2025/05/29 by Kempe, Tobias, S. M. Ali Tabei, Tabei, S. M. Ali +2
Biochemistry, Genetics and Molecular Biology · Computer Science · #Biological Physics (physics.bio-ph) #FOS: Biological sciences #FOS: Physical sciences #Fractal and DNA sequence analysis #Genomics (q-bio.GN) #Genomics and Chromatin Dynamics #Quantum Computing Algorithms and Architecture #Quantum Physics (quant-ph) #Soft Condensed Matter (cond-mat.soft)
paper · pdf · doi:10.48550/arxiv.2505.23289
openalex publication_date 2025/05/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Topologically Associating Chromatin 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 epigenetic 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. Rather than reconstructing exact TAD size distributions or insulation scores, our method reproduces statistical features, such as mean marker incidences and intra-/inter-nucleosome correlations, while generating configurations that exhibit TAD-like structural motifs. These results demonstrate QA as an alternative to explore the chromatin architecture and provide a foundation in epigenetic modeling.