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Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticity
Youngseo Cheon1, Erik Glen Alvstad1, Denis Torre2
1Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.
Nature Structural & Molecular Biology
|February 25, 2026
Summary
Transposable elements (TEs) integrate into genes, influencing cell states and transcriptome plasticity. A novel RNA quality control mechanism prevents aberrant TE expression and differentiation.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Transposable elements (TEs) constitute a significant portion of the human genome, originating from ancient parasitic infections.
- Their repetitive nature presents challenges in studying their positional identity and regulatory functions.
- Limited knowledge exists regarding how TEs integrate into genes and their functional impact.
Purpose of the Study:
- To investigate the timing, location, and mechanisms of transposable element integration into genes.
- To characterize the evolution of TE-derived isoforms across species and their link to gene regulatory networks.
- To identify novel mechanisms controlling TE expression and their impact on cellular processes.
Main Methods:
- Integration of long-read sequencing and multidimensional transcriptional analyses.
- Comparative analysis of TE-derived isoforms across mouse and human genomes.
- Investigation of links between TE elements and gene regulatory networks controlling cell states.
Main Results:
- TEs become integrated into genes, influencing isoforms across species.
- TE-derived isoforms are linked to gene regulatory networks controlling differentiation, organogenesis, aging, and disease.
- A novel RNA degradation- and splicing-dependent quality control mechanism was identified.
- This mechanism operates independently of DNA methylation and heterochromatinization.
- It prevents the expression of TE-chimera transcripts and TE-induced cell differentiation.
Conclusions:
- Transposable elements contribute to transcriptome plasticity through novel integration mechanisms.
- A previously unknown quality control pathway regulates TE expression, distinct from epigenetic silencing.
- These findings reveal how viral-derived elements can enhance cellular adaptability and gene regulation.
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