Genome Organization and Subnuclear Phenomena I: From DNA-Protein Interactions to Higher-Order Structures

Presentations

• Light, CRISPR and DNA repair

  ORAL · Invited

  March 8, 2023, 3:00 PM – March 8, 2023, 3:36 PM

  Publication: R. S. Zou, A. Marin-Gonzalez, Y. Liu, H. B. Liu, L. Shen, R. Dveirin, J.X.J. Luo, R. Kalhor and T. Ha, "Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites" Nature Cell Biology 24, 1433-Y. Liu, R. S. Zou, S. He, Y. Nihongaki, X. Li, S. Razavi, B. Wu and T. Ha, "Very fast CRISPR on demand", Science 368, 1265–1269 (2020).

  Presenters

  • Taekjip Ha

    • Johns Hopkins University

  Authors

  • Taekjip Ha

    • Johns Hopkins University

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• Structural effects of H4K16 acylations characterized by mesoscale simulation

  ORAL

  March 8, 2023, 3:36 PM – March 8, 2023, 3:48 PM

  Presenters

  • Aria E Coraor

    • University of Chicago

  Authors

  • Aria E Coraor

    • University of Chicago

  • Yiheng Wu

    • University of Chicago

  • Juan J De Pablo

    • University of Chicago

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• A polymer model to infer 3D chromosome structures from Hi-C

  ORAL

  March 8, 2023, 3:48 PM – March 8, 2023, 4:00 PM

  Publication: L. Liu, M. H. Kim, C. Hyeon, Biophys. J. (2019) 117, 613-625
  L. Liu, C. Hyeon, Nucl. Acids Res. (2020) 48, 11486-11494
  L. Liu, B. Zhang, C. Hyeon, PLoS Comp. Biol. (2021) 17, e1009669
  L. Liu, X. Cao, B. Zhang, C. Hyeon, Biophys. J. (2022) https://doi.org/10.1016/j.bpj.2022.09.018

  Presenters

  • Changbong Hyeon

    • Korea Inst for Advanced Study
    • Korea Institute for Advanced Study

  Authors

  • Changbong Hyeon

    • Korea Inst for Advanced Study
    • Korea Institute for Advanced Study

  • Lei Liu

    • Zhejiang Sci-Tech University

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• On the origin of the integrity of a subset of Topologically Associating Domains upon Cohesin loss in Interphase Chromosomes

  ORAL

  March 8, 2023, 4:00 PM – March 8, 2023, 4:12 PM

  Presenters

  • DAVIN JEONG

    • University of Texas at Austin

  Authors

  • DAVIN JEONG

    • University of Texas at Austin

  • Guang Shi

    • University of Illinois at Urbana-Champaign

  • Xin Li

    • University of Texas at Austin

  • Devarajan Thirumalai

    • University of Texas at Austin

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• Investigating the epigenetic code through data-driven chromosome structure modeling.

  ORAL

  March 8, 2023, 4:12 PM – March 8, 2023, 4:24 PM

  Presenters

  • Soren C Kyhl

    • University of Chicago

  Authors

  • Soren C Kyhl

    • University of Chicago

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• Interaction energy scales intrinsic to the structural ensemble of chromosomes

  ORAL

  March 8, 2023, 4:24 PM – March 8, 2023, 4:36 PM

  Presenters

  • Sucheol Shin

    • University of Texas at Austin

  Authors

  • Sucheol Shin

    • University of Texas at Austin

  • Guang Shi

    • University of Illinois at Urbana-Champaign

  • Devarajan Thirumalai

    • University of Texas at Austin

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• FRAP calibrated polymer model of chromatin with HP1a predicts heterochromatin domain sizes, 3D organization, and dynamics.

