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...

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Published inNature communications Vol. 16; no. 1; pp. 7670 - 24
Main Authors Babarinde, Isaac A., Fu, Xiuling, Ma, Gang, Li, Yuhao, Liang, Zhangting, Xu, Jianfei, Xiao, Zhen, Qiao, Yu, Lin, Zheng, Oleynikova, Katerina, Akinwole, Mobolaji T., Zhou, Xuemeng, Ruzov, Alexey, Hutchins, Andrew P.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 18.08.2025
Nature Publishing Group
Nature Portfolio
Subjects
13/100
38/91
631/136/532/2064/2117
631/208/199
631/337/2019
631/337/384
Biological activity
Cell differentiation
Chromatin
Ectoderm
Embryogenesis
Embryonic growth stage
Endoderm
Genes
Genomes
Genomics
Humanities and Social Sciences
Localization
Mesoderm
multidisciplinary
Parasites
Pluripotency
Science
Science (multidisciplinary)
Small mammals
Stem cells
Transcriptomes
Transposons
Online AccessGet full text
ISSN2041-1723
2041-1723
DOI10.1038/s41467-025-63080-3

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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. Transposable elements are genetic parasites that have colonised genomes and they express as parts of coding and noncoding RNAs. Here, the authors explore how they are expressed in transcripts in normal human development, and how they alter transcript dynamics.
AbstractList 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.
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. Transposable elements are genetic parasites that have colonised genomes and they express as parts of coding and noncoding RNAs. Here, the authors explore how they are expressed in transcripts in normal human development, and how they alter transcript dynamics.
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.
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.Transposable elements are genetic parasites that have colonised genomes and they express as parts of coding and noncoding RNAs. Here, the authors explore how they are expressed in transcripts in normal human development, and how they alter transcript dynamics.
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.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.
ArticleNumber 7670
Author Fu, Xiuling
Ma, Gang
Babarinde, Isaac A.
Xiao, Zhen
Qiao, Yu
Hutchins, Andrew P.
Akinwole, Mobolaji T.
Ruzov, Alexey
Xu, Jianfei
Lin, Zheng
Liang, Zhangting
Oleynikova, Katerina
Zhou, Xuemeng
Li, Yuhao
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/40825949$$D View this record in MEDLINE/PubMed
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Snippet Transposable elements (TEs) are genomic elements present in multiple copies in mammalian genomes. TEs were thought to have little functional relevance but...
Abstract Transposable elements (TEs) are genomic elements present in multiple copies in mammalian genomes. TEs were thought to have little functional relevance...
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SubjectTerms 13/100
38/91
631/136/532/2064/2117
631/208/199
631/337/2019
631/337/384
Biological activity
Cell differentiation
Chromatin
Ectoderm
Embryogenesis
Embryonic growth stage
Endoderm
Genes
Genomes
Genomics
Humanities and Social Sciences
Localization
Mesoderm
multidisciplinary
Parasites
Pluripotency
Science
Science (multidisciplinary)
Small mammals
Stem cells
Transcriptomes
Transposons
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Title Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages
URI https://link.springer.com/article/10.1038/s41467-025-63080-3
https://www.ncbi.nlm.nih.gov/pubmed/40825949
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https://pubmed.ncbi.nlm.nih.gov/PMC12361454
https://doaj.org/article/f54be1d6d6854969999961558801710e
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