Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

Jiangping He, Isaac A. Babarinde, Li Sun, Shuyang Xu, Ruhai Chen, Junjie Shi, Yuanjie Wei, Yuhao Li, Gang Ma, Qiang Zhuang, Andrew P. Hutchins () and Jiekai Chen ()
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Jiangping He: Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)
Isaac A. Babarinde: Southern University of Science and Technology
Li Sun: Southern University of Science and Technology
Shuyang Xu: Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
Ruhai Chen: Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
Junjie Shi: Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
Yuanjie Wei: Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)
Yuhao Li: Southern University of Science and Technology
Gang Ma: Southern University of Science and Technology
Qiang Zhuang: Southern University of Science and Technology
Andrew P. Hutchins: Southern University of Science and Technology
Jiekai Chen: Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: Abstract Transposable elements (TEs) make up a majority of a typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity.

Date: 2021
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DOI: 10.1038/s41467-021-21808-x

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