The genetic architecture of gene expression in Caenorhabditis elegans

A. Viñuela Rodriguez

Research output: Thesisinternal PhD, WU

Abstract

Most organisms are exposed to a continuously changing environment throughout their life. For instance the ambient temperature is usually not constant and many species are exposed to a diverse range of anthropogenic stressors like toxic compounds. Moreover, individuals are prone to genetic changes due to mutation and allelic recombinations. All these factors might affect particular phenotypes, while others remain unchanged. This thesis provides insight into how phenotypic traits are affected by external stress factors and allelic recombinations in the nematode Caenorhabditis elegans (Nematoda; Rhabditidae).  Because phenotypes and their variation may be explained by variation in gene expression, this thesis explored the architecture of gene expression and some of the elements that contribute to gene expression.

 Chapters 2 and 3 focus on environmental stressors with i) a specific target (two organophosphorus pesticides) and ii) a non-target mode of action (temperature) to study their influence on gene expression. A single genotype, the canonical wild type strain Bristol (N2) was used to study the effect of interacting pesticides by exposing nematodes to a toxicant mixture at two different temperatures Analysis revealed common transcriptional responses related to detoxification, stress, innate immunity, and transport of lipids to all treatments. It was found that for both pesticides these similar processes were regulated by different gene transcripts in single and combined treatments. These results also showed that the effect of a mix of low doses of pesticides is not a summed effect of the single components. Moreover, increased temperature elevates the toxic consequences to the pesticides exposures. This toxicity gain is attributed to an elevated uptake and accumulation of the toxicants in the organisms. These results support the idea that the observed higher toxicity of pesticides with temperature might be a consequence of gene-environment interactions affecting detoxification genes. Together, thefirst part of this thesis illustrates the intense crosstalk between gene pathways in response to interacting environmental stressors in C. elegans.

 The second part of the thesis elaborates on the influence of different genotypes as multiple perturbations on gene expression. How the genotype-phenotype relationship progresses with age was investigated using a quantitative genetics approach (genetical genomics). We performed a genetic mapping strategy of gene transcription variation (expression-QTL, eQTL) to explore the dynamics of regulatory loci affecting genome-wide gene expression at three different ages. We used a recombinant inbred line (RIL) population generated from a cross between the C. elegans strain N2 and the wild type CB4856 in Chapter 4. Also, we investigated the influence of age to reveal a genotype-by-age effect (gxaeQTL) on gene expression. The total number of detected eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms the number of genes with increased variation (1772) was nearly 5 times higher than the number of genes with a decreased expression variation (373). Furthermore, the number of cis-acting eQTL in juveniles decreased by almost 50% in old worms whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network integrity declines with age. To better understand the changes in the gene network with age, gene expression profiles of N2 and CB4856 were generated for Chapter 5. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in different genotypes. The average broad sense heritability was similar in developing and aging worms; but the gene expression variance that can be attributed to genetic variance in each gene changes with age. It can be proposed that regulation became more polygenic in aging worms. These changes explain the decrease in detected eQTLs. Likewise, it explains the imbalance between highly heritable genes and eQTLs in aging worms.

  Chapter 6 discusses the main conclusion of this thesis in the context of the robustness theory. Robustness in biological systems provides the potential to survive severe environmental and genetic perturbations in the form of cryptic genetic variation. The variation we observed in gene transcripts due to external and internal perturbations not always translated to physiological phenotypic variation. In some cases however, the mechanisms underlying phenotypic robustness failed and phenotypic variation was observed. Such genetic cryptic variation was revealed as new molecular and physiological phenotypes.

