title: Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.
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.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. rosengar@bcm.edu.
authors.forename: Rafael David
authors.initials: RD
authors.lastname: Rosengarten
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. santhana@bcm.edu.
authors.forename: Balaji
authors.initials: B
authors.lastname: Santhanam
authors.affiliation: Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. dfuller@ucsd.edu.
authors.forename: Danny
authors.initials: D
authors.lastname: Fuller
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. mkatoh@bcm.edu.
authors.forename: Mariko
authors.initials: M
authors.lastname: Katoh-Kurasawa
authors.affiliation: Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. wloomis@ucsd.edu.
authors.forename: William F
authors.initials: WF
authors.lastname: Loomis
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. blaz.zupan@fri.uni-lj.si.|Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, Ljubljana, SI-1001, Slovenia. blaz.zupan@fri.uni-lj.si.
authors.forename: Blaz
authors.initials: B
authors.lastname: Zupan
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. gadi@bcm.edu.|Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. gadi@bcm.edu.
authors.forename: Gad
authors.initials: G
authors.lastname: Shaulsky
mesh_terms: D000242:Cyclic AMP / Q000378:metabolism; D004023:Dictyostelium / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D009024:Morphogenesis; D012333:RNA, Messenger / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D000242:Cyclic AMP