Intermediate State Formation of Topologically Associated Chromatin Domains using Quantum Annealing

TL;DR

This paper introduces a quantum annealing approach to model the formation of chromatin domains by efficiently sampling complex epigenetic and 3D chromatin folding interactions using quantum processors.

Contribution

It presents the first application of quantum annealing to simulate chromatin domain formation based on epigenetic data, overcoming limitations of classical methods.

Findings

Quantum annealing effectively samples chromatin states with high frustration.

The model links epigenetic markers to 3D chromatin structure.

Demonstrates potential of quantum computing in genomics.

Abstract

Topologically Associating Chromatic Domains are spatially distinct chromatin regions that regulate transcription by segregating active and inactive genomic elements. Empirical studies show that their formation correlates with local patterns of epigenetic markers, yet the precise mechanisms linking 1D epigenetic landscapes to 3D chromatin folding remain unclear. Recent models represent chromatin as a spin system, where nucleosomes are treated as discrete-state variables coupled by interaction strengths derived from genomic and epigenomic data. Classical samplers struggle with these models due to high frustration and dense couplings. Here, we present a quantum annealing (QA) approach to efficiently sample chromatin states, embedding an epigenetic Ising model into the topology of D-Wave quantum processors.