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

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

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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  1. [17]Hoyt SJ From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. bioRxiv 10.1101/2021.07.12.451456v1 (2021). PMC9301658 35357925 · DOI
  2. [41]Carter TA Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. bioRxiv 10.1101/2021.07.08.451617v1 (2021). PMC8912925 35179489 · DOI

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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
Venue
Nature Reviews Molecular Cell Biology
Published
2022-02-28
Volume
23
Issue
7
Pages
481-497
ISSN
  • 1471-0072 (ISSN-L)
  • 1471-0080
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
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 › Agricultural and Biological Sciences › Plant Science › 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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