Spectral graph entropy of chromatin: a von Neumann framework for multiscale polymer organization from Hi-C
Hi-C contact maps encode multiscale chromatin folding, yet extracting quantitative and physically interpretable descriptors directly from these matrices remains challenging due to sparsity, depth variation, and the coexistence of loop-, domain-, and compartment-scale interactions. We introduce VECTO...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article (Journal) |
| Language: | English |
| Published: |
February 9, 2026
|
| In: |
The journal of physical chemistry. B, Biophysics, biomaterials, liquids, and soft matter
Year: 2026, Volume: 130, Issue: 9, Pages: 2699-2709 |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/acs.jpcb.5c08112 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1021/acs.jpcb.5c08112 Verlag, lizenzpflichtig, Volltext: https://pubs.acs.org/doi/10.1021/acs.jpcb.5c08112#Abstract 
|
| Author Notes: | Kavana Priyadarshini Keshava, Dieter W. Heermann, Arnab Bhattacherjee |
| Summary: | Hi-C contact maps encode multiscale chromatin folding, yet extracting quantitative and physically interpretable descriptors directly from these matrices remains challenging due to sparsity, depth variation, and the coexistence of loop-, domain-, and compartment-scale interactions. We introduce VECTOR, a graph-spectral framework that quantifies chromatin organization through the von Neumann entropy of the normalized contact-map Laplacian. By constructing distance-banded egographs for each genomic locus, VECTOR provides scale-resolved measures of configurational disorder spanning ∼102-107 bp. Short-range entropy systematically decreases at topological associating domain (TAD) boundaries, whereas long-range entropy captures compartmental reorganization. Entropy scaling reveals shallow exponents (α ≈ 0.04-0.06) and a monotonic compaction-disorder relation linking P(s) scaling to entropy deficits. Polymer simulations with tunable loop strength and A/B contrast confirm predictable spectral and entropic responses to physically meaningful perturbations. VECTOR is reproducible across replicates, robust to resolution and sequencing depth, and remains informative for sparse single-nucleus Hi-C, offering a compact, physics-grounded framework for multiscale chromatin architecture. |
|---|---|
| Item Description: | Gesehen am 20.05.2026 |
| Physical Description: | Online Resource |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/acs.jpcb.5c08112 |