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Cited by 838Developmental Biology and Gene RegulationGenomics and Phylogenetic StudiesBioinformatics and Genomic Networks

Gene expression across mammalian organ development

Open access
Cardoso-Moreira, Margarida, Halbert, Jean, Valloton, Delphine, Velten, Britta, Chen, Chunyan, Shao, Yi, Liechti, Angélica, Ascenção, Kelly +25 more·2019·Nature
DOI 10.1038/s41586-019-1338-5PMC PMC6658352
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Abstract

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.

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  • 77% (17/22) of heart, brain and liver candidates were expressed at high levels throughout development.

    “77% (17/22) of heart, brain and liver candidates were expressed at high levels throughout development17”

    From Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis (2025) · cites this paper as [17]

    The Organ developmental transcriptomes section and Extended Data Figure 1 discuss expression across development in organs including the heart, brain and liver, but neither reports a set of 22 candidates or says that 17 were highly expressed throughout development. Searches for “17/22,” “17 of 22,” “77%,” and candidate genes found no passage establishing the claimed result. Page numbers are not available in our copy. (LLM, conf=0.72)

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Authors
Cardoso-Moreira, M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascenção, K., Rummel, C., Ovchinnikova, S., Mazin, P. V., Xenarios, I., Harshman, K., Mort, M., Cooper, D. N., Sandi, C., Soares, M. J., Ferreira, P. G., Afonso, S., Carneiro, M., Turner, J. M. A., VandeBerg, J. L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y. E., & Kaessmann, H.
Affiliations
  • Heidelberg University (DE)
  • University of Lausanne (CH)
  • European Molecular Biology Laboratory (DE)
  • Chinese Academy of Sciences (CN)
  • National Research University Higher School of Economics (RU)
  • Cardiff University (GB)
  • École Polytechnique Fédérale de Lausanne (CH)
  • Children’s Mercy Research Institute (US)
  • Universidade do Porto (PT)
  • The Francis Crick Institute (GB)
  • The University of Texas Rio Grande Valley (US)
  • Linköping University (SE)
  • German Primate Center (DE)
  • Newcastle University (GB)
  • Skolkovo Institute of Science and Technology (RU)
  • Stanford Medicine (US)
Corresponding author
  • Cardoso-Moreira, Margarida
  • Kaessmann, Henrik
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2019-06-26
Volume
571
Issue
7766
Pages
505-509
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-019-1338-5
PMC
PMC6658352
OpenAlex
W2954492537
Cited by
838
References
8
Citations by year
2026: 104 · 2025: 136 · 2024: 179 · 2023: 99 · 2022: 114 · 2021: 123 · 2020: 67 · 2019: 15 · 2014: 1
FWCI
28.20
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • SERVAL (Université de Lausanne) (acceptedVersion, other-oa)
  • ScholarWorks @ UTRGV (The University of Texas Rio Grande Valley) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Figshare (submittedVersion, cc-by)
  • ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • IRIS (submittedVersion)
  • The Francis Crick Institute (cc-by)
Funders
  • Wellcome Trust
  • Francis Crick Institute (10193)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (146474)
  • Medical Research Council (MR/R006237/1)
  • National Institute of Environmental Health Sciences (R01ES029280)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD099638, P01HD079363, R01HD020676)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
organogenesis, developmental transcriptome, gene expression evolution, purifying selection, positive selection, de novo genes, developmental trajectories, comparative genomics, brain development, gonad development, heart development, kidney development, liver development, ovarian development, testicular development, mammalian evolution
MeSH terms
Animals, Chickens, Biological Evolution, Female, Humans, Macaca mulatta, Male, Opossums, Rabbits, Gene Expression Regulation, Developmental, Organogenesis, Mice, Rats, Transcriptome

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