  

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Bakker, Jaap, Promotor
  • Kammenga, Jan, Co-promotor
Award date4 Mar 2011
Place of Publication[S.l.]
Publisher
Print ISBNs9789085858386
Publication statusPublished - 2011

Fingerprint

Caenorhabditis elegans
gene expression
pesticides
genes
quantitative trait loci
toxic substances
genotype
Nematoda
phenotypic variation
phenotype
temperature
heritability
Rhabditidae
toxicity
organophosphorus pesticides
loci
genotype-environment interaction
transgressive segregation
organisms
quantitative genetics

Keywords

  • caenorhabditis elegans
  • gene expression
  • stress factors
  • genetic analysis
  • transcription
  • quantitative trait loci
  • genotypes
  • phenotypes
  • genomics
  • polygenic inheritance

Cite this

Viñuela Rodriguez, A.. / The genetic architecture of gene expression in Caenorhabditis elegans. [S.l.] : S.n., 2011. 119 p.
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title = "The genetic architecture of gene expression in Caenorhabditis elegans",
abstract = "Most organisms are exposed to a continuously changing environment throughout their life. For instance the ambient temperature is usually not constant and many species are exposed to a diverse range of anthropogenic stressors like toxic compounds. Moreover, individuals are prone to genetic changes due to mutation and allelic recombinations. All these factors might affect particular phenotypes, while others remain unchanged. This thesis provides insight into how phenotypic traits are affected by external stress factors and allelic recombinations in the nematode Caenorhabditis elegans (Nematoda; Rhabditidae).  Because phenotypes and their variation may be explained by variation in gene expression, this thesis explored the architecture of gene expression and some of the elements that contribute to gene expression.  Chapters 2 and 3 focus on environmental stressors with i) a specific target (two organophosphorus pesticides) and ii) a non-target mode of action (temperature) to study their influence on gene expression. A single genotype, the canonical wild type strain Bristol (N2) was used to study the effect of interacting pesticides by exposing nematodes to a toxicant mixture at two different temperatures Analysis revealed common transcriptional responses related to detoxification, stress, innate immunity, and transport of lipids to all treatments. It was found that for both pesticides these similar processes were regulated by different gene transcripts in single and combined treatments. These results also showed that the effect of a mix of low doses of pesticides is not a summed effect of the single components. Moreover, increased temperature elevates the toxic consequences to the pesticides exposures. This toxicity gain is attributed to an elevated uptake and accumulation of the toxicants in the organisms. These results support the idea that the observed higher toxicity of pesticides with temperature might be a consequence of gene-environment interactions affecting detoxification genes. Together, thefirst part of this thesis illustrates the intense crosstalk between gene pathways in response to interacting environmental stressors in C. elegans.  The second part of the thesis elaborates on the influence of different genotypes as multiple perturbations on gene expression. How the genotype-phenotype relationship progresses with age was investigated using a quantitative genetics approach (genetical genomics). We performed a genetic mapping strategy of gene transcription variation (expression-QTL, eQTL) to explore the dynamics of regulatory loci affecting genome-wide gene expression at three different ages. We used a recombinant inbred line (RIL) population generated from a cross between the C. elegans strain N2 and the wild type CB4856 in Chapter 4. Also, we investigated the influence of age to reveal a genotype-by-age effect (gxaeQTL) on gene expression. The total number of detected eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms the number of genes with increased variation (1772) was nearly 5 times higher than the number of genes with a decreased expression variation (373). Furthermore, the number of cis-acting eQTL in juveniles decreased by almost 50{\%} in old worms whereas the number of trans-acting loci decreased by ~27{\%}, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network integrity declines with age. To better understand the changes in the gene network with age, gene expression profiles of N2 and CB4856 were generated for Chapter 5. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in different genotypes. The average broad sense heritability was similar in developing and aging worms; but the gene expression variance that can be attributed to genetic variance in each gene changes with age. It can be proposed that regulation became more polygenic in aging worms. These changes explain the decrease in detected eQTLs. Likewise, it explains the imbalance between highly heritable genes and eQTLs in aging worms.   Chapter 6 discusses the main conclusion of this thesis in the context of the robustness theory. Robustness in biological systems provides the potential to survive severe environmental and genetic perturbations in the form of cryptic genetic variation. The variation we observed in gene transcripts due to external and internal perturbations not always translated to physiological phenotypic variation. In some cases however, the mechanisms underlying phenotypic robustness failed and phenotypic variation was observed. 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Viñuela Rodriguez, A 2011, 'The genetic architecture of gene expression in Caenorhabditis elegans', Doctor of Philosophy, Wageningen University, [S.l.].

