Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
[Preprint]. 2024 Aug 26:2024.08.15.608164.
doi: 10.1101/2024.08.15.608164.

Robustness and variability in Caenorhabditis elegans dauer gene expression

Johnny Cruz Corchado  1 , Abhishiktha Godthi  1 , Kavinila Selvarasu  1 , Veena Prahlad  1
Affiliations

Robustness and variability in Caenorhabditis elegans dauer gene expression

Johnny Cruz Corchado et al. bioRxiv. .

Abstract

Both plasticity and robustness are pervasive features of developmental programs. The dauer in Caenorhabditis elegans is an arrested, hypometabolic alternative to the third larval stage of the nematode. Dauers undergo dramatic tissue remodeling and extensive physiological, metabolic, behavioral, and gene expression changes compared to conspecifics that continue development and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. Therefore, dauer induction is an example of phenotypic plasticity. However, whether gene expression in dauer larvae induced to arrest development by different genetic or environmental triggers is invariant or varies depending on their route into dauer has not been examined. By using RNA-sequencing to characterize gene expression in different types of dauer larvae and computing the variance and concordance within Gene Ontologies (GO) and gene expression networks, we find that the expression patterns within most pathways are strongly correlated between dauer larvae, suggestive of transcriptional robustness. However, gene expression within specific defense pathways, pathways regulating some morphological traits, and several metabolic pathways differ between the dauer larvae. We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in adaptation, allowing the dauers induced by different stimuli to survive in and exploit different niches.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.. Experimental design.
A, B. Models for phenotypic plasticity (A) and phenotypic robustness (B). C. Schematic of experimental design: RNA sequencing (RNA-seq) of high temperature-induced wild-type dauers (N2; High Temperature Induced Dauers or wild type HID or WT HID), daf-2 (e1370) III, daf-7(e1372) III and ilc-17.1 (syb5296) X dauers, and dauers that result from overexpressing cep-1 (cep-1oe). Samples were collected as described in the text. Wild-type larvae that were grown for 32 hours post-hatching at 25°C to reach the late L2/early L3 stage were used as comparisons. D. Micrographs of dauer larvae as used for RNA-seq. Scale bar=1 mm. E. Pair-wise distance matrix of RNA-seq samples shows the expected clustering of total RNA of the biological triplicates of each strain [Strains used: wild type (N2) L2/L3, wild type (N2) HID, daf-2 (e1370) III, daf-7(e1372) III and ilc-17.1 (syb5296) X and cep-1 (cep-1oe). F. Principal Component Analysis (PCA) of the three repeats of RNA-seq samples.
Figure 2.
Figure 2.. Dauers induced by different environmental and physiological stimuli utilize similar processes for dauer arrest.
A. Venn Diagram showing overlap between differentially expressed genes (DEGs) in wild-type HID, daf-2, daf-7, ilc-17.1 and cep-1oe dauers compared to wild type L2/L3 larvae. B. Dot plot showing comparison of enrichment between downregulated DEGs in wild-type HID, daf-2, daf-7, ilc-17.1 and cep-1oe dauers compared to wild type L2/L3 larvae. Y axis: GO categories (Biological Processes). Color bar: adjusted p-values (Benjamini-Hochberg corrected, p<0.05), lower p-value in red, higher p-value blue. Circle size: Fold Enrichment (Gene Ratio/Background Ratio). C. Dot plot showing comparison of enrichment between upregulated DEGs in wild type HID, daf-2, daf-7, ilc-17.1 or cep-1oe dauers. Y axis: GO categories (Biological Processes). Color bar: adjusted p-values (Benjamini-Hochberg corrected, p<0.05), lower p-value in red, higher p-value blue. Circle size: Fold Enrichment. D. Dot plot showing enrichment of DEGs unique to wild type HID, daf-2, daf-7, ilc-17.1 or cep-1oe dauers. Y axis: GO categories (Wormbase). Color bar: adjusted p-values (Q.value<0.05), lower p-value in red, higher p-value in blue. Circle size: Fold Enrichment.
Figure 3.
Figure 3.. Dauers display high variability in gene expression levels but strong correlation in gene expression patterns.
A. Density plot of the Coefficient of Variation (CV). X-axis: CVs of all expressed genes (mean expression >10 counts) computed by dividing the standard deviation (SD) across all dauers by its mean expression across all dauers. Dotted lines demarcating CVs: low, (CV < 30), moderate (30 < CV < 50), high (CV > 50). Y-axis (left) density, (right): gene count. B. Scatter plots showing pairwise Spearman correlation between the wild type (N2) HID, daf-2 (e1370) III, daf-7(e1372) III and ilc-17.1 (syb5296) X and cep-1 (cep-1oe). Line represents linear regression. TOP: Dauers that are compared, and Spearman rho values shown. p-value is corrected for multiple tests; Benjamini-Hochberg. C. Heatmap depicting relative gene expression (Log10TPM) as Z-scores across the dauers. The five different clusters were obtained by hierarchical clustering (method: complete, distance: Euclidean) between the genes and applying the elbow method to select the optimal number of clusters. TOP: Cluster number. X-axis: dauers. Y-axis: genes. NOTE: Dauer order on X-axis differs in each cluster. Columns are ordered based on the Hierarchical clustering (method: complete, distance: Euclidean) between the different dauers, as shown in the dendrogram on top of the Heatmap. Green-Black-Red Color bar: Z-scores. D. Dot plot comparison of enrichment between of five clusters identified in B. Y-axis: the GO categories. The color bar shows adjusted p-values (Benjamini-Hochberg corrected, p<0.05), lower p-values in red, and higher p-values in blue. Circle size: Fold Enrichment.
