Global analysis of intestine-expressed genes in Caenorhabditis elegans

A major goal of developmental systems biology in the nematode Caenorhabditis elegans is to identify all of the genes expressed in every tissue. We used mRNA tagging to identify most of the genes expressed in the intestine of C. elegans. An intestine-specific promoter (ges-1) was used to drive the expression of an epitope-tagged protein that binds the poly(A) tail of mRNA (FLAG::PAB-1). Intestinal mRNA was immunoprecipitated with antibodies to the FLAG epitope to enrich for FLAG::PAB-1/mRNA complexes. 1938 intestine-expressed genes (p<0.001) were identified using DNA microarrays. We then compared the intestine-expressed genes to those expressed in the muscle and germline, and identified 510 genes enriched in all three tissues and 624 intestine-, 230 muscle-, and 1135 germ line-enriched genes. We also compared the intestine-expressed genes to those identified by another method using intestinal dissection and mRNA profiling with serial analysis of gene expression.; In order to gain insight into the regulation of intestinal gene expression, we searched for regulatory motifs. We found that the promoters of the intestine-expressed genes were enriched for the GATA transcription factor consensus binding sequence. We employed several statistical analyses to show that intestinal expression is correlated with the presence of a GATA motif in the promoters of genes. We experimentally verified these results by showing that the GATA motif is required in cis and that GATA transcription factors are required in trans for expression of promoter::GFP reporters of intestinal genes.; Finally, we showed that the 1938 intestine-expressed genes were physically clustered on the chromosomes, suggesting that the order of genes in the genome is influenced by the effect of chromatin domains on gene expression. Furthermore, the commonly expressed genes showed more chromosomal clustering than the tissue-enriched genes, suggesting that chromatin domains may influence housekeeping genes more than tissue-specific genes. We also analyzed chromosomal clustering and the presence of heat shock DNA regulatory motifs in genes regulated by heat shock. We found that heat shock genes are clustered on the chromosomes, but no further evidence for the chromatin domain model of housekeeping gene expression based on the presence or absence of heat shock motifs.