The genetic architecture of gene expression in Caenorhabditis elegans. / Viñuela Rodriguez, A.

[S.l.] : S.n., 2011. 119 p.

Research output: Thesisinternal PhD, WU

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T1 - The genetic architecture of gene expression in Caenorhabditis elegans

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N1 - WU thesis 4983

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N2 - Most organisms are exposed to a continuously changing environment throughout their life. For instance the ambient temperature is usually not constant and many species are exposed to a diverse range of anthropogenic stressors like toxic compounds. Moreover, individuals are prone to genetic changes due to mutation and allelic recombinations. All these factors might affect particular phenotypes, while others remain unchanged. This thesis provides insight into how phenotypic traits are affected by external stress factors and allelic recombinations in the nematode Caenorhabditis elegans (Nematoda; Rhabditidae).  Because phenotypes and their variation may be explained by variation in gene expression, this thesis explored the architecture of gene expression and some of the elements that contribute to gene expression.  Chapters 2 and 3 focus on environmental stressors with i) a specific target (two organophosphorus pesticides) and ii) a non-target mode of action (temperature) to study their influence on gene expression. A single genotype, the canonical wild type strain Bristol (N2) was used to study the effect of interacting pesticides by exposing nematodes to a toxicant mixture at two different temperatures Analysis revealed common transcriptional responses related to detoxification, stress, innate immunity, and transport of lipids to all treatments. It was found that for both pesticides these similar processes were regulated by different gene transcripts in single and combined treatments. These results also showed that the effect of a mix of low doses of pesticides is not a summed effect of the single components. Moreover, increased temperature elevates the toxic consequences to the pesticides exposures. This toxicity gain is attributed to an elevated uptake and accumulation of the toxicants in the organisms. These results support the idea that the observed higher toxicity of pesticides with temperature might be a consequence of gene-environment interactions affecting detoxification genes. Together, thefirst part of this thesis illustrates the intense crosstalk between gene pathways in response to interacting environmental stressors in C. elegans.  The second part of the thesis elaborates on the influence of different genotypes as multiple perturbations on gene expression. How the genotype-phenotype relationship progresses with age was investigated using a quantitative genetics approach (genetical genomics). We performed a genetic mapping strategy of gene transcription variation (expression-QTL, eQTL) to explore the dynamics of regulatory loci affecting genome-wide gene expression at three different ages. We used a recombinant inbred line (RIL) population generated from a cross between the C. elegans strain N2 and the wild type CB4856 in Chapter 4. Also, we investigated the influence of age to reveal a genotype-by-age effect (gxaeQTL) on gene expression. The total number of detected eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms the number of genes with increased variation (1772) was nearly 5 times higher than the number of genes with a decreased expression variation (373). Furthermore, the number of cis-acting eQTL in juveniles decreased by almost 50% in old worms whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network integrity declines with age. To better understand the changes in the gene network with age, gene expression profiles of N2 and CB4856 were generated for Chapter 5. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in different genotypes. The average broad sense heritability was similar in developing and aging worms; but the gene expression variance that can be attributed to genetic variance in each gene changes with age. It can be proposed that regulation became more polygenic in aging worms. These changes explain the decrease in detected eQTLs. Likewise, it explains the imbalance between highly heritable genes and eQTLs in aging worms.   Chapter 6 discusses the main conclusion of this thesis in the context of the robustness theory. Robustness in biological systems provides the potential to survive severe environmental and genetic perturbations in the form of cryptic genetic variation. The variation we observed in gene transcripts due to external and internal perturbations not always translated to physiological phenotypic variation. In some cases however, the mechanisms underlying phenotypic robustness failed and phenotypic variation was observed. Such genetic cryptic variation was revealed as new molecular and physiological phenotypes.   

