We are using DNA microarrays containing nearly every gene in the C. elegans genome to determine which genes are expressed in the major tissues of the adult hermaphrodite. We use a new method called mRNA tagging to identify most or all of the genes expressed in muscle cells, neurons, skin epithelia, intestinal cells and the vulval precursor cells. We can use the global survey of gene expression in C. elegans development to study entire networks of genes that specify the major tissues.

From cells to molecules: One of the strengths of C. elegans is the completeness of our understanding of the underlying biology. We know the complete cell lineage, the identity of every gene in the genome, and the RNAi phenotypes for virtually all genes. In order to extend our understanding of development from cellular to molecular resolution, we would like to develop a "dictionary of development" by defining most or all of the genes expressed in each of the major tissue types.

Three classes of genes: housekeeping genes (common to all lineages), tissue specific genes (such as epithelial or neuronal), and cellular memory (genes expressed in a progenitor cell remain expressed in the differentiated cell).

Classifying the transcriptome of a cell is the first step toward understanding the underlying transcriptional regulatory logic defining tissue specific gene expression. We can search the upstream regions of the tissue specific genes to find the regulatory sequences controlling their expression.

We have found that genes expressed in a specific tissue are found in clusters on the chromosome. This likely reflects the effect of chromatin domains. In any given tissue, certain regions of the genome are in open chromatin domains and are accessible for expression whereas other parts of the genome are contained in closed chromatin and cannot be expressed.

Publications:

F. Pauli, Y. Liu, Y. A. Kim, P.-J. Chen and S. K. Kim. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. submitted

Roy et al., Chromosomal clustering of muscle-expressed genes in C. elegans Nature, 418, 975-9, 2002.