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Cited by 642Genomics and Chromatin DynamicsDevelopmental Biology and Gene RegulationEpigenetics and DNA Methylation

Enhancer redundancy provides phenotypic robustness in mammalian development

Open access
Osterwalder, Marco, Barozzi, Iros, Tissières, Virginie, Fukuda-Yuzawa, Yoko, Mannion, Brandon J., Afzal, Sarah Y., Lee, Elizabeth A., Zhu, Yiwen +12 more·2018·Nature
DOI 10.1038/nature25461PMC PMC5808607
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Abstract

Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.

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  • In developing mouse limb tissue, genes were regulated by a median of three functional enhancers and some genes had more than ten associated enhancers.

    “In developing mouse limb tissue, for instance, genes were regulated by a median of three functional enhancers and some genes, which coded for limb-specific TFs, had more than ten associated enhancers [480].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [480]

    The Text reports a median of three associated distal enhancers for limb-biased genes and says some limb-biased transcription-factor genes had more than a dozen. But these counts come from a correlation-based estimate of enhancer–gene associations; the paper does not establish that every counted enhancer functionally regulates its assigned gene. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Genes can be affected by a single enhancer or multiple enhancers acting in concert; conversely, individual enhancers can regulate multiple genes.

    “Genes can be affected by a single enhancer or multiple enhancers acting in concert115; conversely, individual enhancers can regulate multiple genes72.”

    From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [115]

  • CRISPR technology has recently made it much more straightforward to delete genomic sequences in the mouse, enabling new insights into enhancer redundancy and consequences of disrupting TADs.

    “Second, CRISPR technology has recently made it much more straightforward to delete genomic sequences in the mouse, enabling new insights into aspects such as enhancer redundancy115 and the consequences of disrupting TADs220.”

    From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [115]

  • CRISPR-based approaches have confirmed that promoters often receive signals from multiple functional enhancers.

    “CRISPR-based approaches have confirmed that promoters often receive signals from multiple functional enhancers [479, 480].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [480]

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Authors
Osterwalder, M., Barozzi, I., Tissières, V., Fukuda-Yuzawa, Y., Mannion, B. J., Afzal, S. Y., Lee, E. A., Zhu, Y., Plajzer-Frick, I., Pickle, C. S., Kato, M., Garvin, T. H., Pham, Q. T., Harrington, A. N., Akiyama, J. A., Afzal, V., Lopez-Rios, J., Dickel, D. E., Visel, A., & Pennacchio, L. A.
Affiliations
  • Lawrence Berkeley National Laboratory (US)
  • University of Basel (CH)
Corresponding author
  • Dickel, Diane E.
  • Visel, Axel
  • Pennacchio, Len A.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2018-01-31
Volume
554
Issue
7691
Pages
239-243
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature25461
PMC
PMC5808607
OpenAlex
W2786174959
Cited by
642
References
10
Citations by year
2026: 45 · 2025: 46 · 2024: 111 · 2023: 80 · 2022: 73 · 2021: 83 · 2020: 87 · 2019: 63 · 2018: 50 · 2017: 1 · 2012: 1
FWCI
25.17
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
  • Spiral (Imperial College London) (submittedVersion)
Funders
  • National Science Foundation (DEAC02-05CH11231)
  • U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
  • Novartis Foundation
  • Universität Basel
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (DEAC02-05CH11231)
  • National Institutes of Health (DE-AC02–05CH11231)
  • National Heart, Lung, and Blood Institute (R24HL123879, UM1HL098166, U01HL131003)
  • National Human Genome Research Institute (U54HG006997, R01HG003988)
  • Lawrence Berkeley National Laboratory (UM1HL098166, AC02‐05CH11231, DE-AC02-05CH11231, R24HL123879, U54HG006997, R01HG003988, 05CH11231)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
enhancer redundancy, phenotypic robustness, limb development, developmental gene regulation, mouse embryo, ENCODE, epigenomics, transcriptomics, gene expression levels, brain development, heart development
MeSH terms
Animals, Brain, Enhancer Elements, Genetic, Extremities, Female, Heart, Male, Phenotype, Genome, Sequence Deletion, Limb Deformities, Congenital, Gene Expression Regulation, Developmental, Mice, Spatio-Temporal Analysis

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