title: Distinct functional constraints partition sequence conservation in a cis-regulatory element.
abstract: Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene. We found that this promoter consists of two distinct domains. The proximal promoter is conserved and is largely sufficient to direct appropriate spatial expression. The distal promoter displays little if any conservation between several closely related nematodes. Despite this divergence, sequences from all species confer robustness of expression, arguing that this function does not require substantial sequence conservation. We showed that even unrelated sequences have the ability to promote robust expression. A prominent feature shared by all of these robustness-promoting sequences is an AT-enriched nucleotide composition consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter.
authors.affiliation: Department of Ecology and Evolution and Institute for Genomics and Systems Biology, Chicago, Illinois, USA.
authors.forename: Antoine
authors.initials: A
authors.lastname: Barrière
authors.forename: Kacy L
authors.initials: KL
authors.lastname: Gordon
authors.forename: Ilya
authors.initials: I
authors.lastname: Ruvinsky
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics