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Science and Mathematics

Chemistry Seminar: Dr. Xingcheng Lin

February 1, 2022 at 4:00pm5:00pm EST

Virtual (See event details)

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The Department of Chemistry in the College of Arts and Sciences is pleased to welcome Dr. Xingcheng Lin, a Postdoctoral Associate at MIT.

The seminar will be held on Zoom. Please email for Zoom info.

Title: Near-atomistic Modeling of Chromatin — Breaking Size Limit to Uncover Mechanistic Insights


Three-dimensional chromatin organization lays the foundation for biological processes involving gene expression and epigenetic regulation. Nevertheless, it is unclear how chromatin is structured at the fundamental level. There is a heated debate over the existence of chromatin fibril structure and its regulation by multiple epigenetic regulators. Controversy also remains on the sol-gel properties of chromatin subject to different environmental conditions. Here, building upon our recently implemented near-atomistic chromatin model, we leveraged computational advances to study structural details of large chromatin systems. Our study with a tetranucleosome, the fundamental unit of chromatin, captures multiple irregular chromatin structures that emerge as intermediates of two chromatin folding pathways. Our further study with a dodecameric nucleosomal array reproduces

the force-extension curve measured by magnetic tweezers. The simulation also reveals a more complicated folding landscape of chromatin under tension than a two-state transition: Whereas the shearing motion of compact chromatin under lower tension constitutes the “linear” response regime, a mixture of trinucleosome and tetranucleosome clutches appears as tension increases, leading to an extended nucleosomal array represented as the “plateau” regime on the force-extension curve. Additional simulations with multiple chromatins reveal a stable interdigitated configuration, thereby suggesting a mechanism initiating the sol-gel transition of chromatin. Finally, we show that Polycomb repressive complex 2 (PRC2), a critical epigenetic modification enzyme, can cooperatively loop DNA via allosteric communication and can bridge non-adjacent nucleosomes to spread histone modifications. Our integrated work demonstrates the usefulness of the near-atomistic model in reconciling the stability of different chromatin conformations under in vitro and in vivo environments and revealing mechanistic insights on the impact of epigenetic regulators on genome organization.

This event was published on January 27, 2022.

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