CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction

article CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction published yes Silvia Galan author Nick N Machnik author 3591A0AA-F248-11E8-B48F-1D18A9856A870000-0001-6617-9742 Kai Kruse author Noelia Díaz author Marc A Marti-Renom author Juan M Vaquerizas author FyKo department Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data. Springer Nature2020 eng Nature Genetics 1061-4036 1546-1718 33077914 00057969350000410.1038/s41588-020-00712-y 521247-1255 https://research-explorer.ista.ac.at/record/18642 Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255. Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. <a href="https://doi.org/10.1038/s41588-020-00712-y">https://doi.org/10.1038/s41588-020-00712-y</a>. S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255. Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:<a href="https://doi.org/10.1038/s41588-020-00712-y">10.1038/s41588-020-00712-y</a>. Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. <a href="https://doi.org/10.1038/s41588-020-00712-y">https://doi.org/10.1038/s41588-020-00712-y</a> Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:<a href="https://doi.org/10.1038/s41588-020-00712-y">10.1038/s41588-020-00712-y</a> S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020. 87072020-10-25T23:01:20Z2026-04-21T22:30:27Z