Direct examination of chromosomal clustering of organ-specific genes in the chordate Ciona intestinalis.

One of challenges in the field of developmental biology is to understand how spatially and/or temporally coordinated expression of genes is controlled at the chromosomal level. It remains controversial whether genes expressed in a given tissue are randomly distributed throughout a given animal genome, or instead resolve into clusters. Here we used microarray analysis to identify more than 1,700 genes that are expressed preferentially in each of 11 organs of the chordate Ciona intestinalis adult, and determined the location of these genes on the 14 pairs of Ciona chromosomes. In spite of extensive mapped gene analysis, we only confirmed small clusters containing two or three genes. Our result indicates that organ-specific genes are distributed rather evenly all over chromosomes, suggesting that the notion of clustering of organ-specific genes in animal genomes is not generally applicable to this chordate.