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Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

ABSTRACT: Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

PROVIDER: PRJNA527284 | ENA |

REPOSITORIES: ENA

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Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

Project description:Background: The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum. Hypotheses to explain this hourglass pattern have focused on purifying the selection of gene regulation. Here, we propose an alternative-genes are regulated in different ways at different stages and have different intrinsic capacities to respond to perturbations on gene expression. Results: To eliminate the influence of natural selection, we quantified the expression variability of isogenetic single embryo transcriptomes throughout fly Drosophila melanogaster embryogenesis. We found that the expression variability is lower at the phylotypic stage, supporting that the underlying regulatory architecture in this stage is more robust to stochastic variation on gene expression. We present evidence that the phylotypic stage is also robust to genetic variations on gene expression. Moreover, chromatin regulation appears to play a key role in the variation and evolution of gene expression. Conclusions: We suggest that a phylum-level pattern of embryonic conservation can be explained by the intrinsic difference of gene regulatory mechanisms in different stages.

2019-12-31 | GSE128370 | GEO

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo.

Project description: Not available

| S-EPMC7502200 | biostudies-literature

Measurement of inter-individual variability in gene expression in mouse neutrophils

Project description:We extracted RNA from C57BL/6 mouse neutrophils to measure inter-individual variability in gene expression. 5 of the 10 blood samples were analyzed separately, the other 5 were pooled then split into 5 technical replicates to measure technical variability. We could then measure inter-individual variability in gene expression and compare it to the amplitude of miRNA-guided repression by miR-223.

2016-09-21 | GSE59549 | GEO

Widespread inter-individual gene expression variability in Arabidopsis thaliana

Project description:A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability over a 24 hours time-course between individual Arabidopsis thaliana plants growing in stable conditions. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene size, the number of transcription factors regulating a gene and the chromatin environment. These results will bring a new light into the impact of transcriptional variability in gene expression regulation in plants.

2018-12-06 | GSE115583 | GEO

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

2023-06-08 | GSE209815 | GEO

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [ATAC-seq]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

2023-06-08 | GSE209810 | GEO

Widespread inter-individual gene expression variability in Arabidopsis thaliana

Project description:Widespread inter-individual gene expression variability in Arabidopsis thaliana

| PRJNA475542 | ENA

Individual variability of protein expression in human tissues

Project description:A retrospective analysis of proteomics data from nine different human tissues, to understand the inter-individual and inter-tissue variability in protein expression. We used the data to build robust classifiers to predict the tissue of origin.

2018-10-22 | PXD010271 | Pride

Inter-layer and inter-subject variability of circadian gene expression in human skin

Project description:This work reports 24 h gene expression rhythms in two skin layers, epidermis and dermis, in a cohort of young, healthy adults, who maintained natural, regular sleep-wake schedules. 10% of the expressed genes showed such diurnal rhythms at the population level, of which only a third differed between the two layers. Amplitude and phases of diurnal gene expression varied more across subjects than layers, with amplitude being more variable than phases. Expression amplitudes in the epidermis were larger and more subject-variable, while they were smaller and more consistent in the dermis. Core clock gene expression was similar across layers at the population-level, but were heterogeneous in their variability across subjects. This work provides a valuable resource to advance our understanding of human skin and presents a novel methodology to quantify sources of variability in human circadian rhythms.

2022-12-12 | GSE205155 | GEO

Autophagy-Mediated Degradation of Integumentary Tapetum Is Critical for Embryo Pattern Formation

Project description:To investigate molecular links and underlying mechanisms between autophagy in the integumentary tapetum and embryo pattern formation, we isolated embryos from wild-type plants, atg5 mutants, and atg5 mutants expressing proTPE8:ATG5-GFP for RNA-sequencing.

2024-02-20 | GSE248624 | GEO

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