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First published online 14 December 2005
doi: 10.1242/dev.02185

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Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans

¹ Department of Genetics, Stanford University, Stanford, CA 94305, USA.
² Stanford Medical Informatics, Stanford University, Stanford, CA 94305, USA.
³ Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
⁴ AbGenomics Corporation, Neihu, Taipei 114, Taiwan.

View larger version (86K): [in a new window]   Fig. 1. ges-1p::FLAG::PAB-1 is expressed exclusively in the intestine. Immunohistochemistry of strain expressing Pges-1::FLAG::PAB-1 with anti-FLAG antibodies shows intestinal expression in fourth larval stage animals. (A) Bright-field image. (B) Antibody immunoflourescence.

View larger version (26K): [in a new window]   Fig. 2. Genes expressed in the intestine by mRNA tagging. Histogram of the average percentile rank of enrichment after intestinal mRNA tagging. The x-axis shows the average percentile rank of enrichment, and the y-axis shows the number of genes.

View larger version (81K): [in a new window]   Fig. 3. Intestinal expression of six genes identified by mRNA tagging. The anatomical expression of six genes chosen from the list of 1938 intestinal genes was visualized by transformation with promoter::GFP transcriptional constructs. B0218.8, C25E10.8, ZK970.2, elo-6 and gst-42 show exclusive intestinal expression and D2030.5 shows expression in the intestine as well as other tissues.

View larger version (34K): [in a new window]   Fig. 4. Distribution of intestine-expressed, intestine-, germ line- and muscle-enriched, and commonly-expressed genes on the C. elegans gene expression topomap. The gene expression topomap is an assembly of data from 553 microarray experiments in which genes that are strongly co-expressed are plotted in close proximity to each other on the map (Kim et al., 2001). The gray triangles represent all the genes in the topomap (17,817) and the red triangles represent the genes in each list.

View larger version (14K): [in a new window]   Fig. 5. A chromosomal cluster of intestine-expressed genes. Genes are represented by vertical bars. The distance between genes is indicated on the x-axis and the log10(p-value) of enrichment in the intestine by mRNA tagging is indicated on the y-axis. Arrows indicate the direction of transcription for each gene.

View larger version (24K): [in a new window]   Fig. 6. The GATA sequence motif is important for intestinal gene expression. (A) Motif logo for the consensus GATA sequence sites identified in 820 out of 1750 intestine-expressed genes by CompareProspector. The y-axis represents the information content for each position. (B) Percentage of genes with GATA sites in the intestine and commonly-expressed gene lists. (C) Histogram of the average percentile rank for intestine enrichment of intestine-expressed genes with 0, 1, 2 or 3+ GATA sequence sites.

View larger version (47K): [in a new window]   Fig. 7. The GATA sequence is necessary for intestinal gene expression. The GATA sequence in the promoters of elo-6, gst-42 and D2030.5 was mutated and used to generate transgenic GFP reporter strains. (+) indicates the wild-type promoter for each gene and (GATA) indicates that one copy of the GATA motif in the promoter was mutated. Mean pixel intensity was calculated by averaging the image pixel intensity of 20 young adult hermaphrodite animals. (A) Bright-field and GFP images of wild-type and mutant strains. (B) Quantification of GFP expression indicates that the variation between lines is less than the variation between wild-type and mutant strains (P<0.001), indicating that the difference between wild-type and GATA mutant expression levels is not due to variability in the transformation procedure. There is little difference in expression between different lines formed from the same DNA construct, not only in the five lines shown here, but also for three other lines used in a different study (Y.L., unpublished).