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Chromosome organisation is increasingly recognised as an essential componentof genome regulation, cell fate and cell health. Within the realm oftransposable elements (TEs) however, the spatial information of how genomes arefolded is still only rarely integrated in experimental studies or accounted forin modelling. Here, we propose a new predictive modelling framework for thestudy of the integration patterns of TEs based on extensions of widely employedpolymer models for genome organisation. Whilst polymer physics is recognised asan important tool to understand the mechanisms of genome folding, we now showthat it can also offer orthogonal and generic insights into the integration anddistribution profiles (or "topography") of TEs across organisms. Here, wepresent polymer physics arguments and molecular dynamics simulations on TEsinserting into heterogeneously flexible polymers and show with a simple modelthat polymer folding and local flexibility affects TE integration patterns. Thepreliminary discussion presented herein lay the foundations for a large-scaleanalysis of TE integration dynamics and topography as a function of thethree-dimensional host genome.

Integrating Transposable Elements in the 3D Genome