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Cited by 30Developmental Biology and Gene RegulationZebrafish Biomedical Research Applicationsmelanin and skin pigmentation

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

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Aman, Andrew J, Saunders, Lauren M, Carr, August A, Srivatasan, Sanjay, Eberhard, Colten, Carrington, Blake, Watkins-Chow, Dawn, Pavan, William J +2 more·2023·eLife
DOI 10.7554/elife.86670PMC PMC10495112

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Abstract

Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding the mechanisms that regulate stripe patterning and scale morphogenesis may lead to the discovery of fundamental mechanisms that govern the development of animal form. To learn about cell types and signaling interactions that govern skin patterning and morphogenesis, we generated and analyzed single-cell transcriptomes of skin from wild-type fish as well as fish having genetic or transgenically induced defects in squamation or pigmentation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial–mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, these comprehensive single-cell transcriptomic data representing skin phenotypes of biomedical relevance should provide a useful resource for accelerating the discovery of mechanisms that govern skin development and homeostasis.

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  • These analyses suggest a new set of high priority candidate genes that may have contributed to species-specific pigmentation, or differences in skin or scale development.

    “but these analyses suggest a new set of high priority candidate genes that may have contributed to species-specific pigmentation, or differences in skin or scale development50.”

    From Genomic and genetic insights into speciation and pigment pattern diversification in <i>Danio</i> fishes (2025) · cites this paper as [50]

    The Results section on hypodermal cells identifies genes involved in zebrafish pigment development, and the Discussion says the transcriptomic data may aid future cross-species comparisons. The paper does not identify a high-priority set of candidate genes as contributors to species-specific pigmentation or skin and scale differences. The available passages have no page numbers. (LLM, conf=0.82)

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Cited by

Sorted by citations

Authors
Aman, A. J., Saunders, L. M., Carr, A. A., Srivatasan, S., Eberhard, C., Carrington, B., Watkins-Chow, D., Pavan, W. J., Trapnell, C., & Parichy, D. M.
Affiliations
  • University of Virginia (US)
  • University of Washington (US)
  • National Human Genome Research Institute (US)
  • National Human Genome Research Institute, National Institutes of Health
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2023-09-11
Volume
12
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.86670
PMC
PMC10495112
OpenAlex
W4367044355
Cited by
30
References
8
Citations by year
2026: 13 · 2025: 7 · 2024: 7 · 2023: 3
FWCI
2.59
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • eLife (acceptedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, public-domain)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institute of General Medical Sciences (R35 GM122471)
  • National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01 AR078320)
  • National Heart, Lung, and Blood Institute (U54 HL145611)
  • National Human Genome Research Institute (UM1 HG011586, R01 HG010632)
  • Paul G. Allen Frontiers Group
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
Keywords
squamation, single-cell transcriptomics, epidermal cell types, enamel matrix proteins, epithelial-mesenchymal signaling, subcutaneous tissue, pigment cell development, hormonal regulation, skin appendages
MeSH terms
Animals, Female, Morphogenesis, Skin, Zebrafish, Gene Expression Profiling, Transcriptome

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