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Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
Alison P Lee1, Sze Yen Kerk, Yue Ying Tan
1Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore.
Molecular Biology and Evolution
|November 18, 2010
Summary
Ancient vertebrate conserved noncoding elements (aCNEs) evolved rapidly in teleost fishes, with significant loss attributed to whole-genome duplication. This rapid evolution may alter gene expression patterns across bony vertebrates.
Area of Science:
- Genomics
- Evolutionary Biology
- Comparative Genomics
Background:
- Conserved noncoding elements (CNEs) are crucial regulatory regions in vertebrate genomes, often acting as tissue-specific enhancers.
- Understanding the evolutionary dynamics of CNEs across diverse vertebrate lineages provides insights into genome evolution and gene regulation.
Purpose of the Study:
- To identify and investigate the evolutionary trajectories of ancient vertebrate CNEs (aCNEs) in bony vertebrate lineages.
- To compare the rates of CNE evolution and loss across mammals, birds, and teleost fishes.
Main Methods:
- Comparative genomic analysis of CNEs across human, dog, chicken, Xenopus, and four teleost fishes, using elephant shark as a reference.
- Relative rate tests to assess substitution rates in CNEs.
- Transgenic zebrafish assays to evaluate the function of conserved CNE enhancers.
Main Results:
- aCNEs exhibit differential evolutionary rates across bony vertebrate lineages.
- Teleost fishes show a high rate of CNE loss (78-83%) and accelerated evolution compared to chicken (24% loss) and mammals (40% loss).
- A significant proportion of aCNEs (68%) were lost in ray-finned fishes prior to teleost divergence, linked to fish-specific whole-genome duplication.
Conclusions:
- The fish-specific whole-genome duplication event significantly impacted aCNE evolution in teleosts, leading to accelerated rates and substantial loss.
- Rapid evolution of aCNEs may have functional consequences on gene expression patterns.
- Functional analysis suggests conservation or alteration of trans-acting factors between mammals and fishes for certain CNE enhancers.
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