Conservation of mRNA and Protein Expression during Development of C. elegans

Grün, Dominic; Kirchner, Marieluise; Thierfelder, Nadine; Stoeckius, Marlon; Selbach, Matthias; Rajewsky, Nikolaus

doi:10.1016/j.celrep.2014.01.001

Cited by 104 publications

(127 citation statements)

References 43 publications

Supporting

Mentioning

107

Contrasting

Order By: Relevance

“…The overall correlations for both protein and mRNA abundances were close to one between the strains. This is consistent with the quantitative comparison of C. elegans and C. briggsae (27), but it is different for C. elegans and D. melanogaster, where the conservation in expression was found only on protein level (26). Thus, in this intraspecies comparison, we observed a strong selective pressure to maintain protein levels, an effect that was also shown for closely (27) and even distantly related species (26).…”

Section: Discussionsupporting

confidence: 78%

“…More than 1,400 proteins were reliably quantified in worm samples using size exclusion chromatography (28), and 3,470 proteins were quantified using LysC digestion followed by hydrophilic interaction liquid chromatography separation of the peptides (29). Between 1,461 and 4,072 proteins were identified in different developmental stages of C. elegans and C. briggsae after separation on SDS gels (27). To quantify less abundant proteins, additional separation methods would be required, as was done for the quantitative comparison of distantly related species (26).…”

Section: Discussionmentioning

confidence: 99%

“…This suggests that protein levels are under evolutionary selection acting post-transcriptionally (26). In a recent interspecies comparison of the two nematodes C. elegans and Caenorhabditis briggsae, the protein and transcript changes were found to be conserved throughout development (27).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans

Kamkina

Snoek

Grossmann

et al. 2016

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

Natural genetic variation is the raw material of evolution and influences disease development and progression. An important question is how this genetic variation translates into variation in protein abundance. To analyze the effects of the genetic background on gene and protein expression in the nematode Caenorhabditis elegans, we quantitatively compared the two genetically highly divergent wild-type strains N2 and CB4856. Gene expression was analyzed by microarray assays, and proteins were quantified using stable isotope labeling by amino acids in cell culture. Among all transcribed genes, we found 1,532 genes to be differentially transcribed between the two wild types. Of the total 3,238 quantified proteins, 129 proteins were significantly differentially expressed between N2 and CB4856. The differentially expressed proteins were enriched for genes that function in insulin-signaling and stress-response pathways, underlining strong divergence of these pathways in nematodes. The protein abundance of the two wild-type strains correlates more strongly than protein abundance versus transcript abundance within each wild type. Our findings indicate that in C. elegans only a fraction of the changes in protein abundance can be explained by the changes in mRNA abundance. These findings corroborate with the observations made across species. Molecular & Cellular Proteomics 15: 10.1074/mcp.M115.052548, 1670-1680, 2016.Natural genetic variation in gene expression shapes the diversity in phenotypic traits and is the raw material for evolutionary processes (1). Variation in gene expression can be very extensive across individuals with different genotypes. The additive effects (narrow-sense heritability) of independent loci on gene expression variation can reach 35% in humans (2). The broad-sense heritable variation in gene expression has been estimated to be up to 70% in the nematode Caenorhabditis elegans (3, 4) and up to 80% in yeast (5). This high heritability and the ability to construct genetically segregating populations facilitate mapping of gene expression regulation and subsequent detection of expression quantitative trait loci (eQTL) 1 (5-11). eQTLs are genomic regions containing a polymorphism associated with variation in transcript abundance between genotypes (12). eQTL analysis provides insight into the underlying genetic architecture of complex traits and is valuable for the identification of pathways and gene networks (10,(13)(14)(15). A key question is whether gene expression variation is translated into variation at the proteome level and whether it affects functionally relevant proteins. Genetic model species provide an ideal platform to explore the relationship between gene expression variation and variation at the proteome level due to their tractability. Although it is well established that there is a correlation between transcript and protein abundances, the relationship between natural variation in gene expression and variation in protein abundance is less well understood. The proteome provides informat...

show abstract

Section: Discussionsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans

Kamkina

Snoek

Grossmann

et al. 2016

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

show abstract

“…22 The DLK-1 promoter (~2 kb upstream from the TSS) contains binding sites for LIN-14, 26 UNC-30 8 and UNC-55, 8 suggesting possible regulation by these transcription factors. DLK-1 transcript levels are globally upregulated from mid L1-L2 stage, 27 and a pulse of DLK-1 at the onset of DD remodeling facilitates new synapse formation. 22 DLK-1 localizes to the perisynaptic region in adult DD neurons, 28 and promotes MT growth and growth cone formation in regenerating axons.…”

Section: The Cellular Changes That Facilitate Dd Remodelingmentioning

confidence: 99%

Neural circuit rewiring: insights from DD synapse remodeling

Kurup

Jin

2015

Worm

View full text Add to dashboard Cite

Nervous systems exhibit many forms of neuronal plasticity during growth, learning and memory consolidation, as well as in response to injury. Such plasticity can occur across entire nervous systems as with the case of insect metamorphosis, in individual classes of neurons, or even at the level of a single neuron. A striking example of neuronal plasticity in C. elegans is the synaptic rewiring of the GABAergic Dorsal D-type motor neurons during larval development, termed DD remodeling. DD remodeling entails multi-step coordination to concurrently eliminate pre-existing synapses and form new synapses on different neurites, without changing the overall morphology of the neuron. This mini-review focuses on recent advances in understanding the cellular and molecular mechanisms driving DD remodeling.

show abstract

“…However, mRNAs are further translated into proteins, which perform the actual cellular functions. It has been shown in multiple species such as Saccharomyces cerevisiae (Griffin et al 2002), Trypanosoma brucei (Butter et al 2013), Caenorhabditis elegans (Grün et al 2014), and human (Schwanhäusser et al 2011), as well as in Drosophila melanogaster (Bonaldi et al 2008), that transcript levels are only a moderate predictor for protein expression as they do not account for post-transcriptional processes such as translational regulation or protein stability (Vogel and Marcotte 2012;Liu et al 2016). Recently, this has also been addressed with a developmental perspective in Caenorhabditis elegans (Grün et al 2014), Xenopus laevis (Peshkin et al 2015), and Trypanosoma brucei (Dejung et al 2016), but not yet in Drosophila.…”

mentioning

confidence: 99%

The developmental proteome of Drosophila melanogaster

et al. 2017

View full text Add to dashboard Cite

Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface.

show abstract

Conservation of mRNA and Protein Expression during Development of C. elegans

Cited by 104 publications

References 43 publications

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans

Neural circuit rewiring: insights from DD synapse remodeling

The developmental proteome of Drosophila melanogaster

Contact Info

Product

Resources

About