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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Additional file 6 of Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation
Cheng, K. C. L., Frost, J. M., Sanchez-Luque, F. J., García-Cañadas, M., Taylor, D., Yang, W. R., Irayanar, B., Sampath, S., Patani, H., Agger, K., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26627302
Additional file 13 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704137
Additional file 16 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704146
Additional file 7 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704119
Additional file 5 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704113
Additional file 4 of SARS-CoV-2 infection induces epigenetic changes in the LTR69 subfamily of endogenous retroviruses
Arora, A., Kolberg, J. E., Srinivasachar Badarinarayan, S., Savytska, N., Munot, D., Müller, M., Krchlíková, V., Sauter, D., & Bansal, V. (2024) · Figshare · doi:10.6084/m9.figshare.26614642
Additional file 4 of Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation
Cheng, K. C. L., Frost, J. M., Sanchez-Luque, F. J., García-Cañadas, M., Taylor, D., Yang, W. R., Irayanar, B., Sampath, S., Patani, H., Agger, K., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26627296
Additional file 3 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704107
Additional file 9 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704125
Additional file 8 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704122
Additional file 3 of Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation
Cheng, K. C. L., Frost, J. M., Sanchez-Luque, F. J., García-Cañadas, M., Taylor, D., Yang, W. R., Irayanar, B., Sampath, S., Patani, H., Agger, K., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26627293
Additional file 2 of Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse
Boyboy, B. A. G., & Ichiyanagi, K. (2024) · Figshare · doi:10.6084/m9.figshare.25801092
Additional file 1 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.25572518
Additional file 4 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704110
Additional file 12 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704134
Additional file 21 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704161
Additional file 7 of SARS-CoV-2 infection induces epigenetic changes in the LTR69 subfamily of endogenous retroviruses
Arora, A., Kolberg, J. E., Srinivasachar Badarinarayan, S., Savytska, N., Munot, D., Müller, M., Krchlíková, V., Sauter, D., & Bansal, V. (2024) · Figshare · doi:10.6084/m9.figshare.26614651
Additional file 15 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704143
Additional file 17 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704149
Additional file 10 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704128
Additional file 1 of Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse
Boyboy, B. A. G., & Ichiyanagi, K. (2024) · Figshare · doi:10.6084/m9.figshare.25800965
Additional file 2 of Asymmetric and parallel subgenome selection co-shape common carp domestication
Wang, M., Li, X., Wang, C., Zou, M., Yang, J., Li, X.-D., & Guo, B. (2024) · Figshare · doi:10.6084/m9.figshare.24934706
Additional file 2 of Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation
Cheng, K. C. L., Frost, J. M., Sanchez-Luque, F. J., García-Cañadas, M., Taylor, D., Yang, W. R., Irayanar, B., Sampath, S., Patani, H., Agger, K., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.24320052
Additional file 20 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704158
Additional file 5 of Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation
Cheng, K. C. L., Frost, J. M., Sanchez-Luque, F. J., García-Cañadas, M., Taylor, D., Yang, W. R., Irayanar, B., Sampath, S., Patani, H., Agger, K., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26627299
Additional file 2 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.25572650
Additional file 6 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704116
Additional file 1 of Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation
Cheng, K. C. L., Frost, J. M., Sanchez-Luque, F. J., García-Cañadas, M., Taylor, D., Yang, W. R., Irayanar, B., Sampath, S., Patani, H., Agger, K., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24319923
Additional file 14 of Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26704140

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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