Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

BMC Genomics

Research Article

Ana Ariza-Cosano¹  José Bessa¹  José Luis Gómez-Skarmeta¹  Hunter B Fraser²  Manuel Irimia³  Len A Pennacchio⁴  Axel Visel⁴ 

[1] Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Ctra. Utrera Km 1, 41013, Seville, Spain;Department of Biology, Stanford University, 94305, Stanford, CA, USA;Department of Biology, Stanford University, 94305, Stanford, CA, USA;The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada;Genomics Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA;U.S. Department of Energy Joint Genome Institute, 94598, Walnut Creek, CA, USA;

关键词: Evolution;    Vertebrates;    Trans-changes;    Trans-evolution;    Enhancers;   

DOI  :  10.1186/1471-2164-13-713

 received in 2012-05-21, accepted in 2012-12-14,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundPhenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in cis- regulatory elements (cis- changes) or from changes in the expression pattern or function of transcription factors (trans- changes). While isolated examples of trans- changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear.ResultsHere, we attempt to examine the prevalence of trans- effects and their potential impact on gene expression patterns in vertebrate evolution by comparing the function of identical human tissue-specific enhancer sequences in two highly divergent vertebrate model systems, mouse and zebrafish. Among 47 human conserved non-coding elements (CNEs) tested in transgenic mouse embryos and in stable zebrafish lines, at least one species-specific expression domain was observed in the majority (83%) of cases, and 36% presented dramatically different expression patterns between the two species. Although some of these discrepancies may be due to the use of different transgenesis systems in mouse and zebrafish, in some instances we found an association between differences in enhancer activity and changes in the endogenous gene expression patterns between mouse and zebrafish, suggesting a potential role for trans- changes in the evolution of gene expression.ConclusionsIn total, our results: (i) serve as a cautionary tale for studies investigating the role of human enhancers in different model organisms, and (ii) suggest that changes in the trans environment may play a significant role in the evolution of gene expression in vertebrates.

【 授权许可】

Unknown   
© Ariza-Cosano et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.