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 journalArticlepeer-review

27 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

Funding

We acknowledge funding from the NSF (Biol & Envir Inter of Nano Mat 1833214, EFRI research project 1830961) and the NIH (National Cancer Institute R01 CA228272 and R01 CA225002). This research was supported, in part, through the computational resources and staff contributions provided by the Genomics Compute Cluster, which is jointly supported by the Feinberg School of Medicine, the Center for Genetic Medicine, and Feinberg’s Department of Biochemistry and Molecular Genetics, the Office of the Provost, the Office for Research, and Northwestern Information Technology. The Genomics Compute Cluster is part of Quest, Northwestern University’s high-performance computing facility, with the purpose to advance research in genomics.

ASJC Scopus subject areas

  • General

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