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Related Experiment Video

Updated: Oct 14, 2025

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Published on: December 19, 2011

Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate

Kun Xiong^1,2, Mark Gerstein^2,3,4,5, Joanna Masel⁶

¹Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.

|November 5, 2021

Summary

Evolutionary accessibility, not just optimal function, shapes transcriptional regulatory network motifs. Incoherent feed-forward loops often evolve before negative feedback loops, influenced by gene expression levels.

Keywords:

adaptationism gene regulatory network mutation-biased adaptation pulse generation transcriptional regulation

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Area of Science:

Systems Biology
Evolutionary Biology
Computational Biology

Background:

Transcriptional regulatory networks (TRNs) feature recurring motifs, often explained by adaptation and optimal function.
However, the ease of evolution for certain motifs may also influence their prevalence.

Purpose of the Study:

To investigate the evolutionary dynamics of TRN motifs computationally.
To compare the evolutionary accessibility and performance of type 1 incoherent feed-forward loops (I1FFLs) and negative feedback loops (NFBLs) in generating a protein pulse.

Main Methods:

Computational evolution of TRNs to produce a specific protein pulse output.
Analysis of motif evolution under varying selection conditions (pulse height, response speed).

Main Results:

Both I1FFLs and NFBLs emerged as primary solutions, achieving similar performance.
I1FFLs generally evolved more frequently than NFBLs.
Selection for pulse speed favored I1FFLs, while selection for pulse height favored NFBLs.
I1FFLs were more evolutionarily accessible early in the process; NFBLs often evolved from I1FFL-NFBL combinations.
In S. cerevisiae, NFBL output genes showed higher expression than I1FFL output genes.

Conclusions:

Evolutionary accessibility, influenced by gene expression levels, plays a critical role in shaping the prevalence of TRN motifs.
The observed motif usage may not solely reflect functional optimization but also the ease of their evolutionary emergence.