Cartography and mechanism of enhanced transcriptome plasticity by transposable elements

ABSTRACT: Transposable elements (TEs) in our genome are the heritage of ancient parasitic infections. While most of human DNA is comprised of TEs and TE-derived elements, their repetitive nature poses technical challenges and thus little is known about their positional identity and regulatory roles. Here, by integrating long-read and multidimensional transcriptional analyses, we investigated when, where and how TEs become part of a gene. We characterized how TE-derived isoform and new genes change across mouse-human variation and are linked to gene regulatory networks controlling cell states during differentiation, organogenesis and health (aging and pathological states). Mechanistically, we identified an RNA degradation-dependent and a splicing-dependent quality control mechanism that operate independently of conventional mechanisms of TE suppression (DNA methylation and heterochromatinization) and prevents TE-exonization and TE-induced cell differentiation. Overall, our findings reveal new mechanisms by which viral-derived elements enhance transcriptome plasticity.

ORGANISM(S): Mus musculus

PROVIDER: GSE297796 | GEO | 2026/01/06

REPOSITORIES: GEO