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Cited by 5Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Conserved noncoding elements evolve around the same genes throughout metazoan evolution

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Gonzalez, Paul, Hauck, Quinn C, Baxevanis, Andreas D·2024·Genome Biology and Evolution
DOI 10.1093/gbe/evae052PMC PMC10988421
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Abstract

Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial roles in embryonic development. To further our knowledge of CNEs in other parts of the animal tree, we conducted a large-scale characterization of CNEs in more than 50 genomes from three of the main branches of the metazoan tree: Cnidaria, Mollusca, and Arthropoda. We identified hundreds of thousands of CNEs and reconstructed the temporal dynamics of their appearance in each lineage, as well as determining their spatial distribution across genomes. We show that CNEs evolve repeatedly around the same genes across the Metazoa, including around homeodomain genes and other transcription factors; they also evolve repeatedly around genes involved in neural development. We also show that transposons are a major source of CNEs, confirming previous observations from vertebrates and suggesting that they have played a major role in wiring developmental gene regulatory mechanisms since the dawn of animal evolution.

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  • Many conserved noncoding elements are consistently located near the same developmental and transcription factor genes in cnidarians and bilaterians, indicating that such regulatory associations predate the origin of their common ancestor.

    “many conserved noncoding elements are consistently located near the same developmental and transcription factor genes in cnidarians and bilaterians, indicating that such regulatory associations predate the origin of their common ancestor”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [51]

    The Significance section (page unavailable) says CNEs cluster around the same developmental and transcription-factor genes across metazoan groups, supporting the location pattern. It describes CNEs as evolving repeatedly around those genes, however, and does not establish that the associations predate the cnidarian–bilaterian common ancestor. (LLM, conf=0.88)

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Cited by

Sorted by citations

Authors
Gonzalez, P., Hauck, Q. C., & Baxevanis, A. D.
Affiliations
National Institutes of Health (US)
Corresponding author
Baxevanis, Andreas D
ORCID
Baxevanis, Andreas D
Venue
Genome Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2024-03-19
Volume
16
Issue
4
ISSN
1759-6653 (ISSN-L)
DOI
10.1093/gbe/evae052
PMC
PMC10988421
OpenAlex
W4392950068
Cited by
5
References
1
Citations by year
2026: 3 · 2025: 2
FWCI
1.10
Type
journal article
Language
en
Open access
Licence
public-domain
Locations
  • Genome Biology and Evolution (publishedVersion, public-domain)
  • PubMed Central (publishedVersion, public-domain)
  • PubMed (publishedVersion)
Funders
National Human Genome Research Institute (ZIA HG000140)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
conserved non-coding elements, enhancers, animal evolution, homeodomain transcription factor, neural development genes, transposable elements, gene regulatory evolution, Cnidaria, Mollusca, arthropods, purifying selection
MeSH terms
Animals, Base Sequence, Regulatory Sequences, Nucleic Acid, Transcription Factors, Vertebrates, Conserved Sequence, Evolution, Molecular

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