scholarly journals Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

2014 ◽  
Vol 24 (7) ◽  
pp. 1115-1124 ◽  
Author(s):  
R. K. Arthur ◽  
L. Ma ◽  
M. Slattery ◽  
R. F. Spokony ◽  
A. Ostapenko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Expression Evolution ◽  
Gene Expression Evolution

scholarly journals Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kenji Fukushima ◽  
David D. Pollock
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Evolutionary Rate ◽  
Expression Patterns ◽  
Vertebrate Species ◽  
Rna Seq ◽  
Organ Specific ◽  
Tightly Coupled ◽  
Expression Evolution ◽  
Gene Expression Evolution

Abstract The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein–Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.

scholarly journals Organ-specific propensity drives patterns of gene expression evolution

2018 ◽  
Author(s):  
Kenji Fukushima ◽  
David D. Pollock
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Evolutionary Rate ◽  
Expression Patterns ◽  
Vertebrate Species ◽  
Rna Seq ◽  
Organ Specific ◽  
Tightly Coupled ◽  
Expression Evolution ◽  
Gene Expression Evolution

AbstractThe origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamated 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminated project-specific biases, and expression shifts were reconstructed using gene-family-wise phylogenetic Ornstein–Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties were tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs were nonrandom, forming modular connections which were reshaped by gene duplication. Thus, if expression shifted, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. This supports a major role for what might be termed “preadaptive” pathways of gene expression evolution.

scholarly journals Relating gene expression evolution with CpG content changes

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 693 ◽  
Author(s):  
Huan Yang ◽  
Dawei Li ◽  
Chao Cheng
Keyword(s):  
Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution

scholarly journals On the relation between promoter divergence and gene expression evolution

2008 ◽  
Vol 4 (1) ◽  
pp. 159 ◽  
Author(s):  
Itay Tirosh ◽  
Adina Weinberger ◽  
Dana Bezalel ◽  
Mark Kaganovich ◽  
Naama Barkai
Keyword(s):  
Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution ◽  
Promoter Divergence

scholarly journals Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes

2020 ◽  
Author(s):  
Soumitra Pal ◽  
Brian Oliver ◽  
Teresa M. Przytycka
Keyword(s):  
Gene Expression ◽  
Evolutionary Dynamics ◽  
Computational Method ◽  
Specific Gene ◽  
Species Variation ◽  
Evolutionary Divergence ◽  
Sequence Evolution ◽  
Study Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution

AbstractWhile DNA sequence evolution has been well studied, the expression of genes is also subject to evolution. Yet the evolution of gene expression is currently not well understood. In recent years, new tissue/organ specific gene expression datasets spanning several organisms across the tree of life, have become available providing the opportunity to study gene expression evolution in more detail. However, while a theoretical model to study evolution of continuous traits exist, in practice computational methods often cannot distinguish, with confidence, between alternative evolutionary scenarios. This lack of power has been attributed to the modest number of species with available expression data.To solve this challenge, we introduce EvoGeneX, a computationally efficient method to uncover the mode of gene expression evolution based on the Ornstein-Uhlenbeck process. Importantly, EvoGeneX in addition to modelling expression variations between species, models within species variation. To estimate the within species variation, EvoGeneX formally incorporates the data from biological replicates as a part of the mathematical model. We show that by modelling the within species diversity EvoGeneX significantly outperforms the currently available computational method. In addition, to facilitate comparative analysis of gene expression evolution, we introduce a new approach to measure the dynamics of evolutionary divergence of a group of genes.We used EvoGeneX to analyse the evolution of expression across different organs, species and sexes of the Drosophila genus. Our analysis revealed differences in the evolutionary dynamics of male and female gonads, and uncovered examples of adaptive evolution of genes expressed in the head and in the thorax.

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