Limits...
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G - BMC Genomics (2015)

Bottom Line: 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.Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. rosengar@bcm.edu.

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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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Related in: MedlinePlus

Temporal resolution affects the interpretation of transcription profiles. The standardized mRNA abundance of four developmentally regulated genes (y-axis) is plotted versus time (hours, x-axis). Data are from the filter development experiment. For each gene—gtaC(A), csaA(B), cotB(C), and ecmB(D)—expression values are included for time points at 1-, 2- and 4-hour intervals, as indicated in the legend below the figure. Each data point represents the average of 2 independent biological replicates. The y-axis scale varies between plots. The insets in (C) and (D) highlight the 8 h – 12 h time frame.
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Fig2: Temporal resolution affects the interpretation of transcription profiles. The standardized mRNA abundance of four developmentally regulated genes (y-axis) is plotted versus time (hours, x-axis). Data are from the filter development experiment. For each gene—gtaC(A), csaA(B), cotB(C), and ecmB(D)—expression values are included for time points at 1-, 2- and 4-hour intervals, as indicated in the legend below the figure. Each data point represents the average of 2 independent biological replicates. The y-axis scale varies between plots. The insets in (C) and (D) highlight the 8 h – 12 h time frame.

Mentions: The master transcriptional regulator gtaC, and several of its putative target genes involved in aggregation (such as the cell-cell adhesion gene csaA), looked markedly different at different time scales (Figures 2A, B). The shape of the expression curve, as well as amplitude and timing of peak expression, varied between 1-hour and 4-hour sampling. However, 2-hour sampling was nearly identical to the 1-hour curve, suggesting that 2-hour intervals are sufficiently frequent to accurately describe population-level changes in mRNA abundance.Figure 2


Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G - BMC Genomics (2015)

Temporal resolution affects the interpretation of transcription profiles. The standardized mRNA abundance of four developmentally regulated genes (y-axis) is plotted versus time (hours, x-axis). Data are from the filter development experiment. For each gene—gtaC(A), csaA(B), cotB(C), and ecmB(D)—expression values are included for time points at 1-, 2- and 4-hour intervals, as indicated in the legend below the figure. Each data point represents the average of 2 independent biological replicates. The y-axis scale varies between plots. The insets in (C) and (D) highlight the 8 h – 12 h time frame.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4403905&req=5

Fig2: Temporal resolution affects the interpretation of transcription profiles. The standardized mRNA abundance of four developmentally regulated genes (y-axis) is plotted versus time (hours, x-axis). Data are from the filter development experiment. For each gene—gtaC(A), csaA(B), cotB(C), and ecmB(D)—expression values are included for time points at 1-, 2- and 4-hour intervals, as indicated in the legend below the figure. Each data point represents the average of 2 independent biological replicates. The y-axis scale varies between plots. The insets in (C) and (D) highlight the 8 h – 12 h time frame.
Mentions: The master transcriptional regulator gtaC, and several of its putative target genes involved in aggregation (such as the cell-cell adhesion gene csaA), looked markedly different at different time scales (Figures 2A, B). The shape of the expression curve, as well as amplitude and timing of peak expression, varied between 1-hour and 4-hour sampling. However, 2-hour sampling was nearly identical to the 1-hour curve, suggesting that 2-hour intervals are sufficiently frequent to accurately describe population-level changes in mRNA abundance.Figure 2

Bottom Line: 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.Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. rosengar@bcm.edu.

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

Show MeSH
Related in: MedlinePlus