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Integrating transposable elements in the 3D genome

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journal contribution
posted on 2023-06-09, 20:49 authored by Alexandros BousiosAlexandros Bousios, Hans-Wilhelm Nützmann, Dorothy Buck, Davide Michieletto
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.

Funding

Analysing Transposable Element integration patterns in the 3D genome; G2942; ROYAL SOCIETY; RGF\EA\201030

History

Publication status

  • Published

File Version

  • Published version

Journal

Mobile DNA

ISSN

1759-8753

Publisher

BMC

Volume

11

Article number

a8

Department affiliated with

  • Evolution, Behaviour and Environment Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2020-03-12

First Open Access (FOA) Date

2020-03-12

First Compliant Deposit (FCD) Date

2020-03-10

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