Physical and data structure of 3D genome

Kai Huang*, Yue Li, Anne R. Shim, Ranya K.A. Virk, Vasundhara Agrawal, Adam Eshein, Rikkert J. Nap, Luay M. Almassalha, Vadim Backman, Igal Szleifer

*Corresponding author for this work

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi–self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.

Original languageEnglish (US)
Article numbereaay4055
JournalScience Advances
Volume6
Issue number2
DOIs
StatePublished - Jan 10 2020

ASJC Scopus subject areas

  • General

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    Huang, K., Li, Y., Shim, A. R., Virk, R. K. A., Agrawal, V., Eshein, A., Nap, R. J., Almassalha, L. M., Backman, V., & Szleifer, I. (2020). Physical and data structure of 3D genome. Science Advances, 6(2), [eaay4055]. https://doi.org/10.1126/sciadv.aay4055