Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years with advances in microscopy and genomics technologies. Computational methods have played a pivotal role in the structural interpretation of experimental data, which helped unravel some organizational principles of genome folding. Here, we give an overview of current computational efforts in mechanistic and data-driven 3D chromatin structure modeling. We discuss strengths and limitations of different methods and evaluate the added value and benefits of computational approaches to infer the 3D structural and dynamic properties of the genome and its underlying mechanisms at different scales and resolution, ranging from the dynamic formation of chromatin loops and topological associated domains to nuclear compartmentalization of chromatin and nuclear bodies.

中文翻译：

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通过 3D 染色质建模揭示基因组折叠的原理

近年来，随着显微镜和基因组学技术的进步，我们对基因组 DNA 如何在细胞核内紧密排列，但仍可用于重要的细胞过程的理解急剧增加。计算方法在实验数据的结构解释中发挥了关键作用，这有助于揭示基因组折叠的一些组织原理。在这里，我们概述了当前在机械和数据驱动的 3D 染色质结构建模中的计算工作。我们讨论了不同方法的优势和局限性，并评估了计算方法的附加价值和好处，以推断基因组的 3D 结构和动态特性及其在不同尺度和分辨率下的潜在机制，