Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages
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.
Authors
- Mobolaji T. Akinwole
- Alexey Ruzov (ORCID: https://orcid.org/0000-0002-1247-6634)
- Gang Ma (ORCID: https://orcid.org/0000-0002-8302-124X)
- Lin Zheng (ORCID: https://orcid.org/0000-0002-7585-6968)
- Isaac A. Babarinde (ORCID: https://orcid.org/0000-0002-8503-2460)
- Xuemeng Zhou (ORCID: https://orcid.org/0000-0001-6458-1770)
- Andrew P. Hutchins (ORCID: https://orcid.org/0000-0001-7784-2255)
- Zhen Xiao (ORCID: https://orcid.org/0000-0002-6132-6149)
- Katerina Oleynikova
- Yuhao Li (ORCID: https://orcid.org/0000-0002-9608-0193)
- Yu Qiao (ORCID: https://orcid.org/0000-0002-2747-7357)
- Jianfei Xu (ORCID: https://orcid.org/0000-0002-7890-3264)
- Xiuling Fu
- Zhendong Liang
Institutions
- Russian Academy of Sciences (RU)
- The University of Queensland (AU)
- ITMO University (RU)
- University of Ibadan (NG)
- Chinese Academy of Sciences (CN)
- Columbia University Irving Medical Center (US)
- Southern University of Science and Technology (CN)
- Shenzhen Institutes of Advanced Technology (CN)
- Southern Medical University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-08-18
- DOI
- https://doi.org/10.1038/s41467-025-63080-3
- Citations
- 1
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- National Natural Science Foundation of China
- Russian Science Foundation
- Southern University of Science and Technology
- Basic and Applied Basic Research Foundation of Guangdong Province