The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level

Barroso, Gustavo; Puzović, Nataša; Dutheil, Julien

doi:10.1534/genetics.117.300467

Cited by 43 publications

(57 citation statements)

References 87 publications

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“…We also observed a high number of stress responsive TFs with targets enriched in HVGs. This is in agreement with previous observations in mammals and Yeast that HVGs are enriched in stress responsive genes 6,29,30 , and that LVGs are enriched in housekeeping genes 31 . This is also further supported by previous results showing a positive correlation between gene expression variability and plasticity 32 , the latter corresponding to environmentally triggered gene expression changes.…”

Section: Discussionsupporting

confidence: 93%

Widespread inter-individual gene expression variability inArabidopsis thaliana

Cortijo

Aydın

Ahnert

et al. 2018

Preprint

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Section: Discussionsupporting

confidence: 93%

Widespread inter-individual gene expression variability inArabidopsis thaliana

Cortijo

Aydın

Ahnert

et al. 2018

Preprint

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“…We also observed a high number of stress‐responsive TFs with targets enriched in HVGs. This is in agreement with previous observations in mammals and yeast that HVGs are enriched in stress‐responsive genes (Newman et al , ; Yin et al , ; Gasch et al , ) and that LVGs are enriched in housekeeping genes (Barroso et al , ). This is also further supported by previous results showing a positive correlation between gene expression variability and plasticity (Hirao et al , ), the latter corresponding to environmentally triggered gene expression changes.…”

Section: Discussionsupporting

confidence: 93%

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Cortijo

Aydın

Ahnert

et al. 2019

Molecular Systems Biology

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A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform, and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about inter‐individual transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24‐h time course. We identified hundreds of genes that exhibit high inter‐individual variability and found that many are involved in environmental responses, with different classes of genes variable between the day and night. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

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“…Despite many studies providing evidence that natural selection can (Tǎnase-Nicola and Ten Wolde 2008; Wang and Zhang 2011;Barroso et al 2018) and has (Fraser et al 2004;Lehner 2008;Zhang et al 2009;Metzger et al 2015) acted on expression noise, the precise effects of expression noise on fitness have proven difficult to measure empirically. This difficulty arises from the facts that (1) most mutations that alter expression noise also alter mean expression in a correlated fashion, making it difficult to isolate the effects of changes in expression noise on fitness (Hornung et al 2012;Keren et al 2016;Liu et al 2016), and (2) the magnitude of fitness effects resulting from changes in expression noise is expected to be smaller than that resulting from changes in mean expression level (Zhang et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Fitness effects of altering gene expression noise inSaccharomyces cerevisiae

Duveau

Hodgins‐Davis

Metzger

et al. 2018

Preprint

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Gene expression noise is an evolvable property of biological systems that describes differences in gene expression among genetically identical cells in the same environment. Prior work has shown that expression noise is heritable and can be shaped by natural selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for the TDH3 gene in Saccharomyces cerevisiae. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns that are consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise.

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The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level

Abstract: Gene expression is a noisy process: in constant environment and genotype, cell to cell variability occurs because of randomness of biochemical reactions...

Cited by 43 publications

References 87 publications

Widespread inter-individual gene expression variability inArabidopsis thaliana

Widespread inter-individual gene expression variability inArabidopsis thaliana

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Fitness effects of altering gene expression noise inSaccharomyces cerevisiae

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