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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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			Action	DRS
	SRR8734410.fastq.gz	Fastqsanger.gz
	SRR8734420.fastq.gz	Fastqsanger.gz
	SRR8734430.fastq.gz	Fastqsanger.gz
	SRR8734440.fastq.gz	Fastqsanger.gz
	SRR8734450.fastq.gz	Fastqsanger.gz

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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:BackgroundThe 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.ResultsTo 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.ConclusionsWe suggest that a phylum-level pattern of embryonic conservation can be explained by the intrinsic difference of gene regulatory mechanisms in different stages.

| S-EPMC7502200 | biostudies-literature

[E-MTAB-366] Transcription profiling by array of chicken embryos at 15 different stages

2011-04-05 | GSE28388 | GEO

[E-MTAB-368] Transcription profiling by array of mouse embryos at 8 different stages

Project description:Transcription profiling of mouse development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

2011-04-05 | GSE28389 | GEO

[E-MTAB-369] Transcription profiling by array of Xenopus laevis embryos at 15 different stages

Project description:Transcription profiling of X.laevis development. The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

2011-04-05 | GSE28390 | GEO

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

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

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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

Transcription profiling by array of chicken embryos at 15 different stages

Project description:The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to A-AFFY-103 Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.

2011-08-01 | E-MTAB-366 | biostudies-arrayexpress

[E-MTAB-366] Transcription profiling by array of chicken embryos at 15 different stages

Project description:Transcription profiling of chicken development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to the Affymetrix Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.

2011-04-05 | E-GEOD-28388 | biostudies-arrayexpress

Transcription profiling by array of mouse embryos at 8 different stages

Project description:The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type C57BL/6 mice, whole embryos at 8 different stages (Stages:E7.5, E8.5, E9.5, E10.5, E12.5, E14.5, E16.5, E18.5), and hybridized to A-AFFY-45 Mouse Genome 430 2.0 Array. All the stages contains data from 2 to 3 biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.

2011-08-01 | E-MTAB-368 | biostudies-arrayexpress

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