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On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero]

ABSTRACT: A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs expressed over time during embryogenesis. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most proteins change very little and duplicated genes are expressed similarly. While the correlation between mRNA levels and protein expression is poor, a mass action kinetics model parametrized by the protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides a rich resource for developmental biologists, unveiling detailed data for absolute levels of ~10K proteins and ~28K transcripts via convenient web portal. It underscores the lasting impact of maternal dowry, finds surprisingly few cases where degradation alone drives a change in protein level, and highlights the importance of transcription in shaping the proteome.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE73904 | GEO | 2015/11/06

SECONDARY ACCESSION(S): PRJNA298393

REPOSITORIES: GEO

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On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA]

Project description:A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs expressed over time during embryogenesis. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most proteins change very little and duplicated genes are expressed similarly. While the correlation between mRNA levels and protein expression is poor, a mass action kinetics model parametrized by the protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides a rich resource for developmental biologists, unveiling detailed data for absolute levels of ~10K proteins and ~28K transcripts via convenient web portal. It underscores the lasting impact of maternal dowry, finds surprisingly few cases where degradation alone drives a change in protein level, and highlights the importance of transcription in shaping the proteome.

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On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA]

2015-11-06 | E-GEOD-73870 | biostudies-arrayexpress

On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero]

2015-11-06 | E-GEOD-73904 | biostudies-arrayexpress

Dynamic profiling of the protein life cycle in response to pathogens (protein)

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Dynamic profiling of the protein life cycle in response to pathogens (RNA-seq)

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On the relationship of protein and mRNA dynamics in vertebrate embryonic development

Project description:How the fertilized egg develops the anatomy of an adult ultimately must be explained at the biochemical level. Deeply connected to the anatomy is the complement of proteins and RNAs expressed during embryogenesis. The relationship of mRNA and respective protein expression dynamics during development has never been systematically explored. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus, between unfertilized egg and early tadpole stage. Surprisingly, most proteins change very little; there is an inverse correlation between abundance and rate of change. While the correlation of mRNA and protein expression is poor, a simple mass action kinetics model connects protein to RNA. Parameterized by two fixed parameters the median protein synthesis and degradation rates, the model depends on RNA dynamics, and initial protein concentration. Associated mRNA datasets in GEO: GSE73905 and GSE73870.

2015-10-20 | PXD002349 | Pride

Dynamic profiling of the protein life cycle in response to pathogens (protein)

Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

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