Figure 4.
Figure 4.. Gene expression in the core dauer pathway is robust.
A. Density plot of the Coefficient of Variation (CV) of genes in the core dauer pathway. Labels of the pathway on top. X-axis: CVs of all genes in the pathway computed by dividing the standard deviation (SD) of its expression across all dauers by its mean expression across all dauers. Dotted lines demarcating CVs: low, (CV < 30), moderate (30 < CV < 50), high (CV > 50). Y-axis (left) density. B. Dumbbell Plot showing Spearman’s correlation coefficient (rho) between pairs of dauers in ‘core’ dauer pathways. TOP labels: the pair of dauers compared. Y-axis: pathway. X-axis: rho value and confidence interval (CI): blue dot represents lower CI, yellow dot represents rho value, and red dot represents high CI. p-values, Bonferroni corrected. *p-value <0.05; ns, not-significant.
Figure 5.
Figure 5.. Correlation within GO categories enriched by genes differentially expressed by all dauers shows variation in a small subset of categories.
A. Scatter plot showing summarized GO categories (Biological Process) enriched from 13210 differentially expressed genes (DEGs) common to all dauers [dauers compared to wild type L2/L3 larvae]. Axes are represented by two UMAP components. Distance between points represents similarity between terms. Size of the points: score in the dissimilarity matrix. B. Heatmap depicting Spearman’s correlation coefficient (rho) for pairwise comparisons between all dauers in each GO category enriched, as in A. Colorbar: Black-white: rho >0.6, purple: rho<0.6 or padj Bonferroni corrected >0.05 (indicates low correlation). C. Dumbbell Plot showing Spearman’s correlation coefficient (rho) between ‘common dauer genes’ compared between pairs of dauers and analyzed within GO categories depicted in A. TOP labels: the pair of dauers compared. Y-axis: GO categories that were collapsed in A. X-axis: rho values and confidence interval (CI): blue dot represents lower CI, yellow dot represents rho value, and red dot depicts high CI. p-values, Bonferroni corrected. *p-value <0.05; ns, not-significant.
Figure 6.
Figure 6.. Correlation within categories of co-expressed genes in the C. elegans gene expression map [Kim et al. (2001)] and the iCEL1314 metabolic network [Nanda et al. (2023)] shows that dauers vary in stress and metabolic pathways.
A. Heatmap depicting Spearman’s correlation coefficient (rho) for pairwise comparisons between all dauers in Kim ‘mountains’ from the C. elegans gene expression map [Kim et al (2001)]. Colorbar: Black-white: rho >0.6, purple: rho<0.6 or padj Bonferroni corrected >0.05 (indicates low correlation). B. Dumbbell Plot showing Spearman’s correlation coefficient (rho) between pairs of dauers compared within ‘Kim mountains’. TOP labels: the pair of dauers compared. Y-axis: pathway. X-axis: rho value and confidence interval (CI): blue dot represents lower CI, yellow dot represents rho value, and red dot depicts high CI. p-values, Bonferroni corrected. *p-value <0.05; ns, not-significant. C. Heatmap depicting Spearman’s correlation coefficient (rho) for pairwise comparisons between all dauers within metabolic pathways in the iCEL1314 metabolic network [Nanda et al. (2023)]. Colorbar: Black-white: rho >0.6, purple: rho<0.6 or padj Bonferroni corrected >0.05 (indicates low correlation).
Figure 7.
Figure 7.. Correlation between dauer larvae in metabolic pathway-gene expression reveals broad variation.
A. Dumbbell Plot showing Spearman’s correlation coefficient (rho) between pairs of dauers compared within metabolic pathways identified in the iCEL1314 metabolic network [Nanda et al. (2023)]. TOP labels: the pair of dauers compared. Y-axis: pathway. X-axis: rho value and confidence interval (CI): blue dot represents lower CI, yellow dot represents rho value, and red dot depicts high CI. p-values, Bonferroni corrected. *p-value <0.05; ns, not-significant.
Figure 8.
Figure 8.. Gene expression differences between dauer larvae induced to arrest development by different stimuli.
A limited number of gene expression pathways that regulate specific morphological features, and specific stress, immune, detoxification and metabolic programs vary between the different dauer larvae. These are summarized here.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Wagner G. P. & Zhang J. The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nat Rev Genet 12, 204–213 (2011). 10.1038/nrg2949 - DOI - PubMed
    1. Sommer R. J. Phenotypic Plasticity: From Theory and Genetics to Current and Future Challenges. Genetics 215, 1–13 (2020). 10.1534/genetics.120.303163 - DOI - PMC - PubMed
    1. Felix M. A. & Barkoulas M. Pervasive robustness in biological systems. Nat Rev Genet 16, 483–496 (2015). 10.1038/nrg3949 - DOI - PubMed
    1. Braendle C. & Felix M. A. The other side of phenotypic plasticity: a developmental system that generates an invariant phenotype despite environmental variation. J Biosci 34, 543–551 (2009). 10.1007/s12038-009-0073-8 - DOI - PubMed
    1. Wagner A. Robustness and evolvability: a paradox resolved. Proc Biol Sci 275, 91–100 (2008). 10.1098/rspb.2007.1137 - DOI - PMC - PubMed

Publication types

LinkOut - more resources