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A transcriptional profile of multicellular development in Dictyostelium discoideum

Nancy Van Driessche^1,2,*, Chad Shaw^1,*, Mariko Katoh^6,*, Takahiro Morio⁶, Richard Sucgang³, Miroslava Ibarra¹, Hidekazu Kuwayama⁶, Tamao Saito⁷, Hideko Urushihara⁶, Mineko Maeda⁸, Ikuo Takeuchi⁹, Hiroshi Ochiai⁷, William Eaton⁵, Jeffrey Tollett^1,4, John Halter⁵, Adam Kuspa^1,2,3, Yoshimasa Tanaka⁶ and Gad Shaulsky^1,2,

¹ Department of Molecular and Human Genetics,
² Graduate Program in Developmental Biology,
³ Department of Biochemistry and Molecular Biology,
⁴ DNA Array Core Facility,
⁵ Department of PM&R and Division of Neuroscience, Baylor College of Medicine, Houston TX 77030, USA
⁶ Institute of Biological Sciences, University of Tsukuba, Tsukuba, Japan
⁷ Division of Biological Sciences, Hokkaido University, Sapporo, Japan
⁸ Department of Biology, Osaka University, Osaka, Japan
⁹ Novartis Foundation for the Promotion of Science, Takarazuka, Japan
^* These authors contributed equally to this work

View larger version (92K): [in a new window]   Fig. 1. Morphological transitions in Dictyostelium development. Dictyostelium development is characterized by a series of coordinated changes. The process is highly synchronous as most of the multicellular structures are at the same morphological stage at each time point (Sussman, 1987). A top view of cells developing on dark nitrocellulose filters is shown. No multicellular structures can be seen at 0 hours. Ripples (6 hours), loose aggregates (10 hours), tipped aggregates (14 hours), fingers (18 hours) and fruiting bodies (24 hours) are shown. Time (h) is indicated in each panel. Bar, 1 mm.

View larger version (28K): [in a new window]   Fig. 2. Transcriptional transitions during Dictyostelium development. Cells were starved on filters and samples collected at 2-hour intervals as indicated. (A) The dendrogram represents the dissimilarity between the RNA samples based on all values of gene expression for each time point. The two most dissimilar groups of samples are indicated as red and green clades, which correspond to the unicellular and the multicellular stages, respectively. (B) The color chart represents the pattern of expression for genes that are highly regulated during development. The order of 2021 genes from top to bottom was determined by the fit between their pattern of expression and the function (y=x/12–1). The chart and the dendrogram are derived from an average of four independent experiments from different strains and growth conditions. The positions of several previously characterized genes are indicated: A, cotA; B, cotB; C, cotC; D, cprD; P, pspA; V, vegetative ribosomal genes. The supplemental data (http://dev.biologists.org/supplemental/) contains a complete list of the genes. Each column represents a time point (hours) and each row represents an array target. The color scale represents the standardized log2 of the ratio between the tested sample and the standard relative to the gene mean, where blue indicates a lower-than-average level of expression and yellow indicates a higher-than-average level of expression.

View larger version (37K): [in a new window]   Fig. 3. The transcriptional profile of development is robust. Data from the individual strain/nutrition conditions were analyzed separately as in Fig. 2B and the order from each condition was imposed on the other data sets. Strain/nutrition conditions are indicated on the left, orders are indicated on the top. Data from the two most different strain/nutrition conditions are shown. The complete data set is shown in the supplemental data (http://dev.biologists.org/supplemental/). Each column represents a time point (hours) and each row represents an array target. The color scale is as in Fig. 2.

View larger version (56K): [in a new window]   Fig. 4. Expression patterns of cell type enriched genes. (A) RNA samples from spores (SP) prespore cells (PSP) prestalk cells (PST) and stalks (ST) were analyzed with the expression array. Targets were tested for differential expression among the four cell types and defined as cell-type-enriched if they exhibited a higher-than-average level of expression in one or two related cell types (yellow) relative to the other cell types (blue), as determined by a test of linear contrast. Tissues highlighted in yellow in the cartoons were those investigated. (B) The expression patterns of the cell-type-enriched genes were traced in the time-course experiments described in Fig. 2B. Data from prespore and prestalk genes were ordered as in Fig. 2B. The order of the targets from top to bottom in the spore and stalk samples is determined by a linear contrast of the pattern of gene expression against the coefficient vector (–1, 1.6, 1.6, 1.6, –1, –1, –1, –1, –1, –1, –1, 1.6, 1.6). Every other time point (hours, columns) is indicated on the top. The cell type is indicated on the left and a few previously characterized cell-type specific genes are indicated on the right: B, cotB; C, cotC; E, ecmA. In both A and B, the columns represent RNA samples and the rows represent individual targets. The color scheme is as in Fig. 2.