Evolution of gene regulatory network architectures: Examples of subcircuit conservation and plasticity between classes of echinoderms
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Developmental gene regulatory networks (GRNs) explain how regulatory states are established in particular cells during development and how these states then determine the final form of the embryo. Evolutionary changes to the sequence of the genome will direct reorganization of GRN architectures, which in turn will lead to the alteration of developmental programs. A comparison of GRN architectures must consequently reveal the molecular basis for the evolution of developmental programs among different organisms. This review highlights some of the important findings that have emerged from the most extensive direct comparison of GRN architectures to date. Comparison of the orthologous GRNs for endomesodermal specification in the sea urchin and sea star, provides examples of several discrete, functional GRN subcircuits and shows that they are subject to diverse selective pressures. This demonstrates that different regulatory linkages may be more or less amenable to evolutionary change. One of the more surprising findings from this comparison is that GRN-level functions may be maintained while the factors performing the functions have changed, suggesting that GRNs have a high capacity for compensatory changes involving transcription factor binding to cis regulatory modules.
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Certain remarkably conserved regulatory sub-circuits located near the top of developmental GRN hierarchy may serve to lock down developmental processes specific to given phyla or classes (GRN kernels).
“Certain remarkably conserved regulatory sub-circuits that are located near the top of developmental GRN hierarchy may serve to lock down developmental process specific to given phyla or classes (GRN kernels)86–91.”
From Emerging properties of animal gene regulatory networks (2010) · cites this paper as [91]
Cites
Gene Regulatory Networks and the Evolution of Animal Body Plans
Davidson, E. H., & Erwin, D. H. (2006) · Science · doi:10.1126/science.1113832 · Cited by 1,207 · cited 6× · see citing works
“In the echinoid lineage, Delta-N signaling took on a new role in specifying mesodermal cell types and activating gcm. Davidson and Erwin [25] suggested that signaling pathways are likely to constitute an evolutionarily promiscuous subcircuitry and are hence likely to be utilized in different contexts.”
InfluentialAn ancient role for nuclear β-catenin in the evolution of axial polarity and germ layer segregation
Wikramanayake, A. H., Hong, M., Lee, P. N., Pang, K., Byrum, C. A., Bince, J. M., Xu, R., & Martindale, M. Q. (2003) · Nature · doi:10.1038/nature02113 · Cited by 324 · see citing works
Evolvability and hierarchy in rewired bacterial gene networks
Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga-Canut, M., & Serrano, L. (2008) · Nature · doi:10.1038/nature06847 · Cited by 307 · see citing works
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
Hinman, V. F., Nguyen, A. T., Cameron, R. A., & Davidson, E. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235868100 · Cited by 272 · see citing works
Self-citationThe evolution of combinatorial gene regulation in fungi
Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H., & Johnson, A. D. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060038 · Cited by 228 · see citing works
Darwin's dilemma: the realities of the Cambrian ‘explosion’
Conway Morris, S. (2006) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2006.1846 · Cited by 179 · cited 2× · see citing works
“Such subcircuits provide a molecular explanation as to why phyletic body plans have remained essentially unchanged since their first appearance in the Cambrian or Precambrian [26].”
Evolutionary plasticity of developmental gene regulatory network architecture
Hinman, V. F., & Davidson, E. H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709994104 · Cited by 154 · see citing works
Self-citationRepression of mesodermal fate by<i>foxa</i>, a key endoderm regulator of the sea urchin embryo
Oliveri, P., Walton, K. D., Davidson, E. H., & McClay, D. R. (2006) · Development · doi:10.1242/dev.02577 · Cited by 141 · see citing works
Calestani, C., Rast, J. P., & Davidson, E. H. (2003) · Development · doi:10.1242/dev.00647 · Cited by 137 · cited 1× · see citing works
“These factors are required to specify various mesodermal cells types, including pigment and blastocoelar cells [63,64].”
Larval stages of a living sea lily (stalked crinoid echinoderm)
Nakano, H., Hibino, T., Oji, T., Hara, Y., & Amemiya, S. (2003) · Nature · doi:10.1038/nature01236 · Cited by 123 · see citing works
<i>Xenopus</i> as a model system to study transcriptional regulatory networks
Koide, T., Hayata, T., & Cho, K. W. Y. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408125102 · Cited by 96 · see citing works
Hinman, V. F., Nguyen, A., & Davidson, E. H. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.09.006 · Cited by 67 · see citing works
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Emerging properties of animal gene regulatory networks
Davidson, E. H. (2010) · Nature · doi:10.1038/nature09645 · Cited by 579 · see citing works
Was the Ediacaran–Cambrian radiation a unique evolutionary event?
Erwin, D. H. (2015) · Paleobiology · doi:10.1017/pab.2014.2 · Cited by 40 · see citing works
- Authors
- Hinman, V. F., Yankura, K. A., & McCauley, B. S.
- Affiliations
- Carnegie Mellon University (US)
- Corresponding author
- Hinman, Veronica F.
- ORCID
- Hinman, Veronica F.
- Venue
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Publisher
- Elsevier BV
- Published
- 2009-04
- Volume
- 1789
- Issue
- 4
- Pages
- 326-332
- ISSN
- 1874-9399 (ISSN-L)
- OpenAlex
- W2013395775
- Cited by
- 32
- References
- 12
- Citations by year
- 2024: 2 · 2023: 3 · 2021: 1 · 2020: 1 · 2019: 1 · 2017: 1 · 2016: 4 · 2015: 3 · 2014: 5 · 2012: 5
- FWCI
- 0.28
- Type
- journal article
- Language
- en
- Open access
- green
- figshare.com
- Licence
- Locations
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (publishedVersion)
- PubMed (publishedVersion)
- Figshare (submittedVersion, cc-by)
- KiltHub Repository
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- gene regulatory networks, Echinodermata, sea urchins, sea stars, cis-regulatory modules, transcription factor binding, compensatory evolution
- MeSH terms
- Animals, Echinodermata, Evolution, Molecular, Gene Regulatory Networks
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