  ORAL

  March 8, 2023, 4:36 PM – March 8, 2023, 4:48 PM

  Presenters

  • Ramin Basir

    • University of Pennsylvania

  Authors

  • Ramin Basir

    • University of Pennsylvania

  • Vivek b Shenoy

    • University of Pennsylvania

  • Vinayak Vinayak

    • University of Pennsylvania

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• Extended and dynamic linker histone-DNA interactions control chromatosome compaction

  ORAL

  March 8, 2023, 4:48 PM – March 8, 2023, 5:00 PM

  Publication: - S. Rudnizky, H. Khamis, Y. Ginosar, E. Goren, P. Melamed and A. Kaplan, "Extended and dynamic linker histone-DNA interactions control chromatosome compaction", Molecular Cell 81, 3410 (2021)
  
  - B. Bar-Sadeh, S. Rudnizky, L. Pnueli, G. R. Bentley, R. Stöger, A. Kaplan and P. Melamed, "Unravelling the role of epigenetics in reproductive adaptations to early-life environment", Nature Reviews Endocrinology (2020)
  
  - S. Rudnizky*, H. Khamis*, O. Malik, P. Melamed, and A. Kaplan, "The base pair-scale diffusion of nucleosomes modulates binding of transcription factors", PNAS 116, 12161 (2019).

  Presenters

  • Ariel Kaplan

    • Technion - Israel Institute of Technology

  Authors

  • Ariel Kaplan

    • Technion - Israel Institute of Technology

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• Quantitative Link Between Chromatin Compaction and Epigenetic Memory at the Single-cell Level

  ORAL

  March 8, 2023, 5:00 PM – March 8, 2023, 5:12 PM

  Presenters

  • Taihei Fujimori

    • Stanford University

  Authors

  • Taihei Fujimori

    • Stanford University

  • Minhee Park

    • Korea Advanced Institute of Science and Technology

  • Derek Le

    • Stanford University

  • Antonia Hafner

    • Stanford University

  • Joydeb Sinha

    • Stanford University

  • Alistair N Boettiger

    • Stanford University

  • Lacramioara Bintu

    • Stanford University

  View abstract →

• Higher-order genetic interactions in sequence-function relationships

  ORAL

  March 8, 2023, 5:12 PM – March 8, 2023, 5:24 PM

  Publication: Juannan Zhou, Mandy S. Wong, Wei-Chia Chen, Adrian R. Krainer, Justin B. Kinney and David M. McCandlish, 2022. Higher-order epistasis and phenotypic prediction, PNAS, 119(39).
  Wei-Chia Chen, Juannan Zhou, Jason M Sheltzer, Justin B. Kinney, and David M. McCandlish, 2020. Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer, PNAS, 118(40).
  Juannan Zhou and David M. McCandlish, 2020. Minimum epistasis interpolation for sequence-function relationships, Nature Communications, 11(1), pp.1-14.

  Presenters

  • Juannan Zhou

    • University of Florida

  Authors

  • Juannan Zhou

    • University of Florida

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• Multi-scale simulations to assess chromatin organization along the nuclear periphery

  ORAL

  March 8, 2023, 5:24 PM – March 8, 2023, 5:36 PM

  Presenters

  • James T Glazar

    • University of Pennsylvania

  Authors

  • James T Glazar

    • University of Pennsylvania

  • Vivek b Shenoy

    • University of Pennsylvania

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• Investigating human chromosome organization by whole-genome simulations

  ORAL

  March 8, 2023, 5:36 PM – March 8, 2023, 5:48 PM

  Presenters

  • Matheus F Mello

    • Rice University

  Authors

  • Matheus F Mello

    • Rice University

  • Esteban Dodero Rojas

    • Rice University

  • Antonio Oliveira Junior

    • Rice University

  • Vinicius Contessoto

    • Rice University

  • Jose N Onuchic

    • Rice University

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• Statistical physics models of transcriptional state

  ORAL

  March 8, 2023, 5:48 PM – March 8, 2023, 6:00 PM

  Presenters

  • Camilla Sarra

    • Princeton University

  Authors

  • Camilla Sarra

    • Princeton University

  • Yaojun Zhang

    • Johns Hopkins University

  • William S Bialek

    • Princeton University

  • Trevor K GrandPre

    • Princeton University

  View abstract →