Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Friday Speaker Abstracts

DECIPHERING HI-C DATA INTO POLYMER DYNAMICS Soya Shinkai 1,2 ; Masaki Nakagawa 2,3 ; Takeshi Sugawara 2,4 ; Yuichi Togashi 2,5 ; Hiroshi Ochiai 5 ; Ryuichiro Nakato 6 ; Yuichi Taniguchi 7 ; Shuichi Onami 1 ; 1 RIKEN, Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan 2 Hiroshima University, Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Higashi-Hiroshima, Hiroshima, Japan 3 The University of Electro-Communications, Graduate School of Informatics and Engineering, Tokyo, Tokyo, Japan 4 The University of Tokyo, Graduate School of Medicine and Faculty of Medicine, Tokyo, Tokyo, Japan 5 Hiroshima University, Graduate School of Science, Higashi-Hiroshima, Hiroshima, Japan 6 The University of Tokyo, Institute for Quantitative Biosciences (IQB), Tokyo, Tokyo, Japan 7 RIKEN, Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan Genome-wide chromosome conformation capture methods have uncovered 3D genome organization in cell nuclei, and associated polymer modeling have revealed 3D genome structure. However, it is challenging to unravel 4D features from Hi-C data, as observed in live cell imaging experiments. We will show our recent progress on deciphering Hi-C data into polymer dynamics in terms of polymer physics. Firstly, we mathematically defined the contacts of Hi-C experiments. Next, we derived matrix transformations between the contact matrix and a polymer model. Based on the analytical matrix transformations, we developed an optimization algorithm for Hi-C data. Finally, here, we propose a 4D simulation method, PHi-C (Polymer dynamics deciphered from Hi-C data), that depicts dynamic organization of chromatin domains and provides physical insights into alterations in Hi-C patterns.

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