Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.

中文翻译：

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在3D基因组中整合转座因子。

染色体组织越来越被认为是基因组调控，细胞命运和细胞健康的重要组成部分。然而，在转座因子（TEs）领域内，关于基因组如何折叠的空间信息仍然很少在实验研究中整合或在建模中说明。尽管高分子物理学被认为是了解基因组折叠机制的重要工具，但在这篇评论中，我们讨论了其在TE生物学方面的潜在适用性。基于有关基因组组织与TE整合之间关系的最新研究，我们认为可以扩展现有的聚合物模型以创建用于TE整合模式研究的预测框架。我们建议这些模型可能会提供有关集成配置文件（或“地形”）的正交和通用见解 ）跨生物体的TE。此外，我们提供了简单的聚合物物理学论证和插入异质柔性聚合物中的TE的初步分子动力学模拟。通过考虑这个简单的模型，我们展示了聚合物折叠和局部柔韧性如何一般性地影响TE集成模式。本评论中的初步讨论旨在为大规模分析TE整合动力学和地形作为三维宿主基因组的功能奠定基础。