Functional Evolution of a cis-Regulatory Module

Michael Z Ludwig,Martin Kreitman,Elena Alekseeva,Arnar Palsson,Casey M Bergman,Janaki Nathan,Michael Levine

doi:10.1371/journal.pbio.0030093

Michael Z Ludwig, Martin Kreitman + Show 5 more

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https://doi.org/10.1371/journal.pbio.0030093

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Journal: PLoS Biology	Publication Date: Mar 15, 2005
Citations: 215	License type: CC BY 4.0

Affiliation: University of Chicago, University of Cambridge

Abstract

Lack of knowledge about how regulatory regions evolve in relation to their structure–function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module—the even-skipped stripe 2 enhancer—from four Drosophila species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure–function, mechanisms of speciation and computational identification of regulatory modules.

Highlights

The annotation of genes from comparative sequence data rests on a fundamental evolutionary dictum, first elaborated by M
We created the eve stripe 2 enhancer (S2E) deficiency mutant by removing a 480-bp fragment corresponding to the minimal stripe 2 element (MSE; see Figure S1) from a 15-kb cloned copy of the eve locus [12]
Eve stripe 2 corresponds to parasegment 3, which is bordered by en stripes 3 and 4

Summary

Introduction

The annotation of genes from comparative sequence data rests on a fundamental evolutionary dictum, first elaborated by M. That the rate of molecular evolution will be inversely related to the level of functional constraint. Knowledge of equivalent scope and depth does not exist for cis-regulatory sequences. These sequences often contain docking sites for transcription factors (TFs), but the number of binding sites and the spacing between them vary, and binding-site sequences are often degenerate to the point that they can only be characterized probabilistically. Even more striking is the lack of data relating functional evolution of gene expression to cis-regulatory sequence evolution. Despite recent progress [4,5], rules have yet to be elucidated for the functional molecular evolution of this critically important component of the genome

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