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00:08
A Rapid In Vivo Bioassay for Developmentally Active Enhancers
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The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape
Aisha Yousaf1, Muhammad Sohail Raza1, Amir Ali Abbasi2
1National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
Genome Biology and Evolution
|August 9, 2015
Summary
Evolutionary studies reveal that enhancer sequences in bony vertebrates evolved rapidly, especially during the transition to land. This accelerated regulatory evolution contrasts with slower coding sequence changes, impacting gene networks during vertebrate land adaptation.
Area of Science:
- Evolutionary genomics
- Developmental biology
- Comparative genomics
Background:
- Enhancers are crucial for gene regulation and development; their sequence changes can cause disease.
- Despite their importance, the evolutionary history of enhancers, particularly in vertebrates, remains understudied.
- Conserved noncoding elements (CNE) are key regulatory regions whose evolution offers insights into genomic adaptation.
Purpose of the Study:
- To investigate the evolutionary dynamics of bony vertebrate enhancers, focusing on conserved noncoding elements (CNE).
- To compare the evolutionary rates of enhancers with coding and nonenhancer CNEs during vertebrate adaptation.
- To understand the role of cis-regulatory evolution in developmental changes during the water-to-land transition.
Main Methods:
- Bayesian phylogenetics was employed to analyze enhancer sequences and infer evolutionary relationships among placental mammals.
- Molecular clock estimates were used to determine the timing and rates of enhancer evolution across bony vertebrates.
- Comparative analysis of evolutionary rates between enhancers, coding sequences, and nonenhancer CNEs was performed.
Main Results:
- Phylogenetic analysis suggested novel interordinal relationships among placental mammals, placing rodents basally.
- Enhancer evolution showed dynamic rate changes across bony vertebrates, with a significant acceleration in land-dwelling tetrapods.
- Land vertebrates exhibited faster evolution in enhancer sequences compared to significantly slower evolution in coding and nonenhancer CNEs.
Conclusions:
- Vertebrate enhancer evolution is distinct from coding sequence evolution, particularly during adaptation to land.
- The accelerated evolution of enhancers in tetrapods likely fine-tuned gene regulatory networks for terrestrial life.
- This study highlights the critical role of cis-regulatory element evolution in shaping developmental circuits during major evolutionary transitions.
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