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Status |
Public on Apr 21, 2015 |
Title |
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum |
Organism |
Dictyostelium discoideum |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
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 fully integrated 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 these 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 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 changes. Considering the whole transcriptome as a single phenotype, we treated each time point as an independent entity and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represent gradual changes in mRNA abundance and the gaps represent times during which many genes are differentially expressed rapidly. Comparing development on solid substrate to development in suspension revealed that gene expression in filter developed cells lagged behind cells 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 showed that the transition to multicellularity at the mound stage coincided with rapid accumulation of transcripts associated with mitosis and DNA replicative processes. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. We observed multiple instances of enrichment of oxidation-reduction and reactive oxygen related terms. Our analysis also demonstrated a high level of synchrony between 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 between 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 future studies of developmental gene expression.
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Overall design |
Dictyosteloium discoideum gene expression (mRNA) profiles from two experimental time courses: development on filters and cAMP signaling in suspension. Filter development consists of 2 replicates of 19 time point samples, while cAMP in suspension contains 3 replicates of 10, 10 and 9 samples each.
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Contributor(s) |
Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G |
Citation(s) |
25887420 |
Submission date |
Sep 30, 2014 |
Last update date |
Mar 09, 2021 |
Contact name |
Gad Shaulsky |
E-mail(s) |
gadi@bcm.edu
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Organization name |
Baylor College of Medicine
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Department |
Molecular and Human Genetics
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Street address |
One Baylor Plaza
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platforms (1) |
GPL9379 |
Illumina Genome Analyzer II (Dictyostelium discoideum) |
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Samples (67)
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GSM1517221 |
Filter development, replicate 1, hour 00 |
GSM1517222 |
Filter development, replicate 1, hour 01 |
GSM1517223 |
Filter development, replicate 1, hour 02 |
GSM1517224 |
Filter development, replicate 1, hour 03 |
GSM1517225 |
Filter development, replicate 1, hour 04 |
GSM1517226 |
Filter development, replicate 1, hour 05 |
GSM1517227 |
Filter development, replicate 1, hour 06 |
GSM1517228 |
Filter development, replicate 1, hour 07 |
GSM1517229 |
Filter development, replicate 1, hour 08 |
GSM1517230 |
Filter development, replicate 1, hour 09 |
GSM1517231 |
Filter development, replicate 1, hour 10 |
GSM1517232 |
Filter development, replicate 1, hour 11 |
GSM1517233 |
Filter development, replicate 1, hour 12 |
GSM1517234 |
Filter development, replicate 1, hour 14 |
GSM1517235 |
Filter development, replicate 1, hour 16 |
GSM1517236 |
Filter development, replicate 1, hour 18 |
GSM1517237 |
Filter development, replicate 1, hour 20 |
GSM1517238 |
Filter development, replicate 1, hour 22 |
GSM1517239 |
Filter development, replicate 1, hour 24 |
GSM1517240 |
Filter development, replicate 2, hour 00 |
GSM1517241 |
Filter development, replicate 2, hour 01 |
GSM1517242 |
Filter development, replicate 2, hour 02 |
GSM1517243 |
Filter development, replicate 2, hour 03 |
GSM1517244 |
Filter development, replicate 2, hour 04 |
GSM1517245 |
Filter development, replicate 2, hour 05 |
GSM1517246 |
Filter development, replicate 2, hour 06 |
GSM1517247 |
Filter development, replicate 2, hour 07 |
GSM1517248 |
Filter development, replicate 2, hour 08 |
GSM1517249 |
Filter development, replicate 2, hour 09 |
GSM1517250 |
Filter development, replicate 2, hour 10 |
GSM1517251 |
Filter development, replicate 2, hour 11 |
GSM1517252 |
Filter development, replicate 2, hour 12 |
GSM1517253 |
Filter development, replicate 2, hour 14 |
GSM1517254 |
Filter development, replicate 2, hour 16 |
GSM1517255 |
Filter development, replicate 2, hour 18 |
GSM1517256 |
Filter development, replicate 2, hour 20 |
GSM1517257 |
Filter development, replicate 2, hour 22 |
GSM1517258 |
Filter development, replicate 2, hour 24 |
GSM1517259 |
Pulsatile cAMP in suspension, replicate 1, hour 00 |
GSM1517260 |
Pulsatile cAMP in suspension, replicate 1, hour 01 |
GSM1517261 |
Pulsatile cAMP in suspension, replicate 1, hour 02 |
GSM1517262 |
Pulsatile cAMP in suspension, replicate 1, hour 03 |
GSM1517263 |
Pulsatile cAMP in suspension, replicate 1, hour 04 |
GSM1517264 |
Pulsatile cAMP in suspension, replicate 1, hour 05 |
GSM1517265 |
Pulsatile cAMP in suspension, replicate 1, hour 06 |
GSM1517266 |
Pulsatile cAMP in suspension, replicate 1, hour 08 |
GSM1517267 |
Pulsatile cAMP in suspension, replicate 1, hour 10 |
GSM1517268 |
Pulsatile cAMP in suspension, replicate 1, hour 12 |
GSM1517269 |
Pulsatile cAMP in suspension, replicate 2, hour 00 |
GSM1517270 |
Pulsatile cAMP in suspension, replicate 2, hour 01 |
GSM1517271 |
Pulsatile cAMP in suspension, replicate 2, hour 02 |
GSM1517272 |
Pulsatile cAMP in suspension, replicate 2, hour 03 |
GSM1517273 |
Pulsatile cAMP in suspension, replicate 2, hour 04 |
GSM1517274 |
Pulsatile cAMP in suspension, replicate 2, hour 05 |
GSM1517275 |
Pulsatile cAMP in suspension, replicate 2, hour 06 |
GSM1517276 |
Pulsatile cAMP in suspension, replicate 2, hour 08 |
GSM1517277 |
Pulsatile cAMP in suspension, replicate 2, hour 10 |
GSM1517278 |
Pulsatile cAMP in suspension, replicate 2, hour 12 |
GSM1517279 |
Pulsatile cAMP in suspension, replicate 3, hour 00 |
GSM1517280 |
Pulsatile cAMP in suspension, replicate 3, hour 01 |
GSM1517281 |
Pulsatile cAMP in suspension, replicate 3, hour 02 |
GSM1517282 |
Pulsatile cAMP in suspension, replicate 3, hour 03 |
GSM1517283 |
Pulsatile cAMP in suspension, replicate 3, hour 04 |
GSM1517284 |
Pulsatile cAMP in suspension, replicate 3, hour 05 |
GSM1517285 |
Pulsatile cAMP in suspension, replicate 3, hour 06 |
GSM1517286 |
Pulsatile cAMP in suspension, replicate 3, hour 08 |
GSM1517287 |
Pulsatile cAMP in suspension, replicate 3, hour 10 |
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Relations |
BioProject |
PRJNA262669 |
SRA |
SRP048533 |
Supplementary file |
Size |
Download |
File type/resource |
GSE61914_RAW.tar |
9.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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