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Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and
Isaac A Babarinde1,2, Xiuling Fu1,3, Gang Ma1,4
1Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
Nature Communications
|August 18, 2025
Summary
Transposable elements (TEs) play a dynamic role in human embryonic development. These genomic sequences show distinct expression patterns and chromatin interactions during early development, influencing biological processes.
Area of Science:
- Genomics
- Developmental Biology
- Molecular Biology
Background:
- Transposable elements (TEs) are repetitive DNA sequences found in multiple copies across mammalian genomes.
- Historically underestimated, TEs are increasingly recognized for their roles in crucial biological processes, including embryonic development.
Purpose of the Study:
- To investigate the dynamic expression patterns of transposable elements during human early development.
- To construct lineage-specific transcriptome assemblies and precisely map TE sequences in differentiating human pluripotent stem cells (hPSCs).
Main Methods:
- Generation of long-read sequence data from hPSCs.
- In vitro differentiation of hPSCs into endoderm, mesoderm, and ectoderm lineages.
- Construction of lineage-specific transcriptome assemblies for accurate TE placement and expression analysis.
Main Results:
- Specific transposable element superfamilies exhibit distinct expression patterns during differentiation.
- Observed "TE switching," where the same TE family is expressed from different transcripts across cell types.
- TE-containing transcripts show varied stability and subcellular localization, with increased chromatin association in germ layer cells.
Conclusions:
- Transposable elements contribute to human embryonic development through dynamic expression and chromatin interactions.
- TEs exhibit complex regulatory roles beyond their genomic sequence.
- This study highlights the functional significance of TEs in early human development.
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