Exploring the regulatory roles of transposable elements in the context of long-range TE-gene chromatin interactions in human cancer

Abstract

Transposable elements (TEs) are mobile DNA sequences that comprise over 45% of the human genome. While the majority are currently inactive, some TE families have active copies still mobilising today. When they insert in a new location, a vast variety of genomic alterations can arise which can lead to disease and cancer. Furthermore, TEs incapable of mobilisation can also play a role in genome regulation. Many TEs carry regulatory sequences that can act as enhancers, alternative promoters, and even insulators. In this thesis, we study the effects of these TE-derived regulatory elements in lung cancer taking into account the 3D organisation of the genome. We captured tumour-specific 3D contacts involving TE-derived regulatory elements and found changes in gene expression associated with their spatial proximity.