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Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages

Author

Listed:
  • Isaac A. Babarinde

    (Southern University of Science and Technology
    Chinese Academy of Sciences)

  • Xiuling Fu

    (Southern University of Science and Technology
    Columbia University Irving Medical Center)

  • Gang Ma

    (Southern University of Science and Technology
    Southern Medical University)

  • Yuhao Li

    (Southern University of Science and Technology
    The University of Queensland)

  • Zhangting Liang

    (Southern University of Science and Technology)

  • Jianfei Xu

    (Southern University of Science and Technology)

  • Zhen Xiao

    (Southern University of Science and Technology)

  • Yu Qiao

    (Southern University of Science and Technology)

  • Zheng Lin

    (Southern University of Science and Technology)

  • Katerina Oleynikova

    (Russian Academy of Sciences
    ITMO University)

  • Mobolaji T. Akinwole

    (University of Ibadan)

  • Xuemeng Zhou

    (Southern University of Science and Technology)

  • Alexey Ruzov

    (Russian Academy of Sciences)

  • Andrew P. Hutchins

    (Southern University of Science and Technology)

Abstract

Transposable elements (TEs) are genomic elements present in multiple copies in mammalian genomes. TEs were thought to have little functional relevance but recent studies report roles in biological processes, including embryonic development. To investigate the expression dynamics of TEs during human early development, we generated long-read sequence data from human pluripotent stem cells (hPSCs) in vitro differentiated to endoderm, mesoderm, and ectoderm lineages to construct lineage-specific transcriptome assemblies and accurately place TE sequences. Our analysis reveals that specific TE superfamilies exhibit distinct expression patterns. Notably, we observed TE switching, where the same family of TE is expressed in multiple cell types, but originates from different transcripts. Interestingly, TE-containing transcripts exhibit distinct levels of transcript stability and subcellular localization. Moreover, TE-containing transcripts increasingly associate with chromatin in germ layer cells compared to hPSCs. This study suggests that TEs contribute to human embryonic development through dynamic chromatin interactions.

Suggested Citation

  • Isaac A. Babarinde & Xiuling Fu & Gang Ma & Yuhao Li & Zhangting Liang & Jianfei Xu & Zhen Xiao & Yu Qiao & Zheng Lin & Katerina Oleynikova & Mobolaji T. Akinwole & Xuemeng Zhou & Alexey Ruzov & Andre, 2025. "Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages," Nature Communications, Nature, vol. 16(1), pages 1-24, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63080-3
    DOI: 10.1038/s41467-025-63080-3
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