Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

Sangram Kadam (), Kiran Kumari, Vinoth Manivannan, Shuvadip Dutta, Mithun K. Mitra and Ranjith Padinhateeri ()
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Sangram Kadam: Indian Institute of Technology Bombay
Kiran Kumari: Indian Institute of Technology Bombay
Vinoth Manivannan: Indian Institute of Technology Bombay
Shuvadip Dutta: Indian Institute of Technology Bombay
Mithun K. Mitra: Indian Institute of Technology Bombay
Ranjith Padinhateeri: Indian Institute of Technology Bombay

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.

Date: 2023
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DOI: 10.1038/s41467-023-39907-2

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