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doi: 10.1242/10.1242/dev.00363

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Global analysis of dauer gene expression in Caenorhabditis elegans

¹ Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
² Department of Genetics, Stanford University, Stanford, CA 94305, USA

View larger version (16K): [in a new window]   Fig. 4. Dauer expression of glyoxylate pathway genes. The glyoxylate pathway genes show increased expression in dauers. Red lettering and boxes refer to genes that are dauer enriched (P<0.01) when comparing dauers at 0 hours with dauers at 12 hours. The corresponding red arrows imply increased levels of enzymatic activity that has not been experimentally verified. Green lettering and boxes refer to genes and enzymatic steps that are downregulated (P<0.01) when comparing dauer at 0 hours to dauer at 12 hours. Black lettering in gray boxes indicates no significant difference in expression. The magnitude of induction or repression for each gene is indicated. Some key metabolic intermediates are shown.

View larger version (28K): [in a new window]   Fig. 5. Dauer expression of glycolysis and gluconeogenesis genes. The glycolytic and gluconeogenic pathways are upregulated in dauers, as inferred from changes in gene expression. None of the C. elegans genes encoding the enzymes that catalyze each step in these two pathways has been explicitly defined, but the ORFs illustrated show significant homology to the respective enzymes. Red lettering and boxes refer to genes that are dauer enriched (P<0.01) when comparing pure dauers at 0 hours to 12 hours. Correspondingly, red arrows indicate inferred high levels of enzyme activity in dauers. Black lettering in gray boxes indicates no significant difference in expression. The magnitude of induction or repression for each gene is indicated. Lines that end in black circles connect genes with the enzymatic step. Some key metabolic intermediates are shown. Glucose-6-phosphatase activity (N4) is depicted as a broken line because there is no clear homolog that encodes that activity. F47B8.10 encodes a glucose-6-phosphate translocase, which functions in a complex with the phosphatase in vertebrates. Glycolysis enzymes: E1, hexokinase; E2, glucose-6-phosphate isomerase; E3, phosphofructokinase; E4, fructose-bisphosphate aldolase; E5, triose phosphate isomerase; E6, glyceraldehyde-3-phosphate dehydrogenase; E7, phosphoglycerate kinase; E8, phosphoglycerate mutase; E9, enolase; E10, pyruvate kinase. Gluconeogenic enzymes: N1, pyruvate carboxylase; N2, phosphenolpyruvate carboxykinase; N3, fructose-1,6-bisphosphatase; N4, glucose-6-phosphatase. Glu-6-P, glucose-6-phosphate; Fru-6-P, fructose-6-phosphate; Fru-1,6-BP, fructose-1,6-bisphosphate; DHAP, dihydroxyacetone phosphate; G3P, glyceraldehyde-3-phosphate; PEP, phosphoenolpyruvate.

View larger version (39K): [in a new window]   Fig. 1. Expression patterns of genes in feeding response. Hierarchical clustering was used to display the ratio of dauer to L1 at 0 hours (D/L1) and the expression ratios of the 446 commonly regulated genes during the dauer exit and L1 starvation timecourses. Rows represent different genes and columns represent different times during the timecourse. Scale shows level of expression. D, Dauer; L1, L1 larvae. Full data for this figure are available at http://dev.biologists.org/supplemental/ and at http://cmgm.stanford.edu/~kimlab/dauer/

View larger version (35K): [in a new window]   Fig. 2. Expression patterns of genes in mounts 40 and 41. Hierarchical clustering was used to display the ratio of dauer to L1 at 0 hours and the expression ratios of the commonly regulated genes during the dauer exit and L1 starvation timecourses for the (A) eight genes in mount 40 and (B) seven genes in mount 41. The genes in mounts 40 and 41 have homogeneous expression patterns. The feeding response genes that are in common with the genes in mounts 40 and 41 are indicated with pink bars to the right of the clusters. Rows represent different genes and columns represent different times during the timecourse. Green and red arrows are the dauer exit and L1 starvation timecourses, respectively. Scale shows level of expression. D, Dauer; L1, L1 larvae. Full data for this figure are available at http://dev.biologists.org/supplemental/ and at http://cmgm.stanford.edu/~kimlab/dauer/

View larger version (43K): [in a new window]   Fig. 6. Expression patterns of genes in four gene expression mountains. Hierarchical clustering was used to display the expression ratio of dauers to L1 worms at 0 hours and the expression ratios during the dauer exit and L1 starvation timecourses for genes in four mountains. (A) Mount 14, 353 genes. Blue bars highlight genes that are not induced late in the dauer exit timecourse. (B) Mount 15, 247 genes. (C) Mount 18, 190 genes. Blue bar highlights genes that do not have a dauer exit timecourse expression pattern that is similar to the L1 starvation timecourse expression pattern. (D) mount 29, 40 genes. Almost all genes in mount 29 are induced at the dauer-L4 (or L3-L4) molt. Rows represent different genes and columns represent different times during the timecourse, except the first column [which is the ratio of dauer to L1 at 0 hours (arrowhead)]. Green and red arrows are the dauer exit and L1 starvation timecourses, respectively. Scale shows level of expression. Full data for this figure are available at http://dev.biologists.org/supplemental/ and at http://cmgm.stanford.edu/~kimlab/dauer/

View larger version (30K): [in a new window]   Fig. 3. A gene expression profile during the dauer exit and L1 starvation timecourses. A self-organizing map was used to cluster the 1984 dauer-specific genes with common normalized expression patterns into 45 nodes using 1.5x107 iterations. Each row represents the average expression pattern of the genes in the node (14-100 genes, average of 45). The columns represent different times during the timecourse except for the first column (D/L1) which is the ratio of dauer to L1 at 0 hours. The nodes have also been aggregated into five groups (vertical axis) based on the dauer exit timecourse expression patterns as labeled. These groups are partitioned into many nodes because the expression patterns in the L1 starvation timecourse and relative dauer-enrichment are different. Because normalized data are shown, there are no units on the scale bar. D, Dauer; L1, L1 larvae. The complete data are available at http://dev.biologists.org/supplemental/ and at http://cmgm.stanford.edu/~kimlab/dauer/

View larger version (16K): [in a new window]   Fig. 7. Differential expression of daf-16 isoforms. Intron and exon structures of the daf-16a and daf-16b isoforms are depicted. Pink boxes correspond to coding sequences and gray boxes are 5' or 3' untranslated regions. Light blue lines with inward facing arrows represent predicted amplified PCR products that are on the microarray. The corresponding expression profile for each PCR product is depicted. Columns represent different times during the timecourse except the first column (D/L1) which is the ratio of dauer to L1 at 0 hours. Scale shows level of expression.

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