The genetic basis of evolutionary change in gene expression levels

Emerson, J. J.; Li, Wen-Hsiung

doi:10.1098/rstb.2010.0005

Cited by 64 publications

(57 citation statements)

References 80 publications

(137 reference statements)

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“…Studying the nature of the regulatory changes ( cis- or trans- acting) that underlie parental divergence and transgressive hybrid segregation can provide insight into the evolutionary forces that influence gene expression variation within and between populations (Lemos et al 2008; Emerson and Li 2010). There is ongoing debate over the relative importance of cis - and trans -regulatory mutations in terms of their contributions toward adaptive evolution (Hoekstra and Coyne 2007; Prud’homme et al 2007).…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

Bell

Kane

Rieseberg

et al. 2013

Genome Biology and Evolution

141

163

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Hybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes in gene expression. The effects of intraspecific hybridization on F1 hybrid gene expression were investigated using parents from divergent, natural populations of Cirsium arvense, an invasive Compositae weed. Using an RNA-seq approach, the expression of 68,746 unigenes was quantified in parents and hybrids. The expression levels of 51% of transcripts differed between parents, a majority of which had less than 1.25× fold-changes. More unigenes had higher expression in the invasive parent (P1) than the noninvasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed nonadditive (transgressive or dominant) modes of gene action in the hybrids. A majority of the dominant cases had P2-like expression patterns in the hybrids. Comparisons of allele-specific expression also enabled a survey of cis- and trans-regulatory effects. Cis- and trans-regulatory divergence was found at 70% and 68% of 62,281 informative single-nucleotide polymorphism sites, respectively. Of the 17% of sites exhibiting both cis- and trans-effects, a majority (70%) had antagonistic regulatory interactions (cis x trans); trans-divergence tended to drive higher expression of the P1 allele, whereas cis-divergence tended to increase P2 transcript abundance. Trans-effects correlated more highly than cis with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared with nonadditive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations.

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Section: Introductionmentioning

confidence: 99%

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

Bell

Kane

Rieseberg

et al. 2013

Genome Biology and Evolution

141

163

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show abstract

“…First, genome-wide allele-specific mRNA expression analyses have revealed that both cis - and trans -regulatory changes contribute to differential expression of mRNAs among closely related species [32-34]. Small RNAs can act as trans -regulatory factors, which contribute to differential mRNA expression [35].…”

Section: Introductionmentioning

confidence: 99%

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks

2013

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BackgroundNon-coding small RNAs, ranging from 20 to 30 nucleotides in length, mediate the regulation of gene expression and play important roles in many biological processes. One class of small RNAs, microRNAs (miRNAs), are highly conserved across taxa and mediate the regulation of the chromatin state and the post-transcriptional regulation of messenger RNA (mRNA). Another class of small RNAs is the Piwi-interacting RNAs, which play important roles in the silencing of transposons and other functional genes. Although the biological functions of the different small RNAs have been elucidated in several laboratory animals, little is known regarding naturally occurring variation in small RNA transcriptomes among closely related species.ResultsWe employed next-generation sequencing technology to compare the expression profiles of brain small RNAs between sympatric species of the Japanese threespine stickleback (Gasterosteus aculeatus). We identified several small RNAs that were differentially expressed between sympatric Pacific Ocean and Japan Sea sticklebacks. Potential targets of several small RNAs were identified as repetitive sequences. Female-biased miRNA expression from the old X chromosome was also observed, and it was attributed to the degeneration of the Y chromosome.ConclusionsOur results suggest that expression patterns of small RNA can differ between incipient species and may be a potential mechanism underlying differential mRNA expression and transposon activity.

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“…Studying cis -regulatory elements has been of great interest over the last years as it has been suggested that phenotypic changes also result from variation in these regions rather than in coding regions [2,81,82]. A relatively straightforward way to investigate this is to first analyze sequence variation and search for specific motifs in promoter regions [83].…”

Section: Discussionmentioning

confidence: 99%

Sequence Evolution and Expression Regulation of Stress-Responsive Genes in Natural Populations of Wild Tomato

Fischer¹,

Steige²,

Stephan³

et al. 2013

PLoS ONE

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The wild tomato species Solanum chilense and S. peruvianum are a valuable non-model system for studying plant adaptation since they grow in diverse environments facing many abiotic constraints. Here we investigate the sequence evolution of regulatory regions of drought and cold responsive genes and their expression regulation. The coding regions of these genes were previously shown to exhibit signatures of positive selection. Expression profiles and sequence evolution of regulatory regions of members of the Asr (ABA/water stress/ripening induced) gene family and the dehydrin gene pLC30-15 were analyzed in wild tomato populations from contrasting environments. For S. chilense, we found that Asr4 and pLC30-15 appear to respond much faster to drought conditions in accessions from very dry environments than accessions from more mesic locations. Sequence analysis suggests that the promoter of Asr2 and the downstream region of pLC30-15 are under positive selection in some local populations of S. chilense. By investigating gene expression differences at the population level we provide further support of our previous conclusions that Asr2, Asr4, and pLC30-15 are promising candidates for functional studies of adaptation. Our analysis also demonstrates the power of the candidate gene approach in evolutionary biology research and highlights the importance of wild Solanum species as a genetic resource for their cultivated relatives.

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The genetic basis of evolutionary change in gene expression levels

Cited by 64 publications

References 80 publications

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks

Sequence Evolution and Expression Regulation of Stress-Responsive Genes in Natural Populations of Wild Tomato

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