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Roles of transposable elements in the regulation of mammalian transcription
Open accessAbstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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“Contrary to the exogenous infectious agents discussed above, transposable elements are endogenous mobile genetic elements that can move and integrate into different locations within the genome [117,118].”
From What would it take to prove that a chronic infection is a causal agent in Alzheimer’s disease? (2025) · cites this paper as [117]
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“Although this study is focused on identifying CREs, there are other non-coding regulatory mechanisms that could alter gene expression in AD including microRNAs (miRNAs),90 long non-coding RNAs (lncRNAs),91 transposable elements,92 etc., that are not assessed.”
From Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements (2023) · cites this paper as [92]
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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
Tissue-based map of the human proteome
Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
Schizophrenia risk from complex variation of complement component 4
Sekar, A., Bialas, A. R., de Rivera, H., Davis, A., Hammond, T. R., Kamitaki, N., Tooley, K., Presumey, J., Baum, M., Van Doren, V., et al. (2016) · Nature · doi:10.1038/nature16549 · Cited by 2,394
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378
An integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354
The diverse roles of DNA methylation in mammalian development and disease
Greenberg, M., & Bourc’his, D. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0159-6 · Cited by 2,272
Gene Regulation for Higher Cells: A Theory
Britten, R. J., & Davidson, E. H. (1969) · Science · doi:10.1126/science.165.3891.349 · Cited by 2,078
Research works printed but not linked: 2
- Hoyt, S. J. et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. bioRxiv https://doi.org/10.1101/2021.07.12.451456v1 (2021). · DOI
- Carter, T. A. et al. Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. bioRxiv https://doi.org/10.1101/2021.07.08.451617v1 (2021). · DOI
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Metadata
- Authors
- Fueyo, R., Judd, J., Feschotte, C., & Wysocka, J.
- Affiliations
- Stanford Medicine (US)
- Cornell University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Wysocka, Joanna
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2022-02-28
- Volume
- 23
- Issue
- 7
- Pages
- 481-497
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC10470143
- OpenAlex
- W4214672693
- Cited by
- 451
- References
- 226
- Citations by year
- 2026: 80 · 2025: 139 · 2024: 119 · 2023: 89 · 2022: 24
- FWCI
- 9.07
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Cancer Research Institute
- Bristol-Myers Squibb
- National Institutes of Health
- National Human Genome Research Institute (U01HG009391, F31HG010820)
- National Cancer Institute (R01CA260691)
- National Institute of General Medical Sciences (R35GM122550, R35GM131757)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- transposable elements, transcriptional regulation, mammalian genomes, cis-regulatory elements, enhancers, promoter, 3D genome organization, non-coding RNA, transcription factors, regulatory evolution, genetic novelty, genomic context, repetitive DNA
- MeSH terms
- Animals, DNA Transposable Elements, Gene Expression Regulation, Mammals, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Transcription Factors, Evolution, Molecular
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