title: Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes.
abstract: Because there is considerable variation in gene expression even between closely related species, it is clear that gene regulatory mechanisms evolve relatively rapidly. Because primary sequence conservation is an unreliable proxy for functional conservation of cis-regulatory elements, their assessment must be carried out in vivo. We conducted a survey of cis-regulatory conservation between C. elegans and closely related species C. briggsae, C. remanei, C. brenneri, and C. japonica. We tested enhancers of eight genes from these species by introducing them into C. elegans and analyzing the expression patterns they drove. Our results support several notable conclusions. Most exogenous cis elements direct expression in the same cells as their C. elegans orthologs, confirming gross conservation of regulatory mechanisms. However, the majority of exogenous elements, when placed in C. elegans, also directed expression in cells outside endogenous patterns, suggesting functional divergence. Recurrent ectopic expression of different promoters in the same C. elegans cells may reflect biases in the directions in which expression patterns can evolve due to shared regulatory logic of coexpressed genes. The fact that, despite differences between individual genes, several patterns repeatedly emerged from our survey, encourages us to think that general rules governing regulatory evolution may exist and be discoverable.
authors: Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America.
authors: Antoine
authors: A
authors: Barrière
authors: Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America; Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America.
authors: Ilya
authors: I
authors: Ruvinsky
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D015870:Gene Expression; D005786:Gene Expression Regulation / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA; D050486:Serotonin Plasma Membrane Transport Proteins / Q000235:genetics; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D050495:Vesicular Inhibitory Amino Acid Transport Proteins / Q000235:genetics
chemical_list: D029742:Caenorhabditis elegans Proteins; D050486:Serotonin Plasma Membrane Transport Proteins; D014157:Transcription Factors; D050495:Vesicular Inhibitory Amino Acid Transport Proteins; C493229:mod-5 protein, C elegans; C522200:unc-46 protein, C elegans; C493420:unc-47 protein, C elegans