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Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes

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 assessmen...

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Autores principales: Barrière, Antoine, Ruvinsky, Ilya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072541/
https://www.ncbi.nlm.nih.gov/pubmed/24968346
http://dx.doi.org/10.1371/journal.pgen.1004435
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author Barrière, Antoine
Ruvinsky, Ilya
author_facet Barrière, Antoine
Ruvinsky, Ilya
author_sort Barrière, Antoine
collection PubMed
description 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.
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spelling pubmed-40725412014-07-02 Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes Barrière, Antoine Ruvinsky, Ilya PLoS Genet Research Article 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. Public Library of Science 2014-06-26 /pmc/articles/PMC4072541/ /pubmed/24968346 http://dx.doi.org/10.1371/journal.pgen.1004435 Text en © 2014 Barrière, Ruvinsky http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Barrière, Antoine
Ruvinsky, Ilya
Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
title Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
title_full Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
title_fullStr Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
title_full_unstemmed Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
title_short Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
title_sort pervasive divergence of transcriptional gene regulation in caenorhabditis nematodes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072541/
https://www.ncbi.nlm.nih.gov/pubmed/24968346
http://dx.doi.org/10.1371/journal.pgen.1004435
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