2017
DOI: 10.1101/229096
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A quantitative model for characterizing the evolutionary history of mammalian gene expression

Abstract: Characterizing the evolutionary history of a gene's expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype.However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein-Uhlenbeck (OU) process. This stochastic process models expression tra… Show more

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Cited by 9 publications
(9 citation statements)
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“…Gene expression profiles have long plays fundamental role in evolution 65 and gene’s expression across tissue could help to reveal the function and important role of those genes 66 . We used the expression profile of candidate epistatic genes across different floral tissues and found majority of them expressed in panicle and other floral tissues (Fig.…”
Section: Discussionmentioning
confidence: 99%
“…Gene expression profiles have long plays fundamental role in evolution 65 and gene’s expression across tissue could help to reveal the function and important role of those genes 66 . We used the expression profile of candidate epistatic genes across different floral tissues and found majority of them expressed in panicle and other floral tissues (Fig.…”
Section: Discussionmentioning
confidence: 99%
“…Gene regulatory network divergence can serve as a substrate for the evolution of phenotypic diversity and adaptation. In both unicellular and multicellular organisms, various mechanisms of regulatory and gene expression divergence underlying phenotypic diversity have been elucidated: horizontal gene transfer and regulatory reorganization in bacteria 33 ; gene duplication in fungi 34 ; cis-regulatory expression divergence in flies 35 ; variable gene co-expression in worms 36 ; dynamic rewiring of TFs in plant leaf shape 9 ; cis-regulatory mutations in stickleback fish 37 ; alternative splicing 38 and differential rate of gene expression evolution shaped by various selective pressures 39,40 in mammals. Despite these changes to genomic and regulatory architecture, some of these groups have remained virtually unvaried for millions of years of evolution, whereas certain organisms, like the near 1,500 species of East African cichlid fish, have rapidly radiated and diversified in an explosive manner.…”
Section: Discussionmentioning
confidence: 99%
“…However, very little is known about the evolution of regulatory networks (genotype) and their potential phenotypic effect across ecologically-diverse cichlid species (ecotype) 41 . To study the various mechanisms of regulatory divergence towards phenotypic diversity as shown in other organisms 9,[33][34][35][36][37][38][39][40]42 and cichlids 17,41 , we developed a novel framework to 1) identify ancestral and extant species co-expression modules and 2) integrate associated regulators (cis-regulatory elements, transcription factors and miRNAs) to dissect gene expression and regulatory contribution to cichlid phenotypic diversity.…”
Section: Eastmentioning
confidence: 99%
“…complex disease) may therefore be reflected in selection on gene expression. Across species, gene expression levels have been shown to evolve more slowly than would be expected under a neutral model (8)(9)(10)(11)). An analysis of mammalian gene duplications also showed that the total expression of gene pairs in species that experienced a duplication event is similar to the expression of the corresponding single gene copy in species without duplication (12).…”
Section: Introductionmentioning
confidence: 99%