Primate transcript and protein expression levels evolve under compensatory selection pressures
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD000419
PROVIDER: PRJNA214703 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR949563.fastq.gz | Fastqsanger.gz | |||
| SRR949564.fastq.gz | Fastqsanger.gz | |||
| SRR949565.fastq.gz | Fastqsanger.gz | |||
| SRR949566.fastq.gz | Fastqsanger.gz | |||
| SRR949567.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 32 |
Similar Datasets
Project description:Variation in gene regulation is thought to have played an important role in the evolution of primates, and many studies have documented differences in mRNA expression levels across primate species. However, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are more directly tied to phenotypic differences. To address this question, we used high-resolution, quantitative mass spectrometry to collect thousands of protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines (LCLs). We also used RNA sequencing to collect transcript expression data from the same samples. Considering the two datasets jointly we found that there is much more inter-species divergence at the mRNA level than at the protein level. Remarkably, we found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest a much stronger evolutionary constraint on protein expression levels than on mRNA levels. We conclude that inter-species mRNA expression differences may often have limited functional consequences due to either buffering or compensatory changes in post-transcriptional or posttranslational regulation of proteins.
2013-10-17 | GSE49682 | GEO
Project description:Variation in gene regulation is thought to have played an important role in the evolution of primates, and many studies have documented differences in mRNA expression levels across primate species. However, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are more directly tied to phenotypic differences. To address this question, we used high-resolution, quantitative mass spectrometry to collect thousands of protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines (LCLs). We also used RNA sequencing to collect transcript expression data from the same samples. Considering the two datasets jointly we found that there is much more inter-species divergence at the mRNA level than at the protein level. Remarkably, we found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest a much stronger evolutionary constraint on protein expression levels than on mRNA levels. We conclude that inter-species mRNA expression differences may often have limited functional consequences due to either buffering or compensatory changes in post-transcriptional or posttranslational regulation of proteins. Gene expression patterns were compared between human, chimpanzee, and rhesus macaque lymphoblastoid cell lines (5 individuals from each species) using RNA-Seq. These gene expression patterns were also compared to protein expression patterns based on mass-spec data, which are available separately (see publication for details).
2013-10-17 | E-GEOD-49682 | biostudies-arrayexpress
Project description:Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.
| S-EPMC3994702 | biostudies-literature
Project description:Purpose: Next-generation transcriptome sequencing was done to understand host and eukaryotic microbiome changes in gene expression in association with defined insecticide selection pressures. The specific goal of this research was to understand whole-body physiological responses in German cockroaches and associated microbiota, at the metatranscriptome level, to defined insecticide selection pressures. Methods: We used the insecticide indoxacarb as the selecting insecticide, which is an important bait active ingredient for cockroach control. Six generations of selection with indoxacarb bait produced a strain with substantial (>20x) resistance relative to inbred control lines originating from the same parental stock. Results: Metatranscriptome sequencing revealed 1123 significantly differentially expressed genes in > two of three statistical models (81 upregulated and 1042 downregulated; FDR p<0.001; log2FC of +/- 1). The majority of upreglated genes were from the host cockroach while the majority of downregulated genes were from associated viruses and the eukaryotic microbiome. Conclusions: We show here significant impacts by insecticide selection on not only host stress-respnses like detoxification, but also on clearace of microbial parasites, pathogens, commensals and/or symbionts.
2021-12-07 | GSE188950 | GEO
Project description:Transcriptome responses to defined insecticide selection pressures in the German cockroach
| PRJNA780882 | ENA
Project description:Adaptation to ecological pressures in Mayflies
| PRJEB60788 | ENA
Project description:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
2012-08-02 | GSE38572 | GEO
Project description:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
2012-08-01 | GSE33960 | GEO
Project description:Cuticular hydrocarbons (CHCs) cover the cuticles of virtually all insects, serving as a waterproofing agent and as a communication signal. The causes for the high CHC variation between species, and the factors influencing CHC profiles, are scarcely understood. Here, we compare CHC profiles of ant species from seven biogeographic regions, searching for physiological constraints and for climatic and biotic selection pressures. Molecule length constrained CHC composition: long-chain profiles contained fewer linear alkanes, but more hydrocarbons with disruptive features in the molecule. This is probably owing to selection on the physiology to build a semi-fluid cuticular layer, which is necessary for waterproofing and communication. CHC composition also depended on the precipitation in the ants' habitats. Species from wet climates had more alkenes and fewer dimethyl alkanes than those from drier habitats, which can be explained by different waterproofing capacities of these compounds. By contrast, temperature did not affect CHC composition. Mutualistically associated (parabiotic) species possessed profiles highly distinct from non-associated species. Our study is, to our knowledge, the first to show systematic impacts of physiological, climatic and biotic factors on quantitative CHC composition across a global, multi-species dataset. We demonstrate how they jointly shape CHC profiles, and advance our understanding of the evolution of this complex functional trait in insects.
| S-EPMC5360911 | biostudies-literature