The insertion of DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of DNA insertions are not random and the physical mechanisms underlying the integration site selection are poorly understood. Here, we perform Molecular Dynamics simulations to study the insertion of DNA elements, such as viral DNA or transposons, into naked DNA or chromatin substrates. More specifically, we explore the role of loops within the polymeric substrate and discover that they act as ‘geometric catalysts’ for DNA integration by reducing the energy barrier for substrate deformation. Additionally, we discover that the 1D pattern and 3D conformation of loops have a marked effect on the distribution of integration sites. Finally, we show that loops may compete with nucleosomes to attract DNA integrations. These results may be tested in vitro and they may help to understand patterns of DNA insertions with implications in genome evolution and engineering.

中文翻译：

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环是 DNA 整合的几何催化剂


DNA 元件在基因组中的插入在不受监管时会支撑遗传多样性和疾病。大多数 DNA 插入不是随机的，并且整合位点选择背后的物理机制人们知之甚少。在这里，我们进行分子动力学模拟来研究 DNA 元素（例如病毒 DNA 或转座子）插入裸露 DNA 或染色质底物的情况。更具体地说，我们探索了聚合物基质中环的作用，并发现它们通过减少基质变形的能量势垒而充当 DNA 整合的“几何催化剂”。此外，我们发现环的 1D 模式和 3D 构象对整合位点的分布有显着影响。最后，我们证明环可能与核小体竞争以吸引 DNA 整合。这些结果可以在体外进行测试，并且可能有助于理解 DNA 插入模式，以及对基因组进化和工程的影响。