  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. Here, we propose a new predictive modelling framework for the
study of the integration patterns of TEs based on extensions of widely employed
polymer models for genome organisation. Whilst polymer physics is recognised as
an important tool to understand the mechanisms of genome folding, we now show
that it can also offer orthogonal and generic insights into the integration and
distribution profiles (or "topography") of TEs across organisms. Here, we
present polymer physics arguments and molecular dynamics simulations on TEs
inserting into heterogeneously flexible polymers and show with a simple model
that polymer folding and local flexibility affects TE integration patterns. The
preliminary discussion presented herein lay the foundations for a large-scale
analysis of TE integration dynamics and topography as a function of the
three-dimensional host genome.
