Cited by 475Chromosomal and Genetic VariationsGenomics and Chromatin DynamicsGenomic variations and chromosomal abnormalities

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Roles of transposable elements in the regulation of mammalian transcription

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Fueyo, Raquel, Judd, Julius, Feschotte, Cedric, Wysocka, Joanna·2022·Nature Reviews Molecular Cell Biology

DOI 10.1038/s41580-022-00457-yPMC PMC10470143

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Abstract

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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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
ORCID: Fueyo, Raquel
Judd, Julius
Feschotte, Cedric
Wysocka, Joanna
Venue: Nature Reviews Molecular Cell Biology
Publisher: Springer Science and Business Media LLC
Published: 2022-02-28
Volume: 23
Issue: 7
Pages: 481-497
ISSN: 1471-0072 (ISSN-L)
1471-0080
DOI: 10.1038/s41580-022-00457-y
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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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Roles of transposable elements in the regulation of mammalian transcription

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