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This thesis provides insight into how phenotypic traits are affected by external stress factors and allelic recombinations in the nematode Caenorhabditis elegans (Nematoda; Rhabditidae).  Because phenotypes and their variation may be explained by variation in gene expression, this thesis explored the architecture of gene expression and some of the elements that contribute to gene expression.  Chapters 2 and 3 focus on environmental stressors with i) a specific target (two organophosphorus pesticides) and ii) a non-target mode of action (temperature) to study their influence on gene expression. A single genotype, the canonical wild type strain Bristol (N2) was used to study the effect of interacting pesticides by exposing nematodes to a toxicant mixture at two different temperatures Analysis revealed common transcriptional responses related to detoxification, stress, innate immunity, and transport of lipids to all treatments. It was found that for both pesticides these similar processes were regulated by different gene transcripts in single and combined treatments. These results also showed that the effect of a mix of low doses of pesticides is not a summed effect of the single components. Moreover, increased temperature elevates the toxic consequences to the pesticides exposures. This toxicity gain is attributed to an elevated uptake and accumulation of the toxicants in the organisms. These results support the idea that the observed higher toxicity of pesticides with temperature might be a consequence of gene-environment interactions affecting detoxification genes. Together, thefirst part of this thesis illustrates the intense crosstalk between gene pathways in response to interacting environmental stressors in C. elegans.  The second part of the thesis elaborates on the influence of different genotypes as multiple perturbations on gene expression. How the genotype-phenotype relationship progresses with age was investigated using a quantitative genetics approach (genetical genomics). We performed a genetic mapping strategy of gene transcription variation (expression-QTL, eQTL) to explore the dynamics of regulatory loci affecting genome-wide gene expression at three different ages. We used a recombinant inbred line (RIL) population generated from a cross between the C. elegans strain N2 and the wild type CB4856 in Chapter 4. Also, we investigated the influence of age to reveal a genotype-by-age effect (gxaeQTL) on gene expression. The total number of detected eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms the number of genes with increased variation (1772) was nearly 5 times higher than the number of genes with a decreased expression variation (373). Furthermore, the number of cis-acting eQTL in juveniles decreased by almost 50% in old worms whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network integrity declines with age. To better understand the changes in the gene network with age, gene expression profiles of N2 and CB4856 were generated for Chapter 5. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in different genotypes. The average broad sense heritability was similar in developing and aging worms; but the gene expression variance that can be attributed to genetic variance in each gene changes with age. It can be proposed that regulation became more polygenic in aging worms. These changes explain the decrease in detected eQTLs. Likewise, it explains the imbalance between highly heritable genes and eQTLs in aging worms.   Chapter 6 discusses the main conclusion of this thesis in the context of the robustness theory. Robustness in biological systems provides the potential to survive severe environmental and genetic perturbations in the form of cryptic genetic variation. The variation we observed in gene transcripts due to external and internal perturbations not always translated to physiological phenotypic variation. In some cases however, the mechanisms underlying phenotypic robustness failed and phenotypic variation was observed. Such genetic cryptic variation was revealed as new molecular and physiological phenotypes.   

KW - caenorhabditis elegans

KW - genexpressie

KW - stressfactoren

KW - genetische analyse

KW - transcriptie

KW - loci voor kwantitatief kenmerk

KW - genotypen

KW - fenotypen

KW - genexpressieanalyse

KW - polygene overerving

KW - caenorhabditis elegans

KW - gene expression

KW - stress factors

KW - genetic analysis

KW - transcription

KW - quantitative trait loci

KW - genotypes

KW - phenotypes

KW - genomics

KW - polygenic inheritance

M3 - internal PhD, WU

SN - 9789085858386

PB - S.n.

CY - [S.l.]

ER -

Viñuela Rodriguez A. The genetic architecture of gene expression in Caenorhabditis elegans. [S.l.]: S.n., 2011. 119 p.