Integrating Transposable Elements in the 3D Genome

TL;DR

This paper introduces a novel predictive model using polymer physics to understand how transposable elements integrate into the 3D genome, revealing the influence of genome folding and flexibility on TE distribution.

Contribution

It extends polymer models to predict TE integration patterns, linking genome 3D structure with TE distribution in a new, physics-based framework.

Findings

Polymer folding influences TE integration sites.

Local flexibility affects TE distribution.

Model provides insights into TE topography across genomes.

Abstract

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.