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Regulatory transposable elements in the encyclopedia of DNA elements

Author

Listed:
  • Alan Y. Du

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Jason D. Chobirko

    (Cornell University)

  • Xiaoyu Zhuo

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Cédric Feschotte

    (Cornell University)

  • Ting Wang

    (Washington University School of Medicine
    Washington University School of Medicine
    Washington University School of Medicine)

Abstract

Transposable elements (TEs) comprise ~50% of our genome, but knowledge of how TEs affect genome evolution remains incomplete. Leveraging ENCODE4 data, we provide the most comprehensive study to date of TE contributions to the regulatory genome. We find 236,181 (~25%) human candidate cis-regulatory elements (cCREs) are TE-derived, with over 90% lineage-specific since the human-mouse split, accounting for 8–36% of lineage-specific cCREs. Except for SINEs, cCRE-associated transcription factor (TF) motifs in TEs are derived from ancestral TE sequence more than expected by chance. We show that TEs may adopt similar regulatory activities of elements near their integration site. Since human-mouse divergence, TEs have contributed 3–56% of TF binding site turnover events across 30 examined TFs. Finally, TE-derived cCREs are similar to non-TE cCREs in terms of MPRA activity and GWAS variant enrichment. Overall, our results substantiate the notion that TEs have played an important role in shaping the human regulatory genome.

Suggested Citation

  • Alan Y. Du & Jason D. Chobirko & Xiaoyu Zhuo & Cédric Feschotte & Ting Wang, 2024. "Regulatory transposable elements in the encyclopedia of DNA elements," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51921-6
    DOI: 10.1038/s41467-024-51921-6
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    References listed on IDEAS

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    1. Adam G. Diehl & Ningxin Ouyang & Alan P. Boyle, 2020. "Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes," Nature Communications, Nature, vol. 11(1), pages 1-18, December.
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    7. Alan Y. Du & Jason D. Chobirko & Xiaoyu Zhuo & Cédric Feschotte & Ting Wang, 2024. "Regulatory transposable elements in the encyclopedia of DNA elements," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    8. Erica C. Pehrsson & Mayank N. K. Choudhary & Vasavi Sundaram & Ting Wang, 2019. "The epigenomic landscape of transposable elements across normal human development and anatomy," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
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    1. Alan Y. Du & Jason D. Chobirko & Xiaoyu Zhuo & Cédric Feschotte & Ting Wang, 2024. "Regulatory transposable elements in the encyclopedia of DNA elements," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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