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Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum

Overview of attention for article published in BMC Genomics, April 2015
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Title
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum
Published in
BMC Genomics, April 2015
DOI 10.1186/s12864-015-1491-7
Pubmed ID
Authors

Rafael David Rosengarten, Balaji Santhanam, Danny Fuller, Mariko Katoh-Kurasawa, William F Loomis, Blaz Zupan, Gad Shaulsky

Abstract

Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under both developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods. Here, we combine the superior depth and specificity of RNA-seq-based analysis of mRNA abundance with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large shifts. For each time point we treated the entire transcriptome as single phenotype, and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represented gradual changes in mRNA abundance, or molecular phenotype, and the gaps represented times during which many genes are differentially expressed rapidly, and thus the phenotype changes dramatically. Comparing developmental experiments revealed that gene expression in filter developed cells lagged behind those treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. Our analysis also demonstrated a high level of synchrony among the developing structures throughout development. Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and among multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for studies of developmental gene expression.

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Mendeley readers

The data shown below were compiled from readership statistics for 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Portugal 1 3%
Unknown 31 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 11 34%
Student > Bachelor 6 19%
Student > Master 4 13%
Professor 3 9%
Student > Doctoral Student 3 9%
Other 5 16%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 14 44%
Agricultural and Biological Sciences 12 38%
Medicine and Dentistry 2 6%
Unspecified 2 6%
Computer Science 1 3%
Other 1 3%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 20 April 2015.
All research outputs
#9,880,895
of 12,378,406 outputs
Outputs from BMC Genomics
#5,640
of 7,251 outputs
Outputs of similar age
#158,640
of 227,834 outputs
Outputs of similar age from BMC Genomics
#181
of 199 outputs
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