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, 6:00 PM – March 8, 2023, 6:36 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, 6:36 PM – March 8, 2023, 6:48 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

  View abstract →

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

  ORAL

  March 8, 2023, 6:48 PM – March 8, 2023, 7:00 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, 7:00 PM – March 8, 2023, 7:12 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, 7:12 PM – March 8, 2023, 7:24 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, 7:24 PM – March 8, 2023, 7:36 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

  View abstract →

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

  ORAL

  March 8, 2023, 7:36 PM – March 8, 2023, 7:48 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, 7:48 PM – March 8, 2023, 8:00 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, 8:00 PM – March 8, 2023, 8:12 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, 8:12 PM – March 8, 2023, 8:24 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, 8:24 PM – March 8, 2023, 8:36 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, 8:36 PM – March 8, 2023, 8:48 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

  View abstract →

• Statistical physics models of transcriptional state

  ORAL

  March 8, 2023, 8:48 PM – March 8, 2023, 9:00 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 →