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bioRxiv · 10.1101/2025.07.13.664622

From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture

Rogers, D. H.·Roth, C. J. N.·Tauxe, C.·Lee, J.·Steadman, C. R.·Sanbonmatsu, K.·Lappala, A.·Starkenburg, S.
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Abstract

BackgroundCharacterizing the physical organization of the genome is essential for understanding long-range gene reg- ulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two- dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological pro- cesses in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. ResultsHerein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. ConclusionsThe 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visual- ization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

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Rogers, D. H., Roth, C. J. N., Tauxe, C., Lee, J., Steadman, C. R., Sanbonmatsu, K., Lappala, A., Starkenburg, S.. 2025-07-18. From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture. https://doi.org/10.1101/2025.07.13.664622

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