Physical and data structure of 3D genome.

Area of Science:

• Molecular Biology
• Polymer Physics
• Genomics

Background:

• The established 30-nm fiber model of chromatin folding is being challenged.
• Interphase DNA exhibits an irregular 10-nm nucleosome polymer structure with unknown folding principles.
• This irregular packing presents puzzling physical properties from a polymer physics perspective.

Purpose of the Study:

• To reconcile the exotic physical properties of interphase DNA packing.
• To propose a new model for three-dimensional genome organization.
• To identify universal folding principles for disordered chromatin fibers.

Main Methods:

• Multiscale theoretical modeling.
• Electron and optical imaging techniques.
• Analysis of DNA polymer physics and topology.

Main Results:

• Three-dimensional genome organization can be modularized into tree data structures.
• Functional genomic modules are connected and isolated by an open backbone.
• This results in porous, heterogeneous, and quasi-self-similar chromatin packing.

Conclusions:

• The proposed tree data structure model reconciles observed physical properties of chromatin.
• Universal folding principles for disordered chromatin fibers likely exist.
• This organization strategy prevents entanglement and supports biological functions.