:30 [13'+7'] Kyeong Kyu Kim (Sungkyunkwan University)
      G-quadruplex-dependent transcriptional regulation by molecular condensation in the Bcl3 promoter
    • 17:30-17:45 [10'+5'] Sucheol Shin (University of Texas at Austin)
      Elucidating biophysical principles in organization-dynamics-function relationship of human chromosome
    • 17:45-18:00 [10'+5'] Qinghong Jiang (The Hong Kong University of Science and Technology)
      Delineating retrotransposon-anchored cis-regulatory interaction domains induced by interferon
    • 18:00-18:25 [15'+10'] Yongdae Shin (Seoul National University)
      Biomolecular condensates in gene regulation
  • Welcome Dinner
Day 2 Timeline

TUESDAY, NOVEMBER 11, 2025

Chung Kunmo Conference Hall

  • Session 4: Spatial Temporal Gene Regulation [Chairperson: Jaecheol Lee (Sungkyunkwan University)]
    • 9:00-9:30 [20'+10'] Anny Xiaobo Zhou (The University of Virginia)
      High dimensional chromatin interaction facilitates the identification of functional variants in COPD
    • 9:30-9:55 [15'+10'] Chul-Hwan Lee (Seoul National University)
      Polycomb, chromatin architecture and cardiomyocyte maturation
    • 9:55-10:15 [13'+7'] Jae-Hyun Yang (Korea Advanced Institute of Science and Technology)
      Epigenetic Strategies for Reversing Mammalian Aging
    • 10:15-10:45 [20'+10'] Wei Xie (Tsinghua University)
      Decoding transcription regulation in early mammalian development
  • Break 10:45–11:00
  • Session 5: Genome Organization and Nuclear Body [Chairperson: Kyoung-Dong Kim (Chung-Ang University)]
    • 11:00-11:25 [15'+10'] Inkyung Jung (Korea Advanced Institute of Science and Technology)
      Aberrantly enhanced nuclear speckle-genome interplay facilitates oncogenic chromosomal translocations
    • 11:25-11:40 [10'+5'] Geun-Seup Shin (Chung-Ang University)
      B-type Lamins safeguard transcriptional fidelity by organizing chromatin-speckle proximity
    • 11:40-12:10 [20'+10'] Jia-Ray Yu (Virginia Polytechnic Institute and State University)
      A novel mechanistic link between nuclear paraspeckle protein NONO and active chromatin formation
    • 12:10-12:30 [13'+7'] Youngdae Gwon (Sungkyunkwan University)
      Condensation of heterochromatin governs both growth and motility dynamics of paraspeckles under cellular senescence
  • Photo time 12:30–12:45
  • Lunch 12:45–14:30
  • Posters Session 14:30–16:30 (John Hannah Hall)
  • Session 6: Chromatin Mechanics within the Nucleus [Chairperson: Kyuha Choi (Pohang University of Science and Technology)]
    • 16:30-17:00 [20'+10'] Yekaterina A Miroshnikova (Max Planck Institute)
      Nuclear mechanotransduction in genome integrity & cell fate regulation
    • 17:00-17:25 [15'+10'] Je-Kyung Ryu (Seoul National University)
      Molecular mechanism of chromatin compartmentalization in Sulfolobus
    • 17:25-17:45 [13'+7'] Yong-Yeon Cho (Catholic University)
      Karyoptosis: Discovery of a new form of regulated cell death and elucidation of its molecular mechanisms
    • 17:45-18:00 [10'+5'] Tyler Blanch (University of Pennsylvania)
      Machine learning-based single molecule analysis of epigenetic enzyme dynamics in live cells
    • 18:00-18:30 [20'+10'] Vivek B. Shenoy (University of Pennsylvania)
      Microenvironment-driven epigenetic and chromatin reorganization in cancer progression
  • Social Hour with Dinner (Invited only)
Day 3 Timeline

