Conservation of core gene expression in vertebrate tissues
Open accessAbstract
Background: Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior. Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates. Results: We measured expression of all known and predicted genes across twenty tissues in chicken, frog and pufferfish. By combining the results with human and mouse data and considering only ten common tissues, we have found evidence of conserved expression for more than a third of unique orthologous genes. We find that, on average, transcription factor gene expression is neither more nor less conserved than that of other genes. Strikingly, conservation of expression correlates poorly with the amount of conserved nonexonic sequence, even using a sequence alignment technique that accounts for non-collinearity in conserved elements. Many genes show conserved human/fish expression despite having almost no nonexonic conserved primary sequence. Conclusions: There are clearly strong evolutionary constraints on tissue-specific gene expression. A major challenge will be to understand the precise mechanisms by which many gene expression patterns remain similar despite extensive cis -regulatory restructuring.
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Previous reports show high constraints of brain gene expression variance across evolution.
“This is in accordance with previous reports showing high constraints of brain gene expression variance across evolution”
From Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program (2019) · cites this paper as Chan et al., 2009
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- Authors
- Chan, E. T., Quon, G. T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R. A., Aubin, J., Ratcliffe, M. J., Wilde, A., Brudno, M., Morris, Q. D., & Hughes, T. R.
- Affiliations
- University of Toronto (CA)
- Corresponding author
- Morris, Quaid D
- Hughes, Timothy R
- ORCID
- Venue
- Journal of Biology
- Published
- 2009-04-16
- Volume
- 8
- Issue
- 3
- Pages
- 33-33
- ISSN
- 1475-4924 (ISSN-L)
- PMC
- PMC2689434
- OpenAlex
- W2148498486
- Cited by
- 190
- References
- 77
- Citations by year
- 2026: 6 · 2025: 6 · 2024: 5 · 2023: 8 · 2022: 13 · 2021: 11 · 2020: 9 · 2019: 6 · 2018: 8 · 2017: 11 · 2016: 10 · 2015: 17 · 2014: 11 · 2013: 7 · 2012: 23
- FWCI
- 8.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Journal of Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- TSpace (University of Toronto) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (R01-GM 1080)
- 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 Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- tissue-specific gene expression, orthologs, transcription factors, cis-regulatory elements, cis-regulatory evolution, vertebrate evolution, chickens, frogs, pufferfish, human, mice
- MeSH terms
- Animals, Anura, Base Sequence, Chickens, DNA, Gene Expression Regulation, Humans, Transcription Factors, Vertebrates, Sequence Alignment, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular, Gene Expression Profiling, Tetraodontiformes, Mice
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