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Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
Open accessAbstract
Advances in vertebrate genomics have uncovered thousands of loci encoding long noncoding RNAs (lncRNAs). While progress has been made in elucidating the regulatory functions of lncRNAs, little is known about their origins and evolution. Here we explore the contribution of transposable elements (TEs) to the makeup and regulation of lncRNAs in human, mouse, and zebrafish. Surprisingly, TEs occur in more than two thirds of mature lncRNA transcripts and account for a substantial portion of total lncRNA sequence (~30% in human), whereas they seldom occur in protein-coding transcripts. While TEs contribute less to lncRNA exons than expected, several TE families are strongly enriched in lncRNAs. There is also substantial interspecific variation in the coverage and types of TEs embedded in lncRNAs, partially reflecting differences in the TE landscapes of the genomes surveyed. In human, TE sequences in lncRNAs evolve under greater evolutionary constraint than their non-TE sequences, than their intronic TEs, or than random DNA. Consistent with functional constraint, we found that TEs contribute signals essential for the biogenesis of many lncRNAs, including ~30,000 unique sites for transcription initiation, splicing, or polyadenylation in human. In addition, we identified ~35,000 TEs marked as open chromatin located within 10 kb upstream of lncRNA genes. The density of these marks in one cell type correlate with elevated expression of the downstream lncRNA in the same cell type, suggesting that these TEs contribute to cis-regulation. These global trends are recapitulated in several lncRNAs with established functions. Finally a subset of TEs embedded in lncRNAs are subject to RNA editing and predicted to form secondary structures likely important for function. In conclusion, TEs are nearly ubiquitous in lncRNAs and have played an important role in the lineage-specific diversification of vertebrate lncRNA repertoires.
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“Notably, 11 of these elements overlapped with the promoters of annotated lncRNAs (Fig. 5a), consistent with the previous finding that LTRs are enriched in the transcription start sites (TSSs) of lncRNAs80.”
From Multi-omic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potential (2025) · cites this paper as [80]
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Cites
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Long non-coding RNAs: insights into functions
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2521 · Cited by 5,654
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
Gupta, R. A., Shah, N., Wang, K., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M.-C., Hung, T., Argani, P., Rinn, J. L., et al. (2010) · Nature · doi:10.1038/nature08975 · Cited by 5,205
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Derrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,135
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Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA–lncRNA classification
García‐Ruano, D., Georges, M., Mohanty, S. K., Baaziz, R., Makova, K. D., Nikolski, M., & Chalopin, D. (2026) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.21203/rs.3.rs-11362934/v1
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Sun, L., Dong, C., Hong, D., Du, M., Xia, S., Fan, H., Lynch, M., Li, Y., & Wei, W. (2026) · Science Advances · doi:10.1126/sciadv.aeb5510
Song, B., Han, P., Li, J., Li, X., Zhang, X., Fan, J., Liu, D., Cai, J., Zhang, L., & Wu, J. (2026) · Advanced Science · doi:10.1002/advs.77091
Long Noncoding RNAs: Characteristics, Microprotein Production, and Genomic Origins
Haseltine, W. A., & Patarca, R. (2026) · Springer eBooks · doi:10.1007/978-3-032-30270-0_1
Ling, W., He, C., Tang, H., Bai, Y., Xi, Y., Qi, J., Guo, S., Yang, Z., Han, X., Huang, A.-X., et al. (2026) · Poultry Science · doi:10.1016/j.psj.2026.107693
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García-Pérez, I., & de la serrana, D. G. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27177861
The “mobile bricks” of human evolution: how transposable elements shaped human phenotypes
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Metadata
- Authors
- Kapusta, A., Kronenberg, Z., Lynch, V. J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M., & Feschotte, C.
- Affiliations
- University of Utah (US)
- University of Chicago (US)
- McGill University and Génome Québec Innovation Centre (CA)
- Corresponding author
- Feschotte, Cédric
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-04-25
- Volume
- 9
- Issue
- 4
- Pages
- e1003470
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3636048
- OpenAlex
- W2029868997
- Cited by
- 687
- References
- 115
- Citations by year
- 2026: 21 · 2025: 27 · 2024: 60 · 2023: 52 · 2022: 57 · 2021: 70 · 2020: 53 · 2019: 52 · 2018: 68 · 2017: 58 · 2016: 50 · 2015: 62 · 2014: 42 · 2013: 13
- FWCI
- 67.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Knowledge@UChicago (University of Chicago) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- University of Chicago (cc-by)
- Funders
- National Science Foundation (1126998)
- National Institutes of Health
- Canadian Institutes of Health Research (115090_1)
- National Human Genome Research Institute (R01HG004694)
- National Institute of General Medical Sciences (T32GM007464, R01GM077582)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- transposable elements, long non-coding RNA, lncRNA evolution, lncRNA biogenesis, cis-regulation, open chromatin, RNA editing, secondary structure, transcription initiation, splicing, polyadenylation, human, mice, zebrafish
- MeSH terms
- Animals, DNA Transposable Elements, Exons, Humans, Introns, Vertebrates, RNA, Long Noncoding
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