Integrating transposable elements in the 3D genome

Bousios, Alexandros, Nützmann, Hans-Wilhelm, Buck, Dorothy and Michieletto, Davide (2020) Integrating transposable elements in the 3D genome. Mobile DNA, 11. a8. ISSN 1759-8753

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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.

Item Type: Article
Schools and Departments: School of Life Sciences > Evolution, Behaviour and Environment
Depositing User: Alexandros Bousios
Date Deposited: 12 Mar 2020 08:26
Last Modified: 21 Feb 2022 13:16

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Project NameSussex Project NumberFunderFunder Ref
Analysing Transposable Element integration patterns in the 3D genomeG2942ROYAL SOCIETYRGF\EA\201030