WEDNESDAY, NOVEMBER 12, 2025

Chung Kunmo Conference Hall

  • Session 7: Chromatin Organization in Cancer [Chairperson: Hong Sook Kim (Sungkyunkwan University)]
    • 9:00-9:30 [20'+10'] Wenbo Li (University of Texas Health Science Center at Houston)
      Enhancer functions and mechanisms: an RNA perspective
    • 9:30-9:55 [15'+10'] Ji Min Lee (Korea Advanced Institute of Science and Technology)
      H2B-Sensing epigenetic remodeling drives STAT1-dependent chemokine activation and tumor microenvironment reprogramming
    • 9:55-10:15 [13'+7'] Anders M Lindroth (National Cancer Center)
      The metabolic influence on chromatin regulation in health and disease
    • 10:15-10:30 [10'+5'] Hanbyeol Kim (Seoul National University)
      EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer
    • 10:30-11:00 [20'+10'] Jiyeon Choi (National Cancer Institute)
      Chromatin interaction and single-cell multiomic approaches to identify context-dependent lung cancer susceptibility genes
  • Break 11:00–11:20
  • Editor session [Chairperson: Danny Leung (Hong Kong University of Science and Technology)]
    • 11:20–11:40 Editor from "Nature Genetics"
    • 11:40-12:00 Editor from "EMBO Reports"
    • 12:00-12:20 Discussion with Editors
  • Lunch 12:20–14:30
  • Session 8: Emerging Technologies in Spatial Genome Organization [Chairperson: Kyuho Kang (Chungbuk National University)]
    • 14:30-14:55 [15'+10'] Sang-Hee Shim (Korea University)
      Atomic-resolution single-molecule localization microscopy for genome mapping and organization
    • 14:55-15:20 [15'+10'] Hajin Kim (Ulsan National Institute of Science and Technology)
      Periodic stiffness encoded in genome governs the looping behavior of DNA
    • 15:20-15:35 [10'+5'] Hyeonkyu kim (Soongsil University)
      TENET+: a tool for reconstructing gene networks by integrating single cell expression and chromatin accessibility data
    • 15:35-15:55 [13'+7'] Chang Ho Sohn (Korea Advanced Institute of Science and Technology)
      Fixative eXchange (FX) seq: scalable single-nucleus and spatial transcriptomics approaches for FFPE clinical tissue
    • 15:55-16:25 [20'+10'] Dong Xing (Peking University)
      Structure and function of eukaryotic genomes at single-cell resolution
  • Break 16:25–16:40
  • Session 9: 4D Nucleome and Disease Relevance [Chairperson: Ji Hun Kim (Korea Advanced Institute of Science and Technology)]
    • 16:40-17:10 [20'+10'] Guohong Li (Wuhan University)
      Structural basis of genome folding and its functions in gene regulation and human diseases
    • 17:10-17:40 [20'+10'] Danny Leung (Hong Kong University of Science and Technology)
      Deciphering the epigenomic impacts of repetitive elements: How do retroviruses control our genes?
    • 17:40-18:10 [20'+10'] Quan Zhu (University of California, San Diego)
      Integrative single-cell analyses reveal a spatial organization program directing the formation of cellular communities in the developing human heart
    • 18:10-18:25 [10'+5'] Juyeong Kang (Sungkyunkwan University)
      Aberrant chromosomal interactions at acrocentric p-arms induce topological changes leading to altered gene expression profiles in GABAergic neurons of Down syndrome
Day 4 Timeline

THURSDAY, NOVEMBER 13, 2025

Chung Kunmo Conference Hall

  • Session 10: Computational 3D Genomics [Chairperson: Keunsoo Kang (Dankook University)]
    • 9:00-9:25 [15'+10'] Minhee Park (Korea Advanced Institute of Science and Technology)
      A computational method to reconstruct 3D chromatin polymer coordinates in single cells
    • 9:25-9:55 [20'+10'] Minji Kim (University of Michigan)
      Algorithms to identify chromatin jets and higher-order interactions
    • 9:55-10:15 [13'+7'] Hyunju Lee (Gwangju Institute of Science and Technology)
      Characterization of 3D genome changes using whole genome sequencing data for Supratentorial ependymoma
    • 10:15-10:30 [10'+5'] Kyukwang Kim (Korea Advanced Institute of Science and Technology)
      Deep learning-based modeling of 3D genome dynamics
    • 10:30-11:00 [20'+10'] Yu Li (Chinese University of Hong Kong)
      Multi-scale virtual cell modelling with artificial intelligence
  • Break 11:00–11:20
  • Session 11: Crosstalk between Chromatin Regulation and Cell Fate Programs [Chairperson: Jung-Shin Lee (Kangwon National University)]
    • 11:20-11:40 [13'+7'] Peng Xu (Soochow University)
      The H3K4 methyltransferase KMT2D is an essential cofactor for GATA1 at erythroid gene enhancers
    • 11:40-12:00 [13'+7'] Woo-jin Kim (Seoul National University, Dentistry)
      Dynamic Regulation of Chromatin Architecture During Osteoblast Differentiation via Ets1-p300 Complex
    • 12:00-12:20 [13'+7'] Xukun Lu (Shandong University)
      Reprogramming of H3K36me2 guides lineage specific post implantation de novo DNA methylation
    • 12:20-12:40 [13'+7'] Ik Soo Kim (Gachon University)
      Single-cell state-recording and tracing unravel the epigenetic regulation of cell fate decisions
  • Lunch 12:40–14:30
  • Session 12: 3D Genome in Neurobiology [Chairperson: Chul-Hwan Lee (Seoul National University)]
    • 14:30-15:00 [20'+10'] Yijun Ruan (Zhejiang University)
      Multi-omics mapping of 3D epigenome and transcriptome in mouse brain cells during maturation and ageing
    • 15:00-15:20 [13'+7'] Tae Wan Kim (Daegu Gyeongbuk Institute of Science and Technology)
      Human stem cell-based cell therapy for Parkinson's diseases
    • 15:20-15:50 [20'+10'] Bogdan Bintu (University of California, San Diego)
      Multimodal spatial transcriptomics connects single-cell pathology with cell type vulnerability in Huntington disease cortex
    • 15:50-16:20 [20'+10'] Tae-Kyung Kim (Pohang University of Science and Technology)
      Leveraging Enhancer RNAs to Understand Brain Organization and Function
  • Meeting Wrap-Up: Outcomes and Future Direction (Organizers), Poster awards
  • Social Hour with Dinner (Invited only)
Day 5 Timeline

FRIDAY, NOVEMBER 14, 2025

Chung Kunmo Conference Hall

  • Council Meeting 9